Genomic characterisation of an extended-spectrum β-Lactamase- producing Klebsiella pneumoniae isolate assigned to a novel sequence type (6914)

Genomic characterisation of an extended-spectrum β-Lactamase- producing Klebsiella pneumoniae isolate assigned to a novel sequence type (6914) | 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 genome-report Genomic characterisation of an extended-spectrum β-Lactamase- producing Klebsiella pneumoniae isolate assigned to a novel sequence type (6914) Muiz O. Akinyemi, Oluwawapelumi A. Oyedele, Mariska S. Kleyn, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4123332/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Cow milk which is sometimes consumed raw host a plethora of microorganisms of beneficial or food safety concern. The draft genome of an extended-spectrum β-Lactamase-producing Klebsiella pneumoniae subsp. pneumoniae strain Cow102, isolated from cow milk used for production of traditional foods in Nigeria, is reported. Result The genome has a total length of 5,359,907 bp with 70 contigs and GC content of 57.35%. A total of 5,244 protein coding sequences were detected with 31% mapped to a subsystem, and genes coding for amino acids and derivatives being the most prevalent. Multilocus sequence typing revealed that the strain had new allelic profile assigned to the novel 6914 sequence type possessing capsular and lipopolysaccharide antigen K locus 122 with an unknown K type (KL122) and O locus O1/O2v2 with type O2afg, respectively. A total of 28 resistance-related genes, 98 virulence-related genes, two plasmids and five phages were identified in the genome. Comparative analysis indicated translocation was the most common structural rearrangements in the genome. Conclusion Whole-genome sequencing and bioinformatics analysis revealed new allelic profile, structural rearrangements, virulence and drug resistance factors in the genome, however, further studies are required to characterize the capsular K type oof Cow102. animal milk draft genome Klebsiella pneumoniae subsp. pneumoniae multidrug resistance Figures Figure 1 Figure 2 Background In recent years, there has been growing concern about the emergence and spread of antibiotic resistance in bacteria [ 1 ]. One of such examples involve the rising incidence of various species, especially strains of Klebsiella pneumoniae , acquiring the capability to synthesize extended-spectrum β-Lactamase (ESBL) enzymes that confer resistance to a broad range of β-lactam antibiotics [ 2 ]. Members of the Klebsiella genus, a Gram-negative non-motile, encapsulated, facultative anaerobic bacterium, within the family Enterobacteriaceae cause a wide range of infections in both humans and animals. Klebsiella pneumoniae is a versatile bacterium that can be found in various environments, including the oral cavity, skin, and gastrointestinal tracts of different mammals [ 3 ]. While normally present as a part of the human microbiota, this bacterium can also act as an opportunistic pathogen, leading to a range of infections such as pneumonia, septicaemia, urinary tract infections, and soft tissue infections, among others [ 3 ]. Beta-lactam antibiotics, e.g., penicillins, cephalosporins, monobactams, and carbapenems, which are widely used as therapeutic agents to combat bacterial infections, exert their antimicrobial effects by cleaving to the penicillin-binding protein [ 2 ]. This binding prevents the biosynthesis of the bacterial cell membrane, ultimately inhibiting the growth and survival of the bacteria [ 2 ]. However, the presence of ESBLs considerably reduces the efficacy of beta-lactam antibiotics, creating a serious problem in the treatment of infection by ESBL-producing bacteria. In recent years, the World Health Organization (WHO) has recognized K. pneumoniae as being among the top priority pathogens due to the significant morbidity and mortality rates associated with its infections and status as a major worldwide reservoir and vector for antibiotic resistance [ 1 , 4 ]. As a result, there is a growing demand for genotyping this important pathogen to better understand its genetic characteristics and transmission patterns. One of the molecular methods commonly employed for this purpose is multilocus sequence typing (MLST) based on housekeeping genes, this allows for the characterization of the genetic relationship between different bacterial strains. Klebsiella strains are largely oligoclonal [ 5 ], which means they can be assigned into several unique sequence types (STs). This method of classification provides unambiguous and reliable data, which allows researchers and healthcare professionals gain valuable insights into the genetic diversity and transmission patterns of this pathogen. In Nigeria, a significant proportion of the available data that employed molecular techniques to identify Klebsiella strain is predominantly derived from studies conducted in healthcare facilities