Complete genome of the barotolerant Listeria monocytogenes RO15 strain and comparison with other strains isolated from food and food processing environments

Complete genome of the barotolerant Listeria monocytogenes RO15 strain and comparison with other strains isolated from food and food processing environments | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research article Complete genome of the barotolerant Listeria monocytogenes RO15 strain and comparison with other strains isolated from food and food processing environments Ilhan Cem Duru, Margarita Andreevskaya, Pia Laine, Tone Mari Rode, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.2.24582/v2 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 02 Jul, 2020 Read the published version in BMC Genomics → Version 2 posted 10 You are reading this latest preprint version Show more versions Abstract Background: High pressure processing (HPP; i.e. 100 - 600 MPa pressure depending on product) is a non-thermal preservation technique adopted by the food industry to decrease significantly foodborne pathogens, including Listeria monocytogenes , from food . However, susceptibility towards pressure differs among diverse strains of L. monocytogenes and it is unclear if this is related to their genomic content. Here, we tested the barotolerance of 10 different L. monocytogenes strains, from food and food processing environments and widely used reference type strains, to pressure treatments with 400 and 600 MPa. Genome sequencing and genome comparison of the tested L. monocytogenes strains were performed to investigate the relation between genomic profile and pressure tolerance. Results : None of the tested strains were tolerant to 600 MPa. A reduction of more than 5 log 10 was observed for all strains after 1 minute 600 MPa pressure treatment. L. monocytogenes strain RO15 showed no significant reduction in viable cell counts after 400 MPa for 1 minute and was therefore defined as barotolerant. Genome analysis of so far unsequenced L. monocytogenes strain RO15, 2HF33, MB5, AB199, AB120, C7, and RO4 allowed us to compare the gene content of all strains tested. This revealed that the three most pressure tolerant strains had more than one CRISPR system with self-targeting spacers. Furthermore, several anti-CRISPR genes were detected in these strains. Pan-genome analysis showed that 10 prophage genes were significantly associated with the three most barotolerant strains. Conclusions: L. monocytogenes strain RO15 was the most pressure tolerant among the selected strains. Genome comparison suggests that there might be a relationship between prophages and pressure tolerance in L. monocytogenes . Epigenetics & Genomics high-pressure processing (HPP) foodborne pathogen CRISPR PacBio comparative genomics pan-genome. Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Background Listeria monocytogenes is a well-known foodborne pathogen that may cause listeriosis, a severe infection with high hospitalization rate which can be fatal in humans and some animal species [1]. Although being a relatively rare foodborne disease, increasing numbers of listeriosis cases have been reported in the EU/EEA countries since 2008 [2]. L. monocytogenes is generally found in agricultural, aquacultural, and food processing environments [3]. Listeriosis outbreaks have been associated with consumption of contaminated food, such as meat, milk, cheese, and fish [4]. The food industry has to process food in such a way to meet food safety microbiological criteria (Commission Regulation (EC) No 1441/2007 amending Commission Regulation (EC) No 2073/2005 [5]), which include the presence in limited numbers (100 cfu/g) or absence of L. monocytogenes (absence in 25 g product). Food processing aimed at L. monocytogenes inactivation is challenging due to its pronounced ability to adapt to different environments, and to survive under various stress conditions [6]. In addition, it is important to preserve the food quality and nutritional value during food processing. High pressure processing (HPP) is an alternative to thermal processes to inactivate pathogens, including L. monocytogenes , and maintain a high quality of the product. Only very small or no quality changes, such as loss of color, nutritional value, flavor, and texture, have been reported for HPP products [7] . Several studies showed that HPP products, such as meat, milk, juice, vegetables, and sauce are well accepted by the consumer, and reported that HPP preserves the taste [8]. Depending on the food products, pressures currently used in the food industry are between 100 and 600 MPa, with a holding time ranging from one to several minutes [9]. HPP has been tested and reported as an effective processing method for several products including fruits (and fruit juices) [10], meat [11], cheese [12], fish [13] and vegetables [14]. It has been shown that HPP has varying effects on different target organisms. For example, a pressure of 300 MPa is sufficient to inactivate most Gram-negative bacteria, while more than 400 MPa is needed for an inactivation of Gram-positive bacteria [15, 16]. It is also known that pressure tolerance can differ even among strains of the same species. Differences in pressure tolerance have been reported for strains of several species including Cronobacter sakazakii (previously Enterobacter sakazakii )[17], 24 different serotypes of Salmonella enterica [18], and L. monocytogenes [19, 20]. In L. monocytogenes strains, pressure tolerance varies between 300 - 500 MPa [19]. To our knowledge, genomic profiling and comparison has not been performed for barotolerant and barosensitive L. monocytogenes strains. In this study, we selected 10 L. monocytogenes strains, isolated from either foods, food processing environments or clinical sources, to test their tolerance towards HPP at 400 and 600 MPa, compared their genomes, and investigated whether genetic traits may be associated with pressure tolerance. Results Pressure treatment and reduction of viable cell counts Reduction of viable cell counts (colony forming units, cfu) after pressure treatment at 400 and 600 MPa for 1 minute showed that pressure tolerance differs between strains. The variance in colony forming units (cfu) of the treated samples was significantly larger (p<0.02, see ANOVA results below) compared to control, indicating a high variance in the level of tolerance of L. monocytogenes . At 400 MPa for 1 minute, the 10 strains exhibited an average log 10 reduction of 0.57 cfu/ml, ranging from 0.05 log 10 cfu/ml for the most barotolerant strain (RO15) to 2.07 log 10 cfu/ml for the most pressure sensitive strain (EGD-e). Similar results were obtained at 600 MPa. Here, the 10 strains exhibited an average log 10 cell number reduction of 7.06 cfu/ml, with a range of 5.42 to 8.27 log 10 cfu/ml (Table 1). Strain RO15 was also the most barotolerant strain based on an initial screening including several other L. monocytogenes strains (Supplementary text 1, Table S1, Figure S1). One-way analysis of variance (ANOVA), comparing the pressure (400 MPa) treated samples of each strain to the control samples, showed that the mean cfu/ml for treated samples was significantly lower than the control for all strains (p<0.02), except for strain RO15 (p=0.15) (Figure 1a). The same statistical analysis for HPP at 600 MPa indicated that all strains including strain RO15 had significantly (p<0.01) lower cfu/ml in treated samples compared to controls (Figure 1b). Genome sequencing, general features and RNA-Seq We sequenced the genomes of seven L. monocytogenes strains for which no genome sequences were available in public databases. Genomes of strains RO15, 2HF33, MB5, AB199, AB120, C7, and RO4 were sequenced using Illumina MiSeq instrument and strain RO15 was sequenced using Pacbio RSII. Sequences of these seven strains were assembled and three additional strains (ScottA, F2365 and EGD-e, genome sequences of which are available in public databases) were used for comparative genome analysis. Assembly of PacBio long reads of strain RO15 resulted in one continuous 3,042,507 bp sized chromosome (Figure 2) at an average 308-fold sequencing coverage. In addition to the chromosome, a contig with a complete circular prophage sequence of 38,811 bp was obtained, which was also found as part of the chromosome (2729417 - 2770759 bp). All genomes had a similar size, GC content and number of coding sequences (CDS) (Table 2). The serotype of the strains was reported in previous studies [21, 22, 23, 24, 25] (Table 2). Although RO15 was reported as a serovar 4b strain using multiplex PCR in a previous study [21], our genome-based prediction suggests that it belongs to serovar 1/2a. Sequences for ORF2110 and ORF2819 primers used for identification of serovar 4b strains [24] were not found in the genome of strain RO15 based on our sequence match analysis, whereas sequences for primers targeting lmo0737 , which are indicators of serovar 1/2a strains [24] were present. Multilocus sequence typing (MLST) based on 7 loci, core genome MLST (cgMLST; based on Moura scheme [26]), and clonal complex (CC) of the strains were also assigned based on the genome sequences (Table 2). Lineage assignment showed that only ScottA and F2365 belonged to lineage I and all other strains were members of lineage II (Table 2). In addition to genome sequencing, transcriptome analysis using RNA-seq for strains RO15 and ScottA provided a basic view of transcriptional activity of the genomes. Differential expression analysis indicated that virulence genes and heat shock genes were upregulated after high pressure treatment in strain ScottA (Table S2). Methylated DNA Motifs High PacBio sequencing coverage allowed us to analyze DNA methylation modification motifs in strain RO15 in addition to assembling the genome. Using the long read modification data, 11 methylated sequence motifs were detected in the genome (Table 3). None of the detected motifs had a partner motif, i.e. a reverse-complementary sequence, but all detected motifs were only partially modified in the genome with less than 50% methylated motifs. While most of the motifs have already been deposited in the REBASE database [29] DADGYATYA, WNNTVVGCNTWNH, AHNBAACA, AGNNARNWW were novel, i.e. they have not been described as potential methylation sites previously. None of the detected motifs have been reported as recognition sequence motif for a restriction enzyme in the REBASE database. We predicted one type II cytosine-5 DNA methyltransferase gene (OCPFDLNE_00657), and three type II N4-cytosine or N6-adenine DNA methyltransferase genes (OCPFDLNE_02168, OCPFDLNE_02626, OCPFDLNE_02808) in the strain RO15 genome. In addition, genes for a type IV methyl-directed restriction enzyme (OCPFDLNE_00324) and type II restriction enzymes (OCPFDLNE_00658, OCPFDLNE_02625, OCPFDLNE_02807) were predicted. These predicted methyltransferases and restriction enzymes had significant (e-value <1E-50) BLASTP hits in the REBASE protein sequences database [29]. However, their recognition sequences are unknown. OCPFDLNE_02625 and OCPFDLNE_02807 type II restriction enzyme genes in prophage regions were expressed based on RNA-seq data. Genomic comparison of the selected strains. In the genome assembly we also identified a circular phage as an independent contig. While looking after phage-originating genome parts, prophage prediction revealed five prophage regions (10.7 kb to 47.9 kb sized) in the RO15 genome (Figure 2). Prophage (region) 5 had the same sequence as the separate circular phage. RNA-Seq count data suggested that most of the genes of prophage 1,3 and 5 in RO15 were transcribed. Subsequently, the prophage prediction was performed for all strains, which showed that all strains had at least one or more prophage regions in the genome with a maximum of six prophage regions in strain C7 (Table 4). One of the predicted prophage regions in ScottA was also transcribed based on the RNA-seq data. Genome alignment of the selected nine strains against the strain RO15 (Figure 3) showed large sequence gaps between strain RO15 and the other strains. The gaps were mainly related to prophage regions with prophage region 3 being specific for strain RO15. Prophage region 2 was only seen in the strain 2HF33. Prophage region 4 was partially seen in strains 2HF33, EGD-e, MB5 and ScottA. Similarly, prophage region 5 was partially seen in strains 2HF33, C7, and RO4. In addition, strains ScottA and F2365 had less aligned regions compared to the other strains. Average nucleotide identity (ANI) results showed that ANI scores of strains ScottA and F2365 with other strains were lower than 95 (Table S3). To study how the large sequence gaps are localized in the other publicly available genomic sequences of L. monocytogenes , all 200 complete L. monocytogenes genomes in RefSeq database [30] were downloaded and aligned to strain RO15 (Figure S2). The visualization of the alignment showed that prophages 2, 3 and 4 were seen only in the minority of the L. monocytogenes strains, while prophages 1 and 5 were seen in the majority of the L. monocytogenes strains. The comparison indicated that these prophage regions were common locations of variance between L. monocytogenes strains. Annotation of CRISPR systems revealed that the RliB-CRISPR system was seen in all the strains, which is in line with previous RliB-CRISPR system studies [31, 32]. Interestingly, CRISPR I or CRISPR II system genes were present only in strains RO15, 2HF33, and MB5 (Figure 4), which exhibited the lowest reduction in log 10 cfu/ml with the 400 MPa pressure treatment (Table 1). Number of spacers in these strains were also significantly (p < 0.001) higher compared to barosensitive strains. The alignment of the spacer sequences of the CRISPR systems back to the genome itself revealed that only strains RO15, 2HF33, and MB5 contained self-targeting spacers with 100% identity. As expected, spacer sequences were aligned to the prophage regions, except one spacer sequence in RO15, which aligned to the addB gene (OCPFDLNE_02427) located in the chromosome encoding an ATP-dependent helicase. Using prediction tools we detected anti-CRISPR genes in the prophage regions (Table 4) of strains RO15, 2HF33, MB5, RO4, and EGD-e. Homologues of all four previously annotated Listeria anti-CRISPR genes, i.e. acrIIA1 , acrIIA2 , acrIIA3 , and acrIIA4 [33], were seen in strain 2HF33. Gene acrIIA4 was not seen in strains MB5, RO4, and EGD-e, but the rest of the anti-CRISPR genes were present. RO15 contains two copies of acrIIA1 (OCPFDLNE_02770, OCPFDLNE_02583) and acrIIA2 (OCPFDLNE_02582) (Figure 2) and we observed expression of these anti-CRISPR genes in strain RO15. As antibiotic resistance and pressure tolerance were linked in a previous study [19], we also searched antibiotic resistance genes in all strains to identify relation of antibiotic resistance genes and pressure tolerance. The same antibiotic resistance gene families were detected in all the 10 strains (Table S4). Multiple sequence alignment of the detected antibiotic resistance genes and the following average distance tree generation showed that amino acid sequence of the norB gene (encoding for a quinolone resistance protein) (OCPFDLNE_03068) was slightly different in barotolerant strain RO15 compared to the other strains (Figure S3). Similarly, for the lin gene (encoding for a lincomycin resistance protein) (OCPFDLNE_00980) amino acid difference was seen for strains 2HF33 and RO15 (Figure S3). Roary pan-genome pipeline suggested that the 10 L. monocytogenes strains contain a total of 4820 orthologous gene clusters. Of these genes, 2247 were core genes found in all strains and 2573 genes were accessory genes found in at least one strain. The core genome was used for constructing a phylogenetic tree, which indicated that the two serovar 4b strains (ScottA and F2365) are closely related to each other and cluster separately from the serovar 1/2a strains in the phylogenetic tree. In addition, there was also a clear difference in accessory genome for serovar 4b strains compared to serovar 1/2a strains (Figure 5). To test any significant association between pressure tolerance and (clusters of) genes in the accessory genome, we performed a pan-genome wide association analysis using Scoary. Based on the pairwise comparison of reduction in log 10 (cfu/ml) against strain RO15 using Student’s t-test (Table S5), a statistically significant difference compared to RO15 was seen in all strains except MB5 and 2HF33. Therefore, strains RO15, 2HF33, MB5 were used as barotolerant strains for the pan-genome association analysis. Scoary results showed that 13 gene clusters (Table S6) had p-values < 0.01 for the association with barotolerant strains, i.e., the genes were only seen in barotolerant strains. Of these, 10 gene clusters were located in the prophage regions, but most of the genes were annotated as hypothetical proteins (Table S6). These prophage genes were also searched for in 200 complete L. monocytogenes strains and found in some strains (Table S6). Interestingly, genes OCPFDLNE_02579 and OCPFDLNE_02580 were only seen in strains that harbored anti-CRISPR genes, Cas type I or II CRISPR system and self-targeting spacers (Table S6). Discussion HPP is commonly used in the food industry to inactivate foodborne pathogens and spoilage organisms. Depending on the type of food product, up to ~600 MPa pressure is applied [9]. It has also been shown that combinations of HPP and biocontrol agents, such as virulent bacteriophages and bacteriocins, have synergistic effects in the inactivation of the target pathogens in food [34, 35]. The pressure tolerance level varies between different species, strains, and even isolates [16, 19, 36, 37]. Here, we tested pressure tolerance of 10 L. monocytogenes strains, compared their genomes and predicted genome features related to pressure tolerance. Pressure treatment using 600 MPa for 1 minute caused more than 5 log 10 reduction in all selected strains, which is generally considered sufficient for food safety regulations. According to the Food Safety and Inspection Service (United States Department of Agriculture), 5 log 10 reduction is considered a full lethality treatment for L. monocytogenes [38]. This suggests that the strains used in this study were relatively sensitive to 600 MPa pressure treatment. Similarly, an earlier study reported that pressure treatment at 500 MPa for 10 minutes provided sufficient reduction in viable counts to reach desired level of safety for all except one L. monocytogenes strains tested [19]. However, the lower pressure levels, such as 400 MPa, would be more relevant for industrial applications, therefore, we focused more on the results obtained with the 400 MPa treatment. Among the strains tested, RO15 was the most barotolerant strain when processed at both 400 and 600 MPa, which is in line with the initial selection process of strains (Supplementary text 1). Based on ANOVA, RO15 was the only strain for which no statistically significant reduction was observed with the 400 MPa treatment (Figure 1a). Therefore, we defined the strain RO15 as barotolerant. It has been shown that the level of inactivation by HPP can be affected by the chemical composition of the food product. Some food products, such as milk and cheese, have baroprotective effects on microorganisms during HPP treatment [39, 40]. However, experiments in this study were performed using TSBYE broth and thus do not take into account the effects of food composition on HPP. Temperature during pressure treatment can have an effect on microbial inactivation depending on treatment time, and it has been shown that increasing the temperature from 25 °C to 35 °C has a significant effect on the viability loss of L. monocytogenes [41]. In this study, temperature during pressure treatment increased up to 33 °C for 400 MPa treatment and 38 °C for 600 MPa treatment due to adiabatic heating. However, since treatment time was only one minute, the effect of temperature rise was expected to be minimal. Serotypes of the selected strains were shown in the earlier studies based on agglutination method, multiplex-PCR and genome sequencing [21, 22, 23, 24, 25] (Table 2). Here, we predicted the serotype of all strains based on their genome sequences. This confirmed the previous serotyping of all strains except RO15, which was reported to be a serotype 4b strain based on multiplex-PCR [21]. Serotype 4b strains should contain serotype 4 marker genes ( ORF2110 and ORF2819 ) and lack lmo0737 marker gene sequence as described by Doumith et al. [24]. However, according to the genome sequence, serotype 4 marker genes were absent, and a lmo0737 homologue was present suggesting that the serotype of strain RO15 is indeed 1/2a. The phylogenetic tree that we created based on the core genome showed that there is considerable genetic variation between serovars. Serovar 4b strains (ScottA and F2365) clustered separately from the other strains (Figure 4). Strain RO15 was not clustered together with other serovar 4b strains hence these results supported our gene-based prediction of serotype 1/2a of strain RO15. PacBio sequencing provides not only the genome sequence but also methylation data [42], which gives an opportunity to analyze restriction-modification systems and their recognition motifs. In this study, we did not observe a genuine methylated motif based on PacBio sequencing data of strain RO15. Similarly, PacBio methylation data of nine other published L. monocytogenes strains without genuine methylated motifs were also seen in REBASE PacBio list database [29], which showed that it is not uncommon to have only partially methylated motifs in L. monocytogenes . Previous studies based on L. monocytogenes strain ScottA and LO28 barotolerant isolates showed that there is a phenotypic and genotypic variation between barotolerant isolates [36, 37, 43], which indicates that there are variety of factors which can lead to pressure tolerance. Therefore, it is a challenge to link a genomic profile with pressure tolerance in different strains. Nevertheless, pan-genome association analysis results suggest that there was a genotypic difference between barotolerant and barosensitive strains. A total of 13 genes were significantly (p<0.01) associated with barotolerant strains. Interestingly, most of the barotolerant strain associated genes (Table S6) were located in the prophage regions in the studied genomes. In addition, extension search of these genes within all complete L. monocytogenes strain genomes showed that some phage genes (OCPFDLNE_02579 and OCPFDLNE_02580) were only seen in strains that contain inactivated CRISPR/Cas system (Table S6). It has been shown that prophages can provide increased biofilm formation and can be beneficial for stress coping in both L. monocytogenes and Escherichia coli [44, 45]. We also observed that barotolerant strains harbored a slightly higher number of prophages compared to barosensitive strains (based on average number of prophages in barotolerant and barosensitive strains). Therefore, we believe that prophages might play a role in barotolerance in L. monocytogenes . It was also interesting to see that two or more CRISPR-Cas systems, self-targeting spacers, and anti-CRISPR genes were seen together only in the three most barotolerant strains (RO15, MB5, and 2HF33). Since the existence of a self-targeting spacer indicates that the activity of the CRISPR/Cas systems is inhibited [46], it can be predicted that anti-CRISPR proteins detected in barotolerant strains inactivate CRISPR/Cas system. Previous studies have also shown that anti-CRISPR proteins are able to inhibit several types of CRISPR systems [33, 47]. The observed active transcription of anti-CRISPR genes in RO15 prophages based on RNA-seq may also support this prediction. It has been shown that bacteria tend to lose CRISPR/Cas systems, since they can be harmful to the host itself. Immunopathological effects through partially matching spacers were reported unless the phage carries anti-CRISPR genes [48]. The anti-CRISPR genes found in prophages and inhibition of the CRISPR/Cas system may be the reason why barotolerant strains carry type I or type II CRISPR/Cas systems. We observed that more than 50% of the L. monocytogenes strains that harboring type I or type II CRISPR/Cas system also had anti-CRISPR genes (Table S6). CRISPR/Cas systems can have alternative roles in bacteria, such as roles in pathogenesis or role in modulating biofilm formation [49], however the role of inhibited CRISPR/Cas system is not known. More studies are required to support the relation between inhibited CRISPR/Cas systems and barotolerance. RNA-seq revealed the general transcriptome profile of strains RO15 and ScottA. Significantly upregulated heat-shock genes after pressure treatment (chaperone and clp protease genes) in ScottA (Table S2) might indicate that proper folding of proteins plays an important role in cell recovery after pressure treatment. A previous study also showed that the expression levels of Clp proteins were significantly higher in mutant HPP-tolerant ScottA isolate compared to wild type ScottA [43]. A previous study concluded that antibiotic resistant L. monocytogenes strains are more tolerant to pressure at 400 MPa [19]. Here, annotation results did not show any strain-specific antibiotic resistance gene. Nevertheless, multiple sequence alignment of predicted antibiotic resistant genes showed that there were slight differences in amino acid sequences across the strains (Figure S3). However, it is not known that these amino acid differences cause antibiotic resistance advantage, and further studies are required to link the amino acid sequence variations of antibiotic resistance genes and pressure tolerance. Conclusions In this study we noticed that barotolerance is manifested at pressures lower than 600MPa. Strain RO15 was identified as the most barotolerant strain for 400 MPa 1 minute pressure treatment. Genome sequence of seven new strains and genome comparison of 10 strains revealed that the three most barotolerant strains have CRISPR-Cas genes and anti-CRISPR genes in their genomes. In addition, the average number of prophages was slightly higher in barotolerant strains compared to barosensitive strains. Furthermore, we have predicted 10 phage genes that might be related to pressure tolerance based on the pan-genome association test. Therefore, we conclude that prophages and inhibited prophage defense systems may be linked to pressure tolerance. The observation described above may argue for the use of phage cocktails as a pretreatment before HPP and will allow to reduce pressure and holding time. Methods Strains, Growth conditions and Pressure Treatment Strains Scott A (CIP103575) and EGD-e (CIP107776) were obtained from Centre de Ressources Biologiques de l'Institut Pasteur, Paris, France, and strain F2365 (LMG23356) from Laboratorium voor Microbiologie, UGent, Gent, Belgium. Strains RO4, RO15, AB120 and AB199 are from Dunarea de Jos University of Galati, Romania, and have been isolated in the Promise FP7 project either from food illegally introduced to Romania or from meat processing environments. All other strains were isolated from the environment as indicated in Table 2. The strains were stored on Microbank beads with cryopreservatives (Pro-Lab Diagnostics, Toronto, Canada) at - 80 °C prior to use. The bacteria were passaged twice in tryptic soy broth (TSB) supplemented with 0.6% (w/v) yeast extract (TSBYE; Oxoid, Basingstoke, Hampshire, England). Prior to pressure treatments, bacteria were grown overnight in 50 mL TSBYE at 37 °C with rotary agitation (150 rpm), resulting in cells in early stationary phase and with a target concentration of approx. 10 9 cfu/mL. Aliquots (10 mL) of the cultures were packaged in sous-vide plastic pouches and sealed without using vacuum, and 10 mL was transferred to 15 mL falcon tubes to serve as untreated controls. HPP was carried out using the QFP 2L-700 (Avure Technologies Inc., Columbus, USA). The cylindrical pressure vessel had 10 x 25.4 cm dimensions, 2 L capacity and 690 MPa upper pressure limit. Temperature of the pressure medium (water) was tracked with a K-type thermocouple located on the external surface of the samples. A holding time of 1 minute was used, pressures of 400 and 600 MPa, and ambient vessel water temperature (20-22 °C). Due to adiabatic heating, water temperatures in the middle of the vessel at the end of pressure treatment had risen to 31-33 °C after the 400 MPa treatment, and 36-38 °C after the 600 MPa treatment. Straight after pressure treatment, 400 MPa pressurized and untreated samples were serially ten-fold diluted in TSBYE and plated in triplicate on tryptic soy agar with 0.6% yeast extract (TSAYE; Oxoid) by using a spiral plater (Eddy Jet; IUL Instruments, Barcelona Spain). Pressurized samples at 600 MPa were additionally plated manually (100 μL) without being diluted. TSAYE plates were incubated at 37 °C for 48 hours prior to counting the colonies and estimating bacterial inactivation. Two consecutive trials of the methodology were performed (Exp. 1 and 2). DNA extraction DNA of each strain was extracted from 5 ml of a culture grown overnight in BHI broth at 37 °C with aeration on a rotary shaker. Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) was used according to the manufacturer's instructions. Library preparation, genome sequencing, de novo assembly, base modification detection and motif analysis L. monocytogenes strain RO15 was sequenced using PacBio RSII (Pacific Bioscience, Menlo Park, CA, USA) and Illumina Miseq (Illumina, San Diego, CA, USA). Genomic DNA PacBio library was prepared according to the manufacturer's Template Preparation and Sequencing Guide using DNA Template Prep Kit 2.0 and DNA/Polymerase Binding Kit P6. The Nextera XT protocol was used for the enzymatic genomic DNA fragmentation and Illumina sequencing library preparation. Pacbio reads were assembled using HGAP3 protocol [50] in SMRTPortal 2.3.0. Obtained assembly of chromosomal and phage sequences were checked and circularized using Gap4 program [51] and finally the chromosomal DNA sequence was set to start from dnaA gene. cutadapt v1.8.1 [52] was used with -m 200 and -q 25 options to trim Nextera adapter sequences and quality filtering. Trimmed reads were mapped against circularized chromosomal and phage sequences using bwa-mem [53]. Short indels within homopolymeric regions were corrected using pilon v1.16 [54]. Average sequencing coverages at the whole genome level were 308X in Pacbio data and 157X in Illumina data, respectively. DNA base modifications and motifs were analyzed using Modification and Motif analysis protocol implemented in SMRTPortal 2.3.0 with default parameters. For L. monocytogenes strain RO4, AB199, and AB120, Nextera DNA Library (Illumina, San Diego, CA, USA) preparation and for strain 2HF33, MB5, and C7, Nextera XT DNA Library preparation was performed. Paired-end sequencing was performed using Illumina Miseq. RTA v1.18.54 and bcl2fastq v2.17.1.14 were used for base calling, demultiplexing and converting data to fastq format. The cutadapt v1.8.1 [52] was used with -m 200 and -q 25 options to trim Nextera adapter sequences and quality filtering. Reads aligning to PhiX genome, which was used as spike-in during Illumina sequencing, were removed by using bbmap v34.56 [55]. Spades v3.13.0 [56] with default options was used for assembling the reads and creating the contigs. Pressure Treatment for RNA-seq experiment and RNA extraction For both strain RO15 and ScottA, 10 ml of cells were grown in TSBYE until early stationary phase (each triplicated with new cultures). Samples were packed in sterile sous-vide pouches and packaged without applying vacuum. They were put in the refrigerator 30 minutes before pressure treatment. After treatment at 200 and 400 MPa for two, eight and sixty minutes at 20-22°C, samples were transferred to sterile 15 ml Falcon tubes. From each sample, 0.5 ml were transferred to a 2 ml Eppendorf tube prefilled with 1 ml RNA Protect (Qiagen, Hilden, Germany). They were vortexed, incubated for 5 minutes at room temperature, and frozen at -80 °C. Cells previously stored in RNA Protect (Qiagen) were pelleted by centrifugation for 10 minutes at 5000 g. RNA extraction was performed with NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany) according to manufacturer’s instructions with some modifications in the cell disruption phase. The cell pellets were suspended with 700 µl RA1 buffer and 7 µl β-mercaptoethanol (Sigma-Aldrich, Saint Louis, MO, USA). Cells were then mechanically disrupted using Lysing Matrix B tubes (MP Biomedicals) and FastPrep 24 tissue homogenizer (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 3 x 30 sec. Cells were rested on ice for five minutes between cycles. After spinning the cells briefly and transferring the supernatant to NucleoSpin filter column, manufacturer’s