and medical settings [ 6 , 7 ]. Studying the genomic characteristics of ESBL-producing K. pneumoniae isolated from alternative sources, such as animal milk, could offer fresh perspectives on the transmission of these opportunistic pathogens across different niches in Nigeria. Moreover, genome typing of Klebsiella strains from various sources will provide resources for bio-surveillance. This research also contributes to understanding antibiotic resistance dissemination as well as the development of targeted interventions and preventive measures to mitigate the spread of K. pneumoniae in both animal and human populations. Results and discussion Antimicrobial susceptibility profile Klebsiella species are major global reservoirs and conduit of drug resistance genes between various bacterial niches [ 8 ]. We report the draft genome sequence of an ESBL-producing K. pneumoniae subsp. pneumoniae strain Cow102 previously isolated from cow milk [ 9 , 10 ]. The phenotypic antimicrobial susceptibility profile of strain cow102 showed resistance to cephalosporins, carbapenem, and drugs from different classes of antibiotics including aminoglycosides (streptomycin), quinolone (ciprofloxacin, nalidixic acid), beta-lactams (amoxicillin + clavulanic acid, ampicillin, cefotaxime, ceftazidime, piperacillin), folic acid synthesis inhibitor (trimethoprim/sulfamethoxazole), monobactams (aztreonam), fosfomycin, and tetracycline. The strain was identified as an ESBL producer due to its resistance to aztreonam, cefotaxime, ceftazidime, and ceftriaxone, which are commonly used as indicators for ESBL production. Haemolysis test The strain reported in this study was non-hemolytic on blood agar and lacked the genes hlyA and cnf-1 that code for this function. General genome features Illumina sequencing of the genomic DNA of strain cow102 generated 12,005,232 total read pairs (2 × 150 bp) giving approximately 336 × coverage. The assembly genome totalled 5,359,907 bp with 70 contigs, an N50 value of 376,296 bp, and a GC content of 57.35%. The assembly was characterized using CheckM as 100% complete with, 0.1% contamination, 99.4% and 97.8% coarse and fine consistencies, respectively. Genome annotation performed using RASTk identified, a total of 5,244 protein coding sequences (CDS), 72 transfer RNA (tRNA) genes, and 5 ribosomal RNA (rRNA) genes. There were 4,605 proteins with functional assignments and 639 hypothetical proteins in the annotation. Among the proteins with functional assignments, 1,457 possessed Enzyme Commission (EC) numbers, 1,208 had Gene Ontology (GO) assignments, and 1,065 contained KEGG pathway mappings. Also, about 31% of the CDS was mapped to a subsystem. Genes responsible for amino acids and derivatives (417 ORFs), protein metabolism (227 ORFs), and cofactors, vitamins, prosthetic groups, and pigments (196 ORFs) were abundant among the SEED subsystem categories. An overview of the subsystem categories and feature counts is shown in Fig. 1A while the genome annotation can be viewed on Figshare. Phylogenetic analysis, Multilocus Sequence typing (MLST) and capsular typing The whole-genome phylogenetic analysis showed that strain Cow102 is closely related to K. pneumoniae subsp. pneumoniae strains IS39, DSM30104, ISC21, and DSM30104, all of which belong to the HS11286 group (Fig. 1B). Multilocus Sequence typing analysis revealed that the current isolate had a new allelic profile [(gapA (2), infB (3), mdh (70) pgi (1) phoE (275), rpoB (44) and tonB (39)], assigned as sequence type 6914 based on the standard 7-gene MLST scheme, initially defined by Diancourt et al [ 11 ]. eBURST analyses showed that ST6914 clustered closely with ST494, ST4138, ST4139 and ST6476 (Figure S1 A). The current strain, ST6914 is a triple-locus variant to all closely clustered ST, differing at the phoE, rpoB and tonB loci. The serotyping of ST6914 revealed a 99.96% match with K locus 122 with an unknown K type (KL122) for the capsular (K typing) antigen (Figure S1 B) using the wzi sequencing K-typing method [ 12 ], and a 98.51% match with O locus O1/O2v2 with type O2afg for the lipopolysaccharide (O typing) antigen (Figure S1 C). Antimicrobial resistance genes Several studies in Nigeria reported drug-resistant Klebsiella strains in raw animal milk and milk products; however, genomic data and serotypes of the reported strains are rare [ 13 , 14 ]. Molecular characterization of the resistance factors associated with strain Cow102 revealed the presence of 38 Antibiotic Resistance Genes (ARGs) (Table 1 and Fig. 2), out of which 24 genes were fully concordant with the phenotypically derived resistance profile. The resistance genes identified in strain Cow102 include core chromosomal resistance genes belonging to the bla SHV family, which transfer resistance to beta-lactam antibiotics. In addition, acquired genes such as aadA2, an aminoglycoside nucleotidyltransferase gene; catA2 and catII, which confer resistance