protocol was followed. Quantity and quality of RNA extractions were analyzed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). RNA-seq library preparation Ribosomal RNAs were removed from the total RNAs (ScottA 9.4 µl; RO15 14 µl) with Ribo-Zero rRNA Removal kit for bacteria (Illumina) according to manufacturer’s instructions with 1/3 (ScottA) or 1/2 (RO15) volumes of kit solutions. rRNA-depleted RNA was purified with RNeasy MinElute Cleanup Kit (Qiagen) according to modified protocol of the Ribo-Zero kit manual and eluted in 12 µl of RNA-free water. Eight µl of rRNA-depleted RNA was used to prepare RNA sequencing libraries with SENSE Total RNA-seq Library Prep Kit for Illumina (Lexogen, Vienna, Austria) according to manufacturer's instructions. In reverse transcription and ligation phase, incubation time was extended to two hours. After second-strand synthesis, purification and size-selection of the libraries were performed with 13 µl of Bead Diluent and 27 µl of Purification Solution. PCR amplification program was slightly modified by increasing the denaturation times: from 30 to 60 sec in the beginning, and from 10 to 30 sec during the cycles; cycle number was increased to 40. Concentration of amplified libraries was measured with Qubit fluorometer and dsDNA HS assay kit (Invitrogen, Waltham, MA, USA), and size distribution visualized with Fragment Analyzer and High Sensitivity NGS Fragment Analysis kit (Advanced Analytical, Parkersburg, WV, USA). Aliquots of amplified libraries were pooled twice for both strains. After pooling, libraries were concentrated using Amicon Ultra 100K columns (Millipore, Burlington, MA, USA). To remove fragments under 200 bp, size selection of ScottA pools was performed using BluePippin and 2% agarose gel cassette (Sage Science, Beverly, MA, USA). In size selection of RO15 library pools, bead purification with 0.9 x AMPure XP beads (Beckman Coulter, Brea, CA, USA) and PEG/NaCl precipitation on MyOne TM carboxylic acid beads (Invitrogen) were additionally used. Concentration of the pooled libraries was measured with Qubit fluorometer, and libraries were sequenced with NextSeq 500 (Illumina). RNA-seq data analysis Quality filtering and adapter trimming for RNA-seq reads was done using Trimmomatic v0.36 [57] using these parameters “TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:3:20 MINLEN:30”. SortMeRNA [58] was used to filter rRNA reads. Reads were mapped to the genomes using Bowtie2 [59] default settings. Aligned reads were sorted using Samtools [60]. HTSeq [61] with union mode was used for read counts. Differentially expressed gene analysis was done using DESeq2 R package [62]. Genes with adjusted p-value (padj) ≤ 0.05 and |log2 Fold Change| ≥ 1 were considered as significantly differentially expressed. Genome annotation, prophage prediction and genome alignment Assembled genomes were annotated using Prokka v1.13 [63] with default options. To improve functional annotation PANNZER2 annotation web server [64] was used. CRISPR repeat regions were detected using CRISPRCasFinder version 4.2.19 [65]. Anti-CRISPR genes were annotated using BLAST alignment against known anti-CRISPR genes [33]. The prophage prediction for all genomes was done using PHASTER web tool [66]. Serotype of the selected strains were predicted by checking the marker primers [24] in the genome using EMBOSS primersearch v 6.6.0 [67]. Multilocus sequence typing (MLST) based on 7 loci (MLST), clonal complex (CC), core genome MLST (cgMLST) and lineages of strains were assigned based on MLST and the cgMLST schemes developed by Moura et al. [26, 68] by uploading the sequences to BIGSdb-Lm webserver (https://bigsdb.pasteur.fr/listeria/listeria.html). Antibiotic resistance genes were detected using Resistance Gene Identifier (RGI) tool with CARD database [69]. Heuristic neighbor-joining phylogeny tree based on concatenated sequences of the MLST gene fragments was created using FastTree v2.1 [70]. Whole genome alignment and ring figure was created using CGView Comparison Tool [71]. The ANIb scores were calculated using JSpeciesWS webtool [72]. Pan-genome and Pan-GWAS analysis The pan-genome analysis was done using Roary Pan-genome Pipeline [73] with default settings, to create alignment of core genes using PRANK [74] the “-e” setting was used. The core genes alignment was used for phylogenetic tree construction using FastTree [70]. Pan-genome-wide association analysis was done using Scoary [75] with default settings. List Of Abbreviations Analysis of variance (ANOVA), average nucleotide identity (ANI), coding sequence (CDS), colony forming units (cfu), high pressure processing (HPP), megapascals (MPa), multilocus sequence typing (MLST) Declarations Ethics approval and consent to participate Not applicable Consent for publication Not applicable Availability of data and material All sequencing data and assembled genomes have been deposited in the European Nucleotide Archive (ENA) under accession code PRJEB35939. Strains RO4, RO15, AB120 and AB199 are from Dunarea de Jos University of Galati, Romania, and are available upon request to [email protected] . Strains C7, MB5, and 2HF33 are from Nofima – Norwegian Institute of Food, and are available upon request to [email protected] . Competing interests The authors declare that they have no competing interests. Funding This study was supported within the ERA-IB2 consortium “SafeFood” (ID: ERA-IB-16- 247 014) by grants from Academy of Finland to PA (307856 and 311717), by a grant of the Executive Agency for Higher Education, Research, Development and Innovation Funding in Romania to AIN (International and European Cooperation – 250 Subprogramme 3.2 – Horizon 2020 – Contract No. 15/2017) and by a grant of the German Ministry for Education and Research to CUR (Grant No: 031B0268). ICD supported by the MBDP doctoral program. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Authors' contributions PA, AIN, TL, CUR, and NB conceived and designed the study. TMR, TL and FIB collected the samples and performed the pressure treatment and viable cell count. ICD, MA, and PL performed the bioinformatics analyses. AY performed RNA extraction and sequencing preparation. PC extracted DNA. NB performed ANOVA statistical analysis. ICD drafted the manuscript. All authors have read, commented, and approved the final manuscript. Acknowledgements We want to thank Kirsi Lipponen and Paula Collin for performing the NGS procedures for this project. Ingrid B. Eri, Karin Tranøy and Laila Budal (Nofima) are acknowledged for technical laboratory assistance. The sequencing service for strains MB5, C7, and 2HF33 was provided by the Norwegian Sequencing Centre ( www.sequencing.uio.no ), a national technology platform hosted by the University of Oslo. Prof. Daniela Borda (Faculty of Food Science and Engineering, Dunarea de Jos University of Galati) is acknowledged for her assistance with the high pressure processing experiments conducted in the equipment purchased in the frame of the RE-SPIA project. We wish to acknowledge CSC – IT Center for Science, Finland, for computational resources. References Schlech WF, Lavigne PM, Bortolussi RA, Allen AC, Haldane EV, Wort AJ, et al. 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Log 10 reduction compared to control -Δlog 10 (cfu/ml) (standard deviation) Strain 400 MPa 600 MPa RO15 0.05 (0.14) 5.42 (0.15) 2HF33 0.15 (0.08) 6.97 (0.10) MB5 0.22 (0.14) 8.27 (0.27) AB199 0.26 (0.12) 6.95 (1.16) AB120 0.35 (0.16) 7.30 (0.59) C7 0.37 (0.17) 7.52 (0.88) F2365 0.47 (0.16) 7.10 (0.26) ScottA 0.68 (0.57) 5.86 (0.39) RO4 1.00 (0.13) 7.70 (1.24) EGD-e 2.07 (0.33) 7.49 (0.70) Table 2. General genome summary of selected L. monocytogenes strains. The table shows the genome size, genome sequence based prediction of clonal complex (CC), multilocus sequence typing (MLST) based on 7 loci, core genome MLST (cgMLST), lineage, and serotypes of selected strains. Strain Size, Mbp (CDS) CC Serotype MLST cgMLST Lineage Genome Source Source Reference RO15 3.04 (3022) CC155 1/2a 155 cg-11632 II This study (Complete) Herring with spices [21] 2HF33 3.11 (3098) CC121 1/2a 121 cg-3328 II This study (Contigs) Salmon filleting section [25, 27] MB5 2.97 (2958) CC7 1/2a 7 cg-9444 II This study (Contigs) Salmon gutting machine [25] AB199 2.99 (2907) CC204 1/2a 204 cg-6821 II This study (Contigs) Drain/processing room [21] AB120 3.00 (2924) CC204 1/2a 204 cg-6821 II This study (Contigs) Sausage filler machine [21] C7 3.09 (3051) CC8 1/2a 8 cg-999 II This study (Contigs) Salmon gutting machine [25] F2365 2.91 (2808) CC1 4b 1 cg-2 I GenBank: AE017262.2 Mexican-style cheese [22] ScottA 3.02 (2966) CC2 4b 290 cg-94 I GenBank: CM001159.1 Clinical isolate [23] RO4 2.88 (2806) CC20 1/2a 20 cg-13510 II This study (Contigs) Dry cured salami [21] EGD-e 2.94 (2875) CC9 1/2a 35 cg-1 II GenBank: AL591824.1 Rabbit tissue [24, 28] Table 3. A summary of motifs. The table shows the detected methylated motifs and the total number of motifs in the RO15 genome. Motifs Type % Motifs Detected # of Motifs Detected # of Motifs in Genome mean Coverage ADGYACYTV m6A 44.03% 420 954 149.9 ADDTGGCA m6A 30.97% 455 1469 148.5 TVVARARG unknown 22.20% 1835 8265 148.8 ANNYASYA m6A 22.10% 3289 14879 149.0 DADGYATYA m6A 21.02% 326 1551 147.7 WNNTVVGCNTWNH unknown 18.14% 582 3208 149.2 AHNBAACA m6A 13.36% 839 6282 150.2 AGNNARNWW m6A 9.85% 2225 22596 148.6 TNNNDNNH unknown 9.22% 114413 1240313 148.9 TNNNCRVHNH unknown 7.59% 6652 87598 149.0 TVNNNNNG unknown 3.26% 7834 240556 149.6 Table 4. Comparison of CRISPR/Cas systems, anti-CRISPR genes, and prophage regions amongst the selected L. monocytogenes strains. Strain Average reduction of log 10 (cfu/ml) at 400 MPa CRISPR/Cas systems Number of spacers Self-targeting spacer predicted anti-CRISPR gene predicted Number of prophage predicted RO15 0.05 RliB-CRISPR, CRISPR I 64 yes AcrIIA1, A2 5 2HF33 0.15 RliB-CRISPR, CRISPR I, CRISPR II 62 yes AcrIIA1, A2, A3, A4 5 MB5 0.22 RliB-CRISPR, CRISPR II 39 yes AcrIIA1, A2, A3 5 AB199 0.26 RliB-CRISPR 3 no no 1 AB120 0.35 RliB-CRISPR 3 no no 1 C7 0.37 RliB-CRISPR 7 no no 6 F2365 0.47 RliB-CRISPR 3 no no 1 ScottA 0.68 RliB-CRISPR 3 no no 3 RO4 1.00 RliB-CRISPR 5 no AcrIIA1, A2, A3 1 EGD-e 2.07 RLIB-CRISPR 4 no AcrIIA1, A2, A3 2 Additional File Legends Additional File 1: Supplementary Text 1. L. monocytogenes st rain selection, including Table S1, Figure S1. Additional File 2: Table S2. Gene count data and differentially expressed gene list for both strains RO15 and ScottA based on RNA-Seq. Additional File 3: Table S3 . Table shows Average Nucleotide Identity (ANI) (based on BLAST) calculation results of each strain. For strains ScottA and F2365 the ANI score with other strains was lower than 95. ANI score between ScottA and F2365 was higher than 95. For the other strains ANI scores between each other were more than 98. Additional File 4: Figure S2 . Genome comparison of 200 L. monocytogenes strains mapped against strain RO15. The genomes were aligned using BLAST and visualized as ring figures. a) Each ring represents the whole genome alignment to strain RO15 (100 most similar genomes (based on BLAST) were displayed in (a) for simplification), b) ring figure zoomed in the prophage 1 region, c) ring figure zoomed in the prophage 2 region, d) ring figure zoomed in the prophage 3 region, e) ring figure zoomed in the prophage 4 region, f) ring figure zoomed in the prophage 5 region. The Refseq identifiers of 200 L. monocytogenes strains can be seen in figure. Genome features can be seen in Table S6. Red colored BLAST hits represent 90–98% identity, blue colored BLAST hits represent 80–90% identity. Black colored BLAST hits represent 100% identity. White gaps represent < 80% identity. Additional File 5: Table S4 and Figure S3. Table S4 shows identified antibiotic resistance genes and percentage identity of matching region in all strains using CARD database. Figure S3 shows average distance trees from alignments of protein sequences of identified antibiotic resistance genes. Additional File 6: Table S5. T-test against RO15 log 10 reduction. Additional File 7: Table S6. Barotolerant strains specific genes based on pan-genome wide association analysis. Table shows genes that have p < 0.01 based on pan-genome wide association analysis for barotolerant strains. Gene IDs of strain RO15 was used for this table. Orthologs of these genes with 95% identity were also seen in strains MB5 and 2HF33. In addition, the list of other publicly available L. monocytogenes genomes, where these genes were seen, are also provided. Supplementary Files AdditionalFile4FigureS2.pdf AdditionalFile1.docx AdditionalFile4FigureS2.pdf AdditionalFile2TableS2.xlsx AdditionalFile3TableS3.xlsx AdditionalFile5TableS4FigureS3.pdf AdditionalFile7TableS6.xlsx AdditionalFile6TableS5.xlsx Cite Share Download PDF Status: Published Journal Publication published 02 Jul, 2020 Read the published version in BMC Genomics → Version 2 posted Review # 1 received at journal 19 May, 2020 Review # 2 received at journal 18 May, 2020 Review # 3 received at journal 18 May, 2020 Reviewer # 1 agreed at journal 28 Apr, 2020 Reviewer # 2 agreed at journal 28 Apr, 2020 Reviewer # 3 agreed at journal 28 Apr, 2020 Editor assigned by journal 27 Apr, 2020 Reviewers invited by journal 27 Apr, 2020 Editor invited by journal 26 Apr, 2020 Submission checks completed at journal 24 Feb, 2020 You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-15141","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research article","associatedPublications":[],"authors":[{"id":530853,"identity":"1f30d5f9-9773-4672-9027-c4afb5aa584a","order_by":1,"name":"Ilhan Cem Duru","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA6UlEQVRIie3PsQrCMBCA4ZNCXU5nJYqvcFKoSAefpQh2qdCxU6mTi+4ZfA5dIwWniqvgoktnQRBBB1MVBcF0dcgPIdOXywHodH+YWcb8MvKzAggAAUsxhKQgxpuYAwB6kVRB4EPQzom85UkVompUlqcAHHfB/fP+SFGjg0kMIlB9rNpnHDx3th0u2pwS7E5Hkqh3IYaQuLw2nDMkgbQpxcZRTazrk/gZu1H0IEVT7NcU32RAcui6+GO2g+RZHDO7PpG7ULqMhYq0xhNrh6HT5OV+VruEUY9S77AXt9/k2febogjodDqdTt0dDNNFzOTZ3JwAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0003-3409-5215","institution":"Institute of Biotechnology, University of Helsinki","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Ilhan","middleName":"Cem","lastName":"Duru","suffix":""},{"id":530854,"identity":"320511d0-2cc7-4e2b-8aa4-12ceb84d975a","order_by":2,"name":"Margarita Andreevskaya","email":"","orcid":"","institution":"Institute of Biotechnology, University of Helsinki","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Margarita","middleName":"","lastName":"Andreevskaya","suffix":""},{"id":530855,"identity":"9815d085-56f4-434d-9bf5-b6cbce114345","order_by":3,"name":"Pia Laine","email":"","orcid":"","institution":"Institute of Biotechnology, University of Helsinki","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Pia","middleName":"","lastName":"Laine","suffix":""},{"id":530856,"identity":"f359aa56-9a71-4cde-85e0-6a1fefc8bd7c","order_by":4,"name":"Tone Mari Rode","email":"","orcid":"","institution":"Department of Process Technology, NOFIMA - Norwegian Institute of Food","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Tone","middleName":"Mari","lastName":"Rode","suffix":""},{"id":530857,"identity":"cebecdc8-cb78-43e4-a907-15a0a0d82174","order_by":5,"name":"Anne Ylinen","email":"","orcid":"","institution":"Institute of Biotechnology, University of Helsinki","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Anne","middleName":"","lastName":"Ylinen","suffix":""},{"id":530858,"identity":"2bc9cde8-8fcf-4d8a-ab9c-16b06f750f4a","order_by":6,"name":"Trond Løvdal","email":"","orcid":"","institution":"Department of Process Technology, Nofima - Norwegian Institute of Food","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Trond","middleName":"","lastName":"Løvdal","suffix":""},{"id":530859,"identity":"2d74a6d0-1f94-42e5-9793-001bdb61b493","order_by":7,"name":"Nadav Bar","email":"","orcid":"","institution":"Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim, Norway","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Nadav","middleName":"","lastName":"Bar","suffix":""},{"id":530860,"identity":"214785c7-f8a6-421b-ab80-597576590e2d","order_by":8,"name":"Peter Crauwels","email":"","orcid":"","institution":"Institute of Microbiology and Biotechnology, Ulm University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Peter","middleName":"","lastName":"Crauwels","suffix":""},{"id":530861,"identity":"6afa4396-3b87-43a9-8f2a-c6e8d6fd45f4","order_by":9,"name":"Christian Riedel","email":"","orcid":"","institution":"Institute of Microbiology and Biotechnology, Ulm University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Christian","middleName":"","lastName":"Riedel","suffix":""},{"id":530862,"identity":"93fff618-9c1a-4e7a-b9b5-4db19dd60ee8","order_by":10,"name":"Florentina Ionela Bucur","email":"","orcid":"","institution":"Universitatea Dunarea de Jos din Galati","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Florentina","middleName":"Ionela","lastName":"Bucur","suffix":""},{"id":530863,"identity":"0e5ebd3b-3fa7-44a4-be4c-f340094f4eca","order_by":11,"name":"Anca Ioana Nicolau","email":"","orcid":"","institution":"Universitatea Dunarea de Jos din Galati","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Anca","middleName":"Ioana","lastName":"Nicolau","suffix":""},{"id":530864,"identity":"368c8d38-a508-4e0c-a3a7-e7f3f6cbc8c3","order_by":12,"name":"Petri Auvinen","email":"","orcid":"","institution":"Institute of Biotechnology, University of Helsinki","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Petri","middleName":"","lastName":"Auvinen","suffix":""}],"badges":[],"createdAt":"2020-02-24 15:24:17","currentVersionCode":2,"declarations":"","doi":"10.21203/rs.2.24582/v2","doiUrl":"https://doi.org/10.21203/rs.2.24582/v2","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12864-020-06819-0","type":"published","date":"2020-07-02T12:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":1084879,"identity":"39fb860f-d1df-45a0-9497-55b05612f1a2","added_by":"auto","created_at":"2020-05-13 14:57:28","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":187270,"visible":true,"origin":"","legend":"Viable cell counts bar chart. Viable cell counts log10(cfu/ml) of untreated controls and samples treated for 1 minute at 400 MPa (a) or 600 MPa (b). Gray bar represents control samples, blue bar represents treated sample. Error bars represent standard deviation (ANOVA; *, p \u003c 0.02).","description":"","filename":"figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/figure1.png"},{"id":1084881,"identity":"566a45ae-cdd8-402e-aeb0-f20b491af3bc","added_by":"auto","created_at":"2020-05-13 14:57:28","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":592074,"visible":true,"origin":"","legend":"Circular map of the L. monocytogenes strain RO15 chromosome with predicted prophage regions, CRISPR region and anti-CRISPR genes. Five prophage regions were predicted in the chromosome of L. monocytogenes strain RO15 using PHASTER tool, shown in figure with blue and green color. Two anti-CRISPR gene regions were annotated within the prophage region 4 and 5. RliB-CRISPR/Cas system was located at position 525-527 kbp, following CRISPR-I system located the position 535-547 kbp with cas1-8 genes and a CRISPR array with 54 spacers.","description":"","filename":"figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/figure2.png"},{"id":1084883,"identity":"f06fee4d-299e-49a6-ae88-75c192fdd450","added_by":"auto","created_at":"2020-05-13 14:57:28","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":240366,"visible":true,"origin":"","legend":"Genome comparison of the selected nine strains mapped against strain RO15. The genomes were aligned using BLAST and visualized as ring figures. Each ring represents the genome alignment to strain RO15. From inside to outside, strains are located according to increasing hits of high percent identity to strain RO15 (Order from inside to outside: strain F2365, ScottA, AB199, AB120, RO4, MB5, EGD-e, C7, and 2HF33. Color represents BLAST hit identity percentage).","description":"","filename":"figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/figure3.png"},{"id":1084885,"identity":"69ebecc9-918e-4811-82a1-8b8a940a7b79","added_by":"auto","created_at":"2020-05-13 14:57:29","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":218935,"visible":true,"origin":"","legend":"Visualization of CRISPR systems in strain RO15, 2HF33, and MB5. The figure shows a representation of CRISPR systems in strain RO15, 2HF33, and MB5. These three strains contained more than one CRISPR system, while the rest of the selected strains in the study contained only the RliB-CRISPR system. Arrows represent genes, rectangles represent repeat/spacer arrays, the numbers below the rectangles indicate number of spacers in the array. For simplification, sizes of the arrows do not correspond to the actual size of the genes.","description":"","filename":"figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/figure4.png"},{"id":1084886,"identity":"0f63baf4-612e-4ebe-a2bc-a642fe2f71a9","added_by":"auto","created_at":"2020-05-13 14:57:29","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":97872,"visible":true,"origin":"","legend":"Pan-genome comparison of selected strains. A phylogenetic tree was created based on core genome alignments of the selected strains. The matrix shows presence (blue) and absence (white) of core and accessory genes. Core genes are found in all strains, accessory genes are found in at least one strain.","description":"","filename":"Figure5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/Figure5.jpg"},{"id":15667007,"identity":"6982c4d5-8530-416b-98df-07239ad02804","added_by":"auto","created_at":"2021-11-18 13:39:52","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1393285,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/1ffa6190-1f4e-4e3b-a9bd-114c518f675c.pdf"},{"id":1084891,"identity":"cd6f6001-afab-41f6-af0c-e7f4b27eb41f","added_by":"auto","created_at":"2020-05-13 14:57:30","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":17807826,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile4FigureS2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile4FigureS2.pdf"},{"id":1084890,"identity":"02dc2c6d-1eb0-4cbf-8996-95d4cc6c74a8","added_by":"auto","created_at":"2020-05-13 14:57:29","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":32055,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile1.docx","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile1.docx"},{"id":1084889,"identity":"e6314579-8e41-4044-8d38-2458e29af7fd","added_by":"auto","created_at":"2020-05-13 14:57:29","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":17807826,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile4FigureS2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile4FigureS2.pdf"},{"id":1084888,"identity":"717d373a-d525-45b7-865c-612665381a95","added_by":"auto","created_at":"2020-05-13 14:57:29","extension":"xlsx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":1119960,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile2TableS2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile2TableS2.xlsx"},{"id":1084887,"identity":"b5096383-b650-4c21-a557-5c6987e9318f","added_by":"auto","created_at":"2020-05-13 14:57:29","extension":"xlsx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":9854,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile3TableS3.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile3TableS3.xlsx"},{"id":1084880,"identity":"79473e96-3abc-4b11-9669-4edb03a10255","added_by":"auto","created_at":"2020-05-13 14:57:28","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":69221,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile5TableS4FigureS3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile5TableS4FigureS3.pdf"},{"id":1084884,"identity":"74c0f621-e8ec-4924-bd84-7c9ca68a10a1","added_by":"auto","created_at":"2020-05-13 14:57:28","extension":"xlsx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":33550,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile7TableS6.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile7TableS6.xlsx"},{"id":1084882,"identity":"c2520ca5-507e-4f60-bc93-f6b67a299367","added_by":"auto","created_at":"2020-05-13 14:57:28","extension":"xlsx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":10263,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile6TableS5.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-15141/v2/AdditionalFile6TableS5.xlsx"}],"financialInterests":"","formattedTitle":"\u003cp\u003eComplete genome of the barotolerant \u003cem\u003eListeria monocytogenes\u003c/em\u003e RO15 strain and comparison with other strains isolated from food and food processing environments\u003c/p\u003e","fulltext":[{"header":"Background","content":"\u003cp\u003e\u003cem\u003eListeria monocytogenes \u003c/em\u003eis a well-known foodborne pathogen that may cause listeriosis, a severe infection with high hospitalization rate which can be fatal in humans and some animal species [1]. Although being a relatively rare foodborne disease, increasing numbers of listeriosis cases have been reported in the EU/EEA countries since 2008 [2]. \u003cem\u003eL. monocytogenes\u003c/em\u003e is generally found in agricultural, aquacultural, and food processing environments [3]. Listeriosis outbreaks have been associated with consumption of contaminated food, such as meat, milk, cheese, and fish [4]. The food industry has to process food in such a way to meet food safety microbiological criteria (Commission Regulation (EC) No 1441/2007 amending Commission Regulation (EC) No 2073/2005 [5]), which include the presence in limited numbers (100 cfu/g) or absence of \u003cem\u003eL. monocytogenes\u003c/em\u003e (absence in 25 g product). Food processing aimed at \u003cem\u003eL. monocytogenes\u003c/em\u003e inactivation is challenging due to its pronounced ability to adapt to different environments, and to survive under various stress conditions [6]. In addition, it is important to preserve the food quality and nutritional value during food processing. High pressure processing (HPP) is an alternative to thermal processes to inactivate pathogens, including \u003cem\u003eL. monocytogenes\u003c/em\u003e, and maintain a high quality of the product. Only very small or no quality changes, such as loss of color, nutritional value, flavor, and texture, have been reported for HPP products [7] . Several studies showed that HPP products, such as meat, milk, juice, vegetables, and sauce are well accepted by the consumer, and reported that HPP preserves the taste [8]. \u0026nbsp;Depending on the food products, pressures currently used in the food industry are between 100 and 600 MPa, with a holding time ranging from one to several minutes [9]. HPP has been tested and reported as an effective processing method for several products including fruits (and fruit juices) [10], meat [11], cheese [12], fish [13] and vegetables [14].\u003c/p\u003e\n\u003cp\u003eIt has been shown that HPP has varying effects on different target organisms. For example, a pressure of 300 MPa is sufficient to inactivate most Gram-negative bacteria, while more than 400 MPa is needed for an inactivation of Gram-positive bacteria [15, 16]. It is also known that pressure tolerance can differ even among strains of the same species. Differences in pressure tolerance have been reported for strains of several species including \u003cem\u003eCronobacter sakazakii\u003c/em\u003e (previously \u003cem\u003eEnterobacter sakazakii\u003c/em\u003e)[17], 24 different serotypes of \u003cem\u003eSalmonella enterica\u003c/em\u003e [18], and \u003cem\u003eL. monocytogenes\u003c/em\u003e [19, 20]. In \u003cem\u003eL. monocytogenes\u003c/em\u003e strains, pressure tolerance varies between 300 - 500 MPa [19]. To our knowledge, genomic profiling and comparison has not been performed for barotolerant and barosensitive \u003cem\u003eL. monocytogenes\u003c/em\u003e strains. In this study, we selected 10 \u003cem\u003eL. monocytogenes\u003c/em\u003e strains, isolated from either foods, food processing environments or clinical sources, to test their tolerance towards HPP at 400 and 600 MPa, compared their genomes, and investigated whether genetic traits may be associated with pressure tolerance.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e\u003cstrong\u003ePressure treatment and reduction of viable cell counts\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eReduction of viable cell counts (colony forming units, cfu) after pressure treatment at 400 and 600 MPa for 1 minute showed that pressure tolerance differs between strains. The variance in colony forming units (cfu) of the treated samples was significantly larger (p\u0026lt;0.02, see ANOVA results below) compared to control, indicating a high variance in the level of tolerance of \u003cem\u003eL. monocytogenes\u003c/em\u003e. At 400 MPa for 1 minute, the 10 strains exhibited an average log\u003csub\u003e10\u003c/sub\u003e reduction of 0.57 cfu/ml, ranging from 0.05 log\u003csub\u003e10\u003c/sub\u003e cfu/ml for the most barotolerant strain (RO15) to 2.07 log\u003csub\u003e10\u003c/sub\u003e cfu/ml for the most pressure sensitive strain (EGD-e). Similar results were obtained at 600 MPa. Here, the 10 strains exhibited an average log\u003csub\u003e10\u003c/sub\u003e cell number reduction of 7.06 cfu/ml, with a range of 5.42 to 8.27 log\u003csub\u003e10\u003c/sub\u003e cfu/ml (Table 1). Strain RO15 was also the most barotolerant strain based on an initial screening including several other \u003cem\u003eL. monocytogenes\u003c/em\u003e strains (Supplementary text 1, Table S1, Figure S1).\u003c/p\u003e\n\u003cp\u003eOne-way analysis of variance (ANOVA), comparing the pressure (400 MPa) treated samples of each strain to the control samples, showed that the mean cfu/ml for treated samples was significantly lower than the control for all strains (p\u0026lt;0.02), except for strain RO15 (p=0.15) (Figure 1a). The same statistical analysis for HPP at 600 MPa indicated that all strains including strain RO15 had significantly (p\u0026lt;0.01) lower cfu/ml in treated samples compared to controls (Figure 1b).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGenome sequencing, general features and RNA-Seq\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe sequenced the genomes of seven \u003cem\u003eL. monocytogenes \u003c/em\u003estrains for which no genome sequences were available in public databases. Genomes of strains RO15, 2HF33, MB5, AB199, AB120, C7, and RO4 were sequenced using Illumina MiSeq instrument and strain RO15 was sequenced using Pacbio RSII. Sequences of these seven strains were assembled and three additional strains (ScottA, F2365 and EGD-e, genome sequences of which are available in public databases) were used for comparative genome analysis. Assembly of PacBio long reads of strain RO15 resulted in one continuous 3,042,507 bp sized chromosome (Figure 2) at an average 308-fold sequencing coverage. In addition to the chromosome, a contig with a complete circular prophage sequence of 38,811 bp was obtained, which was also found as part of the chromosome (2729417 - 2770759 bp). All genomes had a similar size, GC content and number of coding sequences (CDS) (Table 2).\u003c/p\u003e\n\u003cp\u003eThe serotype of the strains was reported in previous studies [21, 22, 23, 24, 25] (Table 2). Although RO15 was reported as a serovar 4b strain using multiplex PCR in a previous study [21], our genome-based prediction suggests that it belongs to serovar 1/2a. Sequences for \u003cem\u003eORF2110\u003c/em\u003e and \u003cem\u003eORF2819\u003c/em\u003e primers used for identification of serovar 4b strains [24] were not found in the genome of strain RO15 based on our sequence match analysis, whereas sequences for primers targeting \u003cem\u003elmo0737\u003c/em\u003e, which are indicators of serovar 1/2a strains [24] were present. Multilocus sequence typing (MLST) based on 7 loci, core genome MLST (cgMLST; based on Moura scheme [26]), and clonal complex (CC) of the strains were also assigned based on the genome sequences (Table 2). Lineage assignment showed that only ScottA and F2365 belonged to lineage I and all other strains were members of lineage II (Table 2).\u003c/p\u003e\n\u003cp\u003eIn addition to genome sequencing, transcriptome analysis using RNA-seq for strains RO15 and ScottA provided a basic view of transcriptional activity of the genomes. Differential expression analysis indicated that virulence genes and heat shock genes were upregulated after high pressure treatment in strain ScottA (Table S2).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethylated DNA Motifs\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eHigh PacBio sequencing coverage allowed us to analyze DNA methylation modification motifs in strain RO15 in addition to assembling the genome. Using the long read modification data, 11 methylated sequence motifs were detected in the genome (Table 3). None of the detected motifs had a partner motif, i.e. a reverse-complementary sequence, but all detected motifs were only partially modified in the genome with less than 50% methylated motifs. While most of the motifs have already been deposited in the REBASE database [29] DADGYATYA, WNNTVVGCNTWNH, AHNBAACA, AGNNARNWW were novel, i.e. they have not been described as potential methylation sites previously. None of the detected motifs have been reported as recognition sequence motif for a restriction enzyme in the REBASE database.\u003c/p\u003e\n\u003cp\u003eWe predicted one type II cytosine-5 DNA methyltransferase gene (OCPFDLNE_00657), and three type II N4-cytosine or N6-adenine DNA methyltransferase genes (OCPFDLNE_02168, OCPFDLNE_02626, OCPFDLNE_02808) in the strain RO15 genome. In addition, genes for a type IV methyl-directed restriction enzyme (OCPFDLNE_00324) and type II restriction enzymes (OCPFDLNE_00658, OCPFDLNE_02625, OCPFDLNE_02807) were predicted. These predicted methyltransferases and restriction enzymes had significant (e-value \u0026lt;1E-50) BLASTP hits in the REBASE protein sequences database [29]. However, their recognition sequences are unknown. OCPFDLNE_02625 and OCPFDLNE_02807 type II restriction enzyme genes in prophage regions were expressed based on RNA-seq data.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGenomic comparison of the selected strains.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn the genome assembly we also identified a circular phage as an independent contig. While looking after phage-originating genome parts, prophage prediction revealed five prophage regions (10.7 kb to 47.9 kb sized) in the RO15 genome (Figure 2). Prophage (region) 5 had the same sequence as the separate circular phage. RNA-Seq count data suggested that most of the genes of prophage 1,3 and 5 in RO15 were transcribed. Subsequently, the prophage prediction was performed for all strains, which showed that all strains had at least one or more prophage regions in the genome with a maximum of six prophage regions in strain C7 (Table 4). One of the predicted prophage regions in ScottA was also transcribed based on the RNA-seq data.\u003c/p\u003e\n\u003cp\u003eGenome alignment of the selected nine strains against the strain RO15 (Figure 3) showed large sequence gaps between strain RO15 and the other strains. The gaps were mainly related to prophage regions with prophage region 3 being specific for strain RO15. Prophage region 2 was only seen in the strain 2HF33. Prophage region 4 was partially seen in strains 2HF33, EGD-e, MB5 and ScottA. Similarly, prophage region 5 was partially seen in strains 2HF33, C7, and RO4. In addition, strains ScottA and F2365 had less aligned regions compared to the other strains. Average nucleotide identity (ANI) results showed that ANI scores of strains ScottA and F2365 with other strains were lower than 95 (Table S3). To study how the large sequence gaps are localized in the other publicly available genomic sequences of \u003cem\u003eL. monocytogenes\u003c/em\u003e, all 200 complete \u003cem\u003eL. monocytogenes\u003c/em\u003e genomes in RefSeq database [30] were downloaded and aligned to strain RO15 (Figure S2). The visualization of the alignment showed that prophages 2, 3 and 4 were seen only in the minority of the \u003cem\u003eL. monocytogenes \u003c/em\u003estrains, while prophages 1 and 5 were seen in the majority of the \u003cem\u003eL. monocytogenes\u003c/em\u003e strains. The comparison indicated that these prophage regions were common locations of variance between \u003cem\u003eL. monocytogenes\u003c/em\u003e strains.\u003c/p\u003e\n\u003cp\u003eAnnotation of CRISPR systems revealed that the RliB-CRISPR system was seen in all the strains, which is in line with previous RliB-CRISPR system studies [31, 32]. Interestingly, CRISPR I or CRISPR II system genes were present only in strains RO15, 2HF33, and MB5 (Figure 4), which exhibited the lowest reduction in log\u003csub\u003e10\u003c/sub\u003e cfu/ml with the 400 MPa pressure treatment (Table 1). Number of spacers in these strains were also significantly (p \u0026lt; 0.001) higher compared to barosensitive strains. The alignment of the spacer sequences of the CRISPR systems back to the genome itself revealed that only strains RO15, 2HF33, and MB5 contained self-targeting spacers with 100% identity. As expected, spacer sequences were aligned to the prophage regions, except one spacer sequence in RO15, which aligned to the \u003cem\u003eaddB\u003c/em\u003e gene (OCPFDLNE_02427) located in the chromosome encoding an ATP-dependent helicase.\u003c/p\u003e\n\u003cp\u003eUsing prediction tools we detected anti-CRISPR genes in the prophage regions (Table 4) of strains RO15, 2HF33, MB5, RO4, and EGD-e. Homologues of all four previously annotated \u003cem\u003eListeria \u003c/em\u003eanti-CRISPR genes, i.e. \u003cem\u003eacrIIA1\u003c/em\u003e, \u003cem\u003eacrIIA2\u003c/em\u003e, \u003cem\u003eacrIIA3\u003c/em\u003e, and \u003cem\u003eacrIIA4\u003c/em\u003e [33], were seen in strain 2HF33. Gene \u003cem\u003eacrIIA4\u003c/em\u003e was not seen in strains MB5, RO4, and EGD-e, but the rest of the anti-CRISPR genes were present. RO15 contains two copies of \u003cem\u003eacrIIA1 \u003c/em\u003e(OCPFDLNE_02770, OCPFDLNE_02583) and \u003cem\u003eacrIIA2 \u003c/em\u003e(OCPFDLNE_02582) (Figure 2) and we observed expression of these anti-CRISPR genes in strain RO15.\u003c/p\u003e\n\u003cp\u003eAs antibiotic resistance and pressure tolerance were linked in a previous study [19], we also searched antibiotic resistance genes in all strains to identify relation of antibiotic resistance genes and pressure tolerance. The same antibiotic resistance gene families were detected in all the 10 strains (Table S4). Multiple sequence alignment of the detected antibiotic resistance genes and the following average distance tree generation showed that amino acid sequence of the \u003cem\u003enorB\u003c/em\u003e gene (encoding for a quinolone resistance protein) (OCPFDLNE_03068) was slightly different in barotolerant strain RO15 compared to the other strains (Figure S3). Similarly, for the \u003cem\u003elin\u003c/em\u003e gene (encoding for a lincomycin resistance protein) (OCPFDLNE_00980) amino acid difference was seen for strains 2HF33 and RO15 (Figure S3).\u003c/p\u003e\n\u003cp\u003eRoary pan-genome pipeline suggested that the 10 \u003cem\u003eL. monocytogenes \u003c/em\u003estrains contain a total of 4820 orthologous gene clusters. Of these genes, 2247 were core genes found in all strains and 2573 genes were accessory genes found in at least one strain. The core genome was used for constructing a phylogenetic tree, which indicated that the two serovar 4b strains (ScottA and F2365) are closely related to each other and cluster separately from the serovar 1/2a strains in the phylogenetic tree. In addition, there was also a clear difference in accessory genome for serovar 4b strains compared to serovar 1/2a strains (Figure 5).\u003c/p\u003e\n\u003cp\u003eTo test any significant association between pressure tolerance and (clusters of) genes in the accessory genome, we performed a pan-genome wide association analysis using Scoary. Based on the pairwise comparison of reduction in log\u003csub\u003e10\u003c/sub\u003e (cfu/ml) against strain RO15 using Student\u0026rsquo;s t-test (Table S5), a statistically significant difference compared to RO15 was seen in all strains except MB5 and 2HF33. Therefore, strains RO15, 2HF33, MB5 were used as barotolerant strains for the pan-genome association analysis. Scoary results showed that 13 gene clusters (Table S6) had p-values \u0026lt; 0.01 for the association with barotolerant strains, i.e., the genes were only seen in barotolerant strains. Of these, 10 gene clusters were located in the prophage regions, but most of the genes were annotated as hypothetical proteins (Table S6). These prophage genes were also searched for in 200 complete \u003cem\u003eL. monocytogenes \u003c/em\u003estrains and found in some strains (Table S6). Interestingly, genes OCPFDLNE_02579 and OCPFDLNE_02580 were only seen in strains that harbored anti-CRISPR genes, Cas type I or II CRISPR system and self-targeting spacers (Table S6).\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eHPP is commonly used in the food industry to inactivate foodborne pathogens and spoilage organisms. Depending on the type of food product, up to ~600 MPa pressure is applied [9]. It has also been shown that combinations of HPP and biocontrol agents, such as virulent bacteriophages and bacteriocins, have synergistic effects in the inactivation of the target pathogens in food [34, 35]. The pressure tolerance level varies between different species, strains, and even isolates [16, 19, 36, 37]. Here, we tested pressure tolerance of 10 \u003cem\u003eL. monocytogenes \u003c/em\u003estrains, compared their genomes and predicted genome features related to pressure tolerance.\u003c/p\u003e\n\u003cp\u003ePressure treatment using 600 MPa for 1 minute caused more than 5 log\u003csub\u003e10\u003c/sub\u003e reduction in all selected strains, which is generally considered sufficient for food safety regulations. According to the Food Safety and Inspection Service (United States Department of Agriculture), 5 log\u003csub\u003e10\u003c/sub\u003e reduction is considered a full lethality treatment for \u003cem\u003eL. monocytogenes\u003c/em\u003e [38]. This suggests that the strains used in this study were relatively sensitive to 600 MPa pressure treatment. Similarly, an earlier study reported that pressure treatment at 500 MPa for 10 minutes provided sufficient reduction in viable counts to reach desired level of safety for all except one \u003cem\u003eL. monocytogenes\u003c/em\u003e strains tested [19]. However, the lower pressure levels, such as 400 MPa, would be more relevant for industrial applications, therefore, we focused more on the results obtained with the 400 MPa treatment. Among the strains tested, RO15 was the most barotolerant strain when processed at both 400 and 600 MPa, which is in line with the initial selection process of strains (Supplementary text 1). Based on ANOVA, RO15 was the only strain for which no statistically significant reduction was observed with the 400 MPa treatment (Figure 1a). Therefore, we defined the strain RO15 as barotolerant. It has been shown that the level of inactivation by HPP can be affected by the chemical composition of the food product. Some food products, such as milk and cheese, have baroprotective effects on microorganisms during HPP treatment [39, 40]. However, experiments in this study were performed using TSBYE broth and thus do not take into account the effects of food composition on HPP. Temperature during pressure treatment can have an effect on microbial inactivation depending on treatment time, and it has been shown that increasing the temperature from 25 \u0026deg;C to 35 \u0026deg;C has a significant effect on the viability loss of \u003cem\u003eL. monocytogenes\u003c/em\u003e [41]. In this study, temperature during pressure treatment increased up to 33 \u0026deg;C for 400 MPa treatment and 38 \u0026deg;C for 600 MPa treatment due to adiabatic heating. However, since treatment time was only one minute, the effect of temperature rise was expected to be minimal.\u003c/p\u003e\n\u003cp\u003eSerotypes of the selected strains were shown in the earlier studies based on agglutination method, multiplex-PCR and genome sequencing [21, 22, 23, 24, 25] (Table 2). Here, we predicted the serotype of all strains based on their genome sequences. This confirmed the previous serotyping of all strains except RO15, which was reported to be a serotype 4b strain based on multiplex-PCR [21]. Serotype 4b strains should contain serotype 4 marker genes (\u003cem\u003eORF2110\u003c/em\u003e and \u003cem\u003eORF2819\u003c/em\u003e) and lack \u003cem\u003elmo0737 \u003c/em\u003emarker gene sequence as described by Doumith et al. [24]. However, according to the genome sequence, serotype 4 marker genes were absent, and a \u003cem\u003elmo0737\u003c/em\u003e homologue was present suggesting that the serotype of strain RO15 is indeed 1/2a. The phylogenetic tree that we created based on the core genome showed that there is considerable genetic variation between serovars. Serovar 4b strains (ScottA and F2365) clustered separately from the other strains (Figure 4). Strain RO15 was not clustered together with other serovar 4b strains hence these results supported our gene-based prediction of serotype 1/2a of strain RO15.\u003c/p\u003e\n\u003cp\u003ePacBio sequencing provides not only the genome sequence but also methylation data [42], which gives an opportunity to analyze restriction-modification systems and their recognition motifs. In this study, we did not observe a genuine methylated motif based on PacBio sequencing data of strain RO15. Similarly, PacBio methylation data of nine other published \u003cem\u003eL. monocytogenes\u003c/em\u003e strains without genuine methylated motifs were also seen in REBASE PacBio list database [29], which showed that it is not uncommon to have only partially methylated motifs in \u003cem\u003eL. monocytogenes\u003c/em\u003e.\u003c/p\u003e\n\u003cp\u003ePrevious studies based on \u003cem\u003eL.\u003c/em\u003e \u003cem\u003emonocytogenes \u003c/em\u003estrain ScottA and LO28 barotolerant isolates showed that there is a phenotypic and genotypic variation between barotolerant isolates [36, 37, 43], which indicates that there are variety of factors which can lead to pressure tolerance. Therefore, it is a challenge to link a genomic profile with pressure tolerance in different strains. Nevertheless, pan-genome association analysis results suggest that there was a genotypic difference between barotolerant and barosensitive strains. A total of 13 genes were significantly (p\u0026lt;0.01) associated with barotolerant strains. Interestingly, most of the barotolerant strain associated genes (Table S6) were located in the prophage regions in the studied genomes. In addition, extension search of these genes within all complete \u003cem\u003eL. monocytogenes\u003c/em\u003e strain genomes showed that some phage genes (OCPFDLNE_02579 and OCPFDLNE_02580) were only seen in strains that contain inactivated CRISPR/Cas system (Table S6). It has been shown that prophages can provide increased biofilm formation and can be beneficial for stress coping in both \u003cem\u003eL. monocytogenes\u003c/em\u003e and \u003cem\u003eEscherichia coli\u003c/em\u003e [44, 45]. We also observed that barotolerant strains harbored a slightly higher number of prophages compared to barosensitive strains (based on average number of prophages in barotolerant and barosensitive strains). Therefore, we believe that prophages might play a role in barotolerance in \u003cem\u003eL. monocytogenes\u003c/em\u003e.\u003c/p\u003e\n\u003cp\u003eIt was also interesting to see that two or more CRISPR-Cas systems, self-targeting spacers, and anti-CRISPR genes were seen together only in the three most barotolerant strains (RO15, MB5, and 2HF33). Since the existence of a self-targeting spacer indicates that the activity of the CRISPR/Cas systems is inhibited [46], it can be predicted that anti-CRISPR proteins detected in barotolerant strains inactivate CRISPR/Cas system. Previous studies have also shown that anti-CRISPR proteins are able to inhibit several types of CRISPR systems [33, 47]. The observed active transcription of anti-CRISPR genes in RO15 prophages based on RNA-seq may also support this prediction. It has been shown that bacteria tend to lose CRISPR/Cas systems, since they can be harmful to the host itself. Immunopathological effects through partially matching spacers were reported unless the phage carries anti-CRISPR genes [48]. The anti-CRISPR genes found in prophages and inhibition of the CRISPR/Cas system may be the reason why barotolerant strains carry type I or type II CRISPR/Cas systems. We observed that more than 50% of the \u003cem\u003eL. monocytogenes\u003c/em\u003e strains that harboring type I or type II CRISPR/Cas system also had anti-CRISPR genes (Table S6). CRISPR/Cas systems can have alternative roles in bacteria, such as roles in pathogenesis or role in modulating biofilm formation [49], however the role of inhibited CRISPR/Cas system is not known. More studies are required to support the relation between inhibited CRISPR/Cas systems and barotolerance.\u003c/p\u003e\n\u003cp\u003eRNA-seq revealed the general transcriptome profile of strains RO15 and ScottA. Significantly upregulated heat-shock genes after pressure treatment (chaperone and clp protease genes) in ScottA (Table S2) might indicate that proper folding of proteins plays an important role in cell recovery after pressure treatment. A previous study also showed that the expression levels of Clp proteins were significantly higher in mutant HPP-tolerant ScottA isolate compared to wild type ScottA [43].\u003c/p\u003e\n\u003cp\u003eA previous study concluded that antibiotic resistant \u003cem\u003eL. monocytogenes \u003c/em\u003estrains are more tolerant to pressure at 400 MPa [19]. Here, annotation results did not show any strain-specific antibiotic resistance gene. Nevertheless, multiple sequence alignment of predicted antibiotic resistant genes showed that there were slight differences in amino acid sequences across the strains (Figure S3). However, it is not known that these amino acid differences cause antibiotic resistance advantage, and further studies are required to link the amino acid sequence variations of antibiotic resistance genes and pressure tolerance.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eIn this study we noticed that barotolerance is manifested at pressures lower than 600MPa. Strain RO15 was identified as the most barotolerant strain for 400 MPa 1 minute pressure treatment. Genome sequence of seven new strains and genome comparison of 10 strains revealed that the three most barotolerant strains have CRISPR-Cas genes and anti-CRISPR genes in their genomes. In addition, the average number of prophages was slightly higher in barotolerant strains compared to barosensitive strains. Furthermore, we have predicted 10 phage genes that might be related to pressure tolerance based on the pan-genome association test. Therefore, we conclude that prophages and inhibited prophage defense systems may be linked to pressure tolerance. The observation described above may argue for the use of phage cocktails as a pretreatment before HPP and will allow to reduce pressure and holding time.\u003c/p\u003e"},{"header":"Methods","content":"\u003cp\u003e\u003cstrong\u003eStrains, Growth conditions and Pressure Treatment\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eStrains Scott A (CIP103575) and EGD-e (CIP107776) were obtained from Centre de Ressources Biologiques de l'Institut Pasteur, Paris, France, and strain F2365 (LMG23356) from Laboratorium voor Microbiologie, UGent, Gent, Belgium. Strains RO4, RO15, AB120 and AB199 are from Dunarea de Jos University of Galati, Romania, and have been isolated in the Promise FP7 project either from food illegally introduced to Romania or from meat processing environments. All other strains were isolated from the environment as indicated in Table 2. The strains were stored on Microbank beads with cryopreservatives (Pro-Lab Diagnostics, Toronto, Canada) at - 80 \u0026deg;C prior to use. The bacteria were passaged twice in tryptic soy broth (TSB) supplemented with 0.6% (w/v) yeast extract (TSBYE; Oxoid, Basingstoke, Hampshire, England). Prior to pressure treatments, bacteria were grown overnight in 50 mL TSBYE at 37 \u0026deg;C with rotary agitation (150 rpm), resulting in cells in early stationary phase and with a target concentration of approx. 10\u003csup\u003e9\u003c/sup\u003e cfu/mL. Aliquots (10 mL) of the cultures were packaged in sous-vide plastic pouches and sealed without using vacuum, and 10 mL was transferred to 15 mL falcon tubes to serve as untreated controls.\u003c/p\u003e\n\u003cp\u003eHPP was carried out using the QFP 2L-700 (Avure Technologies Inc., Columbus, USA). The cylindrical pressure vessel had 10 x 25.4 cm dimensions, 2 L capacity and 690 MPa upper pressure limit. Temperature of the pressure medium (water) was tracked with a K-type thermocouple located on the external surface of the samples. A holding time of 1 minute was used, pressures of 400 and 600 MPa, and ambient vessel water temperature (20-22 \u0026deg;C). Due to adiabatic heating, water temperatures in the middle of the vessel at the end of pressure treatment had risen to 31-33 \u0026deg;C after the 400 MPa treatment, and 36-38 \u0026deg;C after the 600 MPa treatment. Straight after pressure treatment, 400 MPa pressurized and untreated samples were serially ten-fold diluted in TSBYE and plated in triplicate on tryptic soy agar with 0.6% yeast extract (TSAYE; Oxoid) by using a spiral plater (Eddy Jet; IUL Instruments, Barcelona Spain). Pressurized samples at 600 MPa were additionally plated manually (100 \u0026mu;L) without being diluted. TSAYE plates were incubated at 37 \u0026deg;C for 48 hours prior to counting the colonies and estimating bacterial inactivation. Two consecutive trials of the methodology were performed (Exp. 1 and 2).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDNA extraction\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDNA of each strain was extracted from 5 ml of a culture grown overnight in BHI broth at 37 \u0026deg;C with aeration on a rotary shaker. Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) was used according to the manufacturer's instructions.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eLibrary preparation, genome sequencing, \u003cem\u003ede novo \u003c/em\u003eassembly, base modification detection and motif analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eL. monocytogenes\u003c/em\u003e strain RO15 was sequenced using PacBio RSII (Pacific Bioscience, Menlo Park, CA, USA) and Illumina Miseq (Illumina, San Diego, CA, USA). Genomic DNA PacBio library was prepared according to the manufacturer's Template Preparation and Sequencing Guide using DNA Template Prep Kit 2.0 and DNA/Polymerase Binding Kit P6. The Nextera XT protocol was used for the enzymatic genomic DNA fragmentation and Illumina sequencing library preparation. Pacbio reads were assembled using HGAP3 protocol [50] in SMRTPortal 2.3.0. Obtained assembly of chromosomal and phage sequences were checked and circularized using Gap4 program [51] and finally the chromosomal DNA sequence was set to start from \u003cem\u003ednaA\u003c/em\u003e gene. cutadapt v1.8.1 [52] was used with -m 200 and -q 25 options to trim Nextera adapter sequences and quality filtering. Trimmed reads were mapped against circularized chromosomal and phage sequences using bwa-mem [53]. Short indels within homopolymeric regions were corrected using pilon v1.16 [54]. Average sequencing coverages at the whole genome level were 308X in Pacbio data and 157X in Illumina data, respectively. DNA base modifications and motifs were analyzed using Modification and Motif analysis protocol implemented in SMRTPortal 2.3.0 with default parameters.\u003c/p\u003e\n\u003cp\u003eFor \u003cem\u003eL. monocytogenes\u003c/em\u003e strain RO4, AB199, and AB120, Nextera DNA Library (Illumina, San Diego, CA, USA) preparation and for strain 2HF33, MB5, and C7, Nextera XT DNA Library preparation was performed. Paired-end sequencing was performed using Illumina Miseq. RTA v1.18.54 and bcl2fastq v2.17.1.14 were used for base calling, demultiplexing and converting data to fastq format. The cutadapt v1.8.1 [52] was used with -m 200 and -q 25 options to trim Nextera adapter sequences and quality filtering. Reads aligning to PhiX genome, which was used as spike-in during Illumina sequencing, were removed by using bbmap v34.56 [55]. Spades v3.13.0 [56] with default options was used for assembling the reads and creating the contigs.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePressure Treatment for RNA-seq experiment and \u003c/strong\u003e\u003cstrong\u003eRNA extraction\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eFor both strain RO15 and ScottA, 10 ml of cells were grown in TSBYE until early stationary phase (each triplicated with new cultures). Samples were packed in sterile sous-vide pouches and packaged without applying vacuum. They were put in the refrigerator 30 minutes before pressure treatment. After treatment at 200 and 400 MPa for two, eight and sixty minutes at 20-22\u0026deg;C, samples were transferred to sterile 15 ml Falcon tubes. From each sample, 0.5 ml were transferred to a 2 ml Eppendorf tube prefilled with 1 ml RNA Protect (Qiagen, Hilden, Germany). They were vortexed, incubated for 5 minutes at room temperature, and frozen at -80 \u0026deg;C. Cells previously stored in RNA Protect (Qiagen) were pelleted by centrifugation for 10 minutes at 5000 g. RNA extraction was performed with NucleoSpin RNA kit (Macherey-Nagel, D\u0026uuml;ren, Germany) according to manufacturer\u0026rsquo;s instructions with some modifications in the cell disruption phase. The cell pellets were suspended with 700 \u0026micro;l RA1 buffer and 7 \u0026micro;l \u0026beta;-mercaptoethanol (Sigma-Aldrich, Saint Louis, MO, USA). Cells were then mechanically disrupted using Lysing Matrix B tubes (MP Biomedicals) and FastPrep 24 tissue homogenizer (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 3 x 30 sec. Cells were rested on ice for five minutes between cycles. After spinning the cells briefly and transferring the supernatant to NucleoSpin filter column, manufacturer\u0026rsquo;s protocol was followed. Quantity and quality of RNA extractions were analyzed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eRNA-seq library preparation\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eRibosomal RNAs were removed from the total RNAs (ScottA 9.4 \u0026micro;l; RO15 14 \u0026micro;l) with Ribo-Zero rRNA Removal kit for bacteria (Illumina) according to manufacturer\u0026rsquo;s instructions with 1/3 (ScottA) or 1/2 (RO15) volumes of kit solutions. rRNA-depleted RNA was purified with RNeasy MinElute Cleanup Kit (Qiagen) according to modified protocol of the Ribo-Zero kit manual and eluted in 12 \u0026micro;l of RNA-free water. Eight \u0026micro;l of rRNA-depleted RNA was used to prepare RNA sequencing libraries with SENSE Total RNA-seq Library Prep Kit for Illumina (Lexogen, Vienna, Austria) according to manufacturer's instructions. In reverse transcription and ligation phase, incubation time was extended to two hours. After second-strand synthesis, purification and size-selection of the libraries were performed with 13 \u0026micro;l of Bead Diluent and 27 \u0026micro;l of Purification Solution. PCR amplification program was slightly modified by increasing the denaturation times: from 30 to 60 sec in the beginning, and from 10 to 30 sec during the cycles; cycle number was increased to 40. Concentration of amplified libraries was measured with Qubit fluorometer and dsDNA HS assay kit (Invitrogen, Waltham, MA, USA), and size distribution visualized with Fragment Analyzer and High Sensitivity NGS Fragment Analysis kit (Advanced Analytical, Parkersburg, WV, USA). Aliquots of amplified libraries were pooled twice for both strains. After pooling, libraries were concentrated using Amicon Ultra 100K columns (Millipore, Burlington, MA, USA). To remove fragments under 200 bp, size selection of ScottA pools was performed using BluePippin and 2% agarose gel cassette (Sage Science, Beverly, MA, USA). In size selection of RO15 library pools, bead purification with 0.9 x AMPure XP beads (Beckman Coulter, Brea, CA, USA) and PEG/NaCl precipitation on MyOne\u003csup\u003eTM\u003c/sup\u003e carboxylic acid beads (Invitrogen) were additionally used. Concentration of the pooled libraries was measured with Qubit fluorometer, and libraries were sequenced with NextSeq 500 (Illumina).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eRNA-seq data analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eQuality filtering and adapter trimming for RNA-seq reads was done using Trimmomatic v0.36 [57] using these parameters \u0026ldquo;TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:3:20 MINLEN:30\u0026rdquo;. SortMeRNA [58] was used to filter rRNA reads. Reads were mapped to the genomes using Bowtie2 [59] default settings. Aligned reads were sorted using Samtools [60]. HTSeq [61] with union mode was used for read counts. Differentially expressed gene analysis was done using DESeq2 R package [62].\u0026nbsp; Genes with adjusted p-value (padj) \u0026le; 0.05 and |log2 Fold Change| \u0026ge; 1 were considered as significantly differentially expressed.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGenome annotation, prophage prediction and genome alignment\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAssembled genomes were annotated using Prokka v1.13 [63] with default options. To improve functional annotation PANNZER2 annotation web server [64] was used. CRISPR repeat regions were detected using CRISPRCasFinder version 4.2.19 [65]. Anti-CRISPR genes were annotated using BLAST alignment against known anti-CRISPR genes [33]. The prophage prediction for all genomes was done using PHASTER web tool [66]. Serotype of the selected strains were predicted by checking the marker primers [24] in the genome using EMBOSS primersearch v 6.6.0 [67]. Multilocus sequence typing (MLST) based on 7 loci (MLST), clonal complex (CC), core genome MLST (cgMLST) and lineages of strains were assigned based on MLST and the cgMLST schemes developed by Moura et al. [26, 68] by uploading the sequences to BIGSdb-Lm webserver (https://bigsdb.pasteur.fr/listeria/listeria.html). Antibiotic resistance genes were detected using Resistance Gene Identifier (RGI) tool with CARD database [69]. Heuristic neighbor-joining phylogeny tree based on concatenated sequences of the MLST gene fragments was created using FastTree v2.1 [70]. Whole genome alignment and ring figure was created using CGView Comparison Tool [71]. The ANIb scores were calculated using JSpeciesWS webtool [72].\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePan-genome and Pan-GWAS analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe pan-genome analysis was done using Roary Pan-genome Pipeline [73] with default settings, to create alignment of core genes using PRANK [74] the \u0026ldquo;-e\u0026rdquo; setting was used. The core genes alignment was used for phylogenetic tree construction using FastTree [70]. Pan-genome-wide association analysis was done using Scoary [75] with default settings.\u003c/p\u003e"},{"header":"List Of Abbreviations","content":"\u003cp\u003eAnalysis of variance (ANOVA), average nucleotide identity (ANI), coding sequence (CDS), colony forming units (cfu), high pressure processing (HPP), megapascals (MPa), multilocus sequence typing (MLST)\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and material\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll sequencing data and assembled genomes have been deposited in the European Nucleotide Archive (ENA) under accession code PRJEB35939. Strains RO4, RO15, AB120 and AB199 are from Dunarea de Jos University of Galati, Romania, and are available upon request to [email protected]. Strains C7, MB5, and 2HF33 are from Nofima \u0026ndash; Norwegian Institute of Food, and are available upon request to [email protected].\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was supported within the ERA-IB2 consortium \u0026ldquo;SafeFood\u0026rdquo; (ID: ERA-IB-16- 247 014) by grants from Academy of Finland to PA (307856 and 311717), by a grant of the Executive Agency for Higher Education, Research, Development and Innovation Funding in Romania to AIN (International and European Cooperation \u0026ndash; 250 Subprogramme 3.2 \u0026ndash; Horizon 2020 \u0026ndash; Contract No. 15/2017) and by a grant of the German Ministry for Education and Research to CUR (Grant No: 031B0268). ICD supported by the MBDP doctoral program. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors' contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePA, AIN, TL, CUR, and NB conceived and designed the study. TMR, TL and FIB collected the samples and performed the pressure treatment and viable cell count. ICD, MA, and PL performed the bioinformatics analyses. AY performed RNA extraction and sequencing preparation. PC extracted DNA. NB performed ANOVA statistical analysis. ICD drafted the manuscript. All authors have read, commented, and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe want to thank Kirsi Lipponen and Paula Collin for performing the NGS procedures for this project. Ingrid B. Eri, Karin Tran\u0026oslash;y and Laila Budal (Nofima) are acknowledged for technical laboratory assistance. The sequencing service for strains MB5, C7, and 2HF33 was provided by the Norwegian Sequencing Centre (\u003ca href=\"http://www.sequencing.uio.no\"\u003ewww.sequencing.uio.no\u003c/a\u003e), a national technology platform hosted by the University of Oslo. Prof. Daniela Borda (Faculty of Food Science and Engineering, Dunarea de Jos University of Galati) is acknowledged for her assistance with the high pressure processing experiments conducted in the equipment purchased in the frame of the RE-SPIA project. We wish to acknowledge CSC \u0026ndash; IT Center for Science, Finland, for computational resources.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eSchlech WF, Lavigne PM, Bortolussi RA, Allen AC, Haldane EV, Wort AJ, et al. Epidemic Listeriosis \u0026mdash; Evidence for Transmission by Food. New England Journal of Medicine. 1983;308:203\u0026ndash;6.\u003c/li\u003e\n\u003cli\u003eEuropean Centre for Disease Prevention and Control. 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Methods Mol Biol. 2014;1079:155\u0026ndash;70.\u003c/li\u003e\n\u003cli\u003eBrynildsrud O, Bohlin J, Scheffer L, Eldholm V. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biology. 2016;17:238.\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Tables","content":"\u003cp style='margin:0in;margin-bottom:10.0pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cstrong\u003e\u003cspan style=\"font-size: 12px; line-height: 200%; font-family: Helvetica; color: rgb(0, 0, 0);\"\u003eTable 1\u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 200%;\"\u003e. \u003cstrong\u003eReduction in viable cell counts after 1 minute 400 and 600 MPa pressure treatment\u003c/strong\u003e. Table shows the average reduction in log\u003csub\u003e10\u0026nbsp;\u003c/sub\u003e(cfu/ml) of selected \u003cem\u003eL. monocytogenes\u003c/em\u003e strains after 1 minute at 400 or 600 MPa pressure compared to untreated control samples (n = 6 to 9 treated/untreated samples per strain). Standard deviation is shown in brackets.\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003ctable style=\"width: 2.9e+2pt;border-collapse:collapse;border:none;\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border-right: none;border-bottom: none;border-left: none;border-image: initial;border-top: 1pt solid black;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 230.25pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eLog\u003csub\u003e10\u0026nbsp;\u003c/sub\u003ereduction compared to control\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e\u0026nbsp;-\u0026Delta;log\u003csub\u003e10\u0026nbsp;\u003c/sub\u003e(cfu/ml)\u003c/span\u003e \u003cspan style=\"line-height: 115%;\"\u003e(standard deviation)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eStrain\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e400 MPa\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e600 MPa\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRO15\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.05 (0.14)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e5.42 (0.15)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e2HF33\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.15 (0.08)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e6.97 (0.10)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eMB5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.22 (0.14)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e8.27 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style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e7.30 (0.59)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eC7\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: 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\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eF2365\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.47 (0.16)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e7.10 (0.26)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eScottA\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.68 (0.57)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e5.86 (0.39)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRO4\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e1.00 (0.13)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border: none;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e7.70 (1.24)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 58.5pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eEGD-e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 111.75pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e2.07 (0.33)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 118.5pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e7.49 (0.70)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003ch1 style='margin-top:20.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;line-height:200%;font-size:27px;font-family:\"Arial\",sans-serif;font-weight:normal;'\u003e\u003cbr\u003e\u003c/h1\u003e\n\u003cp style='margin:0in;margin-bottom:.0001pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 200%;\"\u003eTable 2.\u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"line-height: 200%;\"\u003e\u0026nbsp;\u003cstrong\u003eGeneral genome summary of selected \u003cem\u003eL. monocytogenes\u0026nbsp;\u003c/em\u003estrains.\u003c/strong\u003e The table shows the genome size, genome sequence based prediction of clonal complex (CC), multilocus sequence typing (MLST) based on 7 loci, core genome MLST (cgMLST), lineage, and serotypes of selected strains.\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 200%;\"\u003e\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003ctable style=\"width: 4.8e+2pt;border: none;border-collapse:collapse;\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eStrain\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eSize, Mbp (CDS)\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eCC\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eSerotype\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eMLST\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 0in 5.4pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003ecgMLST\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eLineage\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eGenome Source\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eSource\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eReference\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eRO15\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e3.04 (3022)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC155\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e155\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;border: none;padding: 0in 5.4pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-11632\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Complete)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eHerring with spices\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;border: none;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[21]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e2HF33\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e3.11 (3098)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC121\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e121\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-3328\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Contigs)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eSalmon filleting section\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[25, 27]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eMB5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e2.97 (2958)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC7\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e7\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-9444\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Contigs)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eSalmon gutting machine\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[25]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eAB199\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e2.99 (2907)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC204\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e204\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-6821\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Contigs)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eDrain/processing room\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 0.25in;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[21]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eAB120\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e3.00 (2924)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC204\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e204\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-6821\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Contigs)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eSausage filler machine\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 33pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[21]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eC7\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e3.09 (3051)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC8\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e8\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-999\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Contigs)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eSalmon gutting machine\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 15pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[25]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eF2365\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e2.91 (2808)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e4b\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-2\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eI\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eGenBank: AE017262.2\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eMexican-style cheese\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 17pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[22]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eScottA\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e3.02 (2966)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC2\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e4b\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e290\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-94\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eI\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eGenBank: CM001159.1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eClinical isolate\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 26pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[23]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eRO4\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e2.88 (2806)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC20\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e20\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;padding: 0in 5.4pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-13510\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eThis study (Contigs)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eDry cured salami\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;padding: 2pt;height: 20pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[21]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 35.45pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eEGD-e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.1pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e2.94 (2875)\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 42.45pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eCC9\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e1/2a\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 35.45pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e35\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 56.7pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 0in 5.4pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003ecg-1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 28.35pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eII\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 70.85pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eGenBank: AL591824.1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003eRabbit tissue\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62.45pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 27pt;vertical-align: top;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:normal;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e[24, 28]\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003cp style='margin:0in;margin-bottom:.0001pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003cp style='margin:0in;margin-bottom:10.0pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 200%;\"\u003eTable 3.\u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"line-height: 200%;\"\u003e\u0026nbsp;\u003cstrong\u003eA summary of motifs.\u003c/strong\u003e The table shows the detected methylated motifs and the total number of motifs in the RO15 genome.\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003ctable style=\"width: 4.5e+2pt;border-collapse:collapse;border:none;\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27.3pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eMotifs\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27.3pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eType\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27.3pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003e% Motifs\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eDetected\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27.3pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003e# of Motifs\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003eDetected\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27.3pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003e# of Motifs\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003ein Genome\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 27.3pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 115%;\"\u003emean Coverage\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eADGYACYTV\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003em6A\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e44.03%\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e420\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e954\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e149.9\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eADDTGGCA\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003em6A\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e30.97%\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e455\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e1469\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e148.5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eTVVARARG\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eunknown\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e22.20%\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e1835\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e8265\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e148.8\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eANNYASYA\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003em6A\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e22.10%\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e3289\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n 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115%;\"\u003e149.0\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eDADGYATYA\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 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rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e1240313\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e148.9\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eTNNNCRVHNH\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eunknown\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e7.59%\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e6652\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e87598\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border: none;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e149.0\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 123pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eTVNNNNNG\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.05pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eunknown\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 59.6pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e3.26%\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e7834\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e240556\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 69.9pt;border-top: none;border-right: none;border-left: none;border-image: initial;border-bottom: 1pt solid black;padding: 2pt;height: 15.15pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:right;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e149.6\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp style='margin:0in;margin-bottom:.0001pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003cp style='margin:0in;margin-bottom:.0001pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cp style='margin:0in;margin-bottom:10.0pt;line-height:200%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cstrong\u003e\u003cspan style=\"line-height: 200%;\"\u003eTable 4.\u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"line-height: 200%;\"\u003e\u0026nbsp;\u003cstrong\u003eComparison of CRISPR/Cas systems, anti-CRISPR genes, and prophage regions amongst the selected \u003cem\u003eL. monocytogenes\u0026nbsp;\u003c/em\u003estrains.\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n\u003ctable style=\"width: 4.8e+2pt;border-collapse:collapse;border:none;\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eStrain\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 84.35pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eAverage reduction of log\u003csub\u003e10\u003c/sub\u003e(cfu/ml) at 400 MPa\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 99pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eCRISPR/Cas systems\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 49.5pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eNumber of spacers\u0026nbsp;\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.5pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eSelf-targeting spacer predicted\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 74.25pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eanti-CRISPR gene predicted\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66.75pt;border-top: 1pt solid black;border-left: none;border-bottom: 1pt solid black;border-right: none;padding: 2pt;height: 53pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eNumber of prophage predicted\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRO15\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 84.35pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.05\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 99pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRliB-CRISPR,\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eCRISPR I\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 49.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e64\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eyes\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 74.25pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:10.0pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eAcrIIA1, A2\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66.75pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e2HF33\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 84.35pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.15\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 99pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRliB-CRISPR,\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eCRISPR I,\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eCRISPR II\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 49.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e62\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eyes\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 74.25pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eAcrIIA1, A2, A3, A4\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66.75pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eMB5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 84.35pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.22\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 99pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRliB-CRISPR,\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eCRISPR II\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 49.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e39\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eyes\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 74.25pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eAcrIIA1, A2, A3\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66.75pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e5\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eAB199\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 84.35pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.26\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 99pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRliB-CRISPR\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 49.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e3\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eno\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 74.25pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eno\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66.75pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eAB120\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 84.35pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;text-align:center;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e0.35\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 99pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eRliB-CRISPR\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 49.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e3\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.5pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eno\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 74.25pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003eno\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66.75pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan style=\"color: rgb(0, 0, 0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e1\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 49.15pt;border: none;padding: 2pt;height: 16pt;vertical-align: bottom;\"\u003e\n \u003cp style='margin:0in;margin-bottom:.0001pt;line-height:115%;font-size:15px;font-family:\"Arial\",sans-serif;'\u003e\u003cspan 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0);\"\u003e\u003cspan style=\"font-size: 12px;\"\u003e\u003cspan style=\"font-family: Helvetica;\"\u003e\u003cspan style=\"line-height: 115%;\"\u003e2\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003ch1 style='margin-top:20.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;line-height:115%;font-size:27px;font-family:\"Arial\",sans-serif;font-weight:normal;'\u003e\u003cstrong\u003e\u003cspan style=\"font-size: 12px; line-height: 115%; font-family: Helvetica; color: rgb(0, 0, 0);\"\u003e\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003c/h1\u003e"},{"header":"Additional File Legends","content":"\u003cp\u003e\u003cstrong\u003eAdditional File 1: Supplementary Text 1. \u003cem\u003eL.\u003c/em\u003e \u003cem\u003emonocytogenes\u003c/em\u003e st\u003c/strong\u003e\u003cstrong\u003erain selection, including Table S1, Figure\u003c/strong\u003e \u003cstrong\u003eS1. \u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAdditional File 2: Table S2.\u003c/strong\u003e Gene count data and differentially expressed gene list for both strains RO15 and ScottA based on RNA-Seq.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAdditional File 3: Table S3\u003c/strong\u003e. \u0026nbsp;Table shows Average Nucleotide Identity (ANI) (based on BLAST) calculation results of each strain. For strains ScottA and F2365 the ANI score with other strains was lower than 95. ANI score between ScottA and F2365 was higher than 95. For the other strains ANI scores between each other were more than 98.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAdditional File 4: Figure S2\u003c/strong\u003e. Genome comparison of 200 \u003cem\u003eL. monocytogenes\u003c/em\u003e strains mapped against strain RO15. The genomes were aligned using BLAST and visualized as ring figures. a) Each ring represents the whole genome alignment to strain RO15 (100 most similar genomes (based on BLAST) were displayed\u0026nbsp; in (a) for simplification), b) ring figure zoomed in the prophage 1 region, c) ring figure zoomed in the prophage 2 region, d) ring figure zoomed in the prophage 3 region, e) ring figure zoomed in the prophage 4 region, f) ring figure zoomed in the prophage 5 region. The Refseq identifiers of 200 \u003cem\u003eL. monocytogenes\u003c/em\u003e strains can be seen in figure. Genome features can be seen in Table S6. Red colored BLAST hits represent 90\u0026ndash;98% identity, blue colored BLAST hits represent 80\u0026ndash;90% identity. Black colored BLAST hits represent 100% identity. White gaps represent \u0026lt; 80% identity.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAdditional File 5: Table S4 and Figure S3. \u003c/strong\u003eTable S4 shows identified antibiotic resistance genes and percentage identity of matching region in all strains using CARD database. Figure S3 shows average distance trees from alignments of protein sequences of identified antibiotic resistance genes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAdditional File 6: Table S5. \u003c/strong\u003eT-test against RO15 log\u003csub\u003e10 \u003c/sub\u003ereduction.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAdditional File 7: Table S6.\u003c/strong\u003e Barotolerant strains specific genes based on pan-genome wide association analysis. Table shows genes that have p \u0026lt; 0.01 based on pan-genome wide association analysis for barotolerant strains. Gene IDs of strain RO15 was used for this table. Orthologs of these genes with 95% identity were also seen in strains MB5 and 2HF33. In addition, the list of other publicly available \u003cem\u003eL. monocytogenes\u003c/em\u003e genomes, where these genes were seen, are also provided.\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"high-pressure processing (HPP), foodborne pathogen, CRISPR, PacBio, comparative genomics, pan-genome.","lastPublishedDoi":"10.21203/rs.2.24582/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.2.24582/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground: \u003c/strong\u003eHigh pressure processing (HPP; i.e. 100 - 600 MPa pressure depending on product) is a non-thermal preservation technique adopted by the food industry to decrease significantly foodborne pathogens, including \u003cem\u003eListeria monocytogenes\u003c/em\u003e,\u003cem\u003e \u003c/em\u003efrom food\u003cem\u003e.\u003c/em\u003e However, susceptibility towards pressure differs among diverse strains of \u003cem\u003eL. monocytogenes\u003c/em\u003e and it is unclear if this is related to their genomic content. Here, we tested the barotolerance of 10 different \u003cem\u003eL. monocytogenes\u003c/em\u003e strains, from food and food processing environments and widely used reference type strains, to pressure treatments with 400 and 600 MPa. Genome sequencing and genome comparison of the tested \u003cem\u003eL. monocytogenes\u003c/em\u003e strains were performed to investigate the relation between genomic profile and pressure tolerance.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: None of the tested strains were tolerant to 600 MPa. A reduction of more than 5 log\u003csub\u003e10\u003c/sub\u003e was observed for all strains after 1 minute 600 MPa pressure treatment. \u003cem\u003eL. monocytogenes\u003c/em\u003e strain RO15 showed no significant reduction in viable cell counts after 400 MPa for 1 minute and was therefore defined as barotolerant. Genome analysis of so far unsequenced \u003cem\u003eL. monocytogenes\u003c/em\u003e strain RO15, 2HF33, MB5, AB199, AB120, C7, and RO4 allowed us to compare the gene content of all strains tested. This revealed that the three most pressure tolerant strains had more than one CRISPR system with self-targeting spacers. Furthermore, several anti-CRISPR genes were detected in these strains. Pan-genome analysis showed that 10 prophage genes were significantly associated with the three most barotolerant strains.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions: \u003c/strong\u003e\u003cem\u003eL. monocytogenes \u003c/em\u003estrain RO15 was the most pressure tolerant among the selected strains. Genome comparison suggests that there might be a relationship between prophages and pressure tolerance in \u003cem\u003eL. monocytogenes\u003c/em\u003e.\u003c/p\u003e","manuscriptTitle":"Complete genome of the barotolerant Listeria monocytogenes RO15 strain and comparison with other strains isolated from food and food processing environments","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2020-05-13 14:57:27","doi":"10.21203/rs.2.24582/v2","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2020-05-19T12:00:00+00:00","index":1,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"editorInvitedReview","content":"","date":"2020-05-18T12:00:00+00:00","index":2,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"editorInvitedReview","content":"","date":"2020-05-18T12:00:00+00:00","index":3,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"reviewerAgreed","content":"","date":"2020-04-28T12:00:00+00:00","index":1,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-04-28T12:00:00+00:00","index":2,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-04-28T12:00:00+00:00","index":3,"fulltext":""},{"type":"editorAssigned","content":"","date":"2020-04-27T12:00:00+00:00","index":"","fulltext":""},{"type":"reviewersInvited","content":"","date":"2020-04-27T12:00:00+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2020-04-26T12:00:00+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2020-02-24T12:00:00+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2020-02-26 16:03:44","doi":"10.21203/rs.2.24582/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major revision","date":"2020-03-25T12:00:00+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2020-03-20T12:00:00+00:00","index":4,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"editorInvitedReview","content":"","date":"2020-03-19T12:00:00+00:00","index":3,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"editorInvitedReview","content":"","date":"2020-03-19T12:00:00+00:00","index":2,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"editorInvitedReview","content":"","date":"2020-03-18T12:00:00+00:00","index":1,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"reviewerAgreed","content":"","date":"2020-03-07T12:00:00+00:00","index":5,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-03-06T12:00:00+00:00","index":3,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-03-06T12:00:00+00:00","index":4,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-03-04T12:00:00+00:00","index":2,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-03-03T12:00:00+00:00","index":1,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2020-03-02T12:00:00+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2020-02-24T12:00:00+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2020-02-24T12:00:00+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2020-02-23T12:00:00+00:00","index":"","fulltext":""},{"type":"submitted","content":"","date":"2020-02-21T12:00:00+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"11576f0a-3355-4caa-98df-7f063dcdb281","owner":[],"postedDate":"May 13th, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":99525,"name":"Epigenetics \u0026 Genomics"}],"tags":[],"updatedAt":"2020-07-05T15:01:09+00:00","versionOfRecord":{"articleIdentity":"rs-15141","link":"https://doi.org/10.1186/s12864-020-06819-0","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2020-07-02 12:00:00","publishedOnDateReadable":"July 2nd, 2020"},"versionCreatedAt":"2020-05-13 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