by enzymatic inactivation of amphenicol antibiotics; TEM families, which transfer resistance through similar mechanisms as bla SHV family; and Escherichia coli FosA and oqxAB gene conferring resistance to fosfomycin and quinolones, respectively, were found. Furthermore, the presence of the efflux pump gene, Tet (D), which provides resistance to tetracycline, was expected (Table 1 and Fig. 2). This is likely due to the common practice among veterinary and para-veterinary professionals in Nigeria to prescribe oxytetracycline for treating diseases [ 15 , 16 ]. Table 1 Antimicrobial resistance genes identified in Klebsiella pneumoniae subsp. pneumoniae strain Cow102 and conferring resistance to tested antibiotics Resistance gene Antibiotic Class Antibiotic (phenotype observed) aadA2b aminoglycoside Streptomycin (resistant) blaSHV-1 a beta-lactam Amoxicillin (resistant) a,b,c,d,f,g,n blaSHV-11 b Amoxicillin + clavulanic acid (resistant) d blaSHV-13 c Ampicillin(resistant) a,b,c,d,f,g,n blaSHV-26 d Ampicillin + clavulanic acid (resistant) d blaSHV-70 e Aztreonam (resistant) c,e,g blaSHV-78 f Cefotaxime (resistant) c,e,g blaSHV-98 g Ceftazidime (resistant) c,e,g blaSHV-145 h Ceftriaxone (resistant) c,e,g blaSHV-161 i Piperacillin (resistant) a,b,c,d,f,g,n blaSHV-179 j blaSHV-185 k blaSHV-194 l blaSHV-199 m blaTEM-1B n catA2 amphenicol Chloramphenicol (intermediate) dfrA16 q folic acid synthesis inhibitor trimethoprim o,q /sulfamethoxazole p (resistant) fosA fosfomycin Fosfomycin (intermediate) fosA5 fosA6 OqxA o Quinolone and folic acid synthesis inhibitor Ciprofloxacin (intermediate) OqxB o Nalidixic acid (resistant) sul1 p folic acid synthesis inhibitor Sul2 p Tet(D) tetracycline Tetracyclin (resistant) Key: Superscripts represent combination of resistance gene conferring resistance to an antibiotic The genome as shown in Fig. 2 includes several additional genes associated with antimicrobial resistance that were not phenotypically tested, and their presence alone does not confirm resistance. These include KatG gene and operons MarA, MarB, and MarR, which are involved in enzymatic catalysis of antibiotics. The BcrC gene serves as a protective protein for antibiotic targets. GdpD and PgsA genes are involved in altering the charge of the cell wall, while OccD6/OprQ and OprB modulate antibiotic permeability. The presence of AcrAB-TolC, EmrAB-TolC, H-NS, and OxyR suggests the role of regulatory factors in modulating the expression of antibiotic resistance genes. Additionally, the genome harbours other ARGs that were acquired through horizontal gene transfer such as the E. coli UhpT gene, which carries a mutation conferring resistance to fosfomycin, mdfA gene, an efflux pump, and multidrug transporter, as well as the Haemophilus influenzae PBP3 gene which confers resistance to beta-lactam antibiotics (Fig. 2). Comprehensive details of ARGs, their orientation and genomic location is presented in Table S1 . Virulence factors Profiling of virulence features in the current strain revealed the presence of 98 virulence factors (Table 2 ) classified into 12 categories: adherence (15 genes), antimicrobial activity/competitive advantage (3 genes), biofilm formation (10 genes), effector delivery system (25 genes), exotoxins (2 genes), immune modulation (16 genes), invasion (2 genes), motility (3 genes), nutritional/metabolic factors (14 genes), regulation (7 genes), and other (1 gene). Table 2 Virulence genes of Klebsiella pneumoniae subsp. pneumoniae strain Cow102. Virulence factor Category Related Gene Product Adherence Type I fimbriae fimC Periplasmic chaperone Adherence Type I fimbriae fimD Outer membrane usher protein Adherence Type I fimbriae fimH Type 1 fimbrial adhesin precursor Adherence Type I fimbriae fimK Transcriptional regulator Adherence Flagella fleQ Transcriptional regulator Adherence Hsp60 htpB Hsp60, heat shock protein Adherence ChiRP pilB Type IV-A pilus assembly Adherence Type IV pili pilR Two-component response regulator Adherence Type IV pili pilT Twitching motility protein Adherence Type IV pili rpoN RNA polymerase factor sigma-54 Adherence Type IV pili rpoS RNA polymerase sigma factor Adherence Type IV pili tapT Twitching Adherence EF-Tu tufA Elongation factor Adherence Type IV pili vfr Camp-regulatory protein Adherence ECP yagX/ecpC E. coli common pilus usher Antimicrobial activity/ Competitive advantage MtrCDE mtrD Multiple transferable resistance system protein Antimicrobial activity/ Competitive advantage AcrAB acrA Acriflavine resistance protein Antimicrobial activity/ Competitive advantage AcrAB acrB Acriflavine resistance protein Biofilm Alginate algW Algw protein Biofilm AI-2 luxS S-ribosylhomocysteinase Biofilm Type 3 fimbriae mrkB Fimbrial chaperone protein mrkB precursor Biofilm Type 3 fimbriae mrkC Fimbrial biogenesis outer membrane usher protein Biofilm Type 3 fimbriae mrkD Fimbrial adhesin protein precursor Biofilm Type 3 fimbriae mrkF Type 3 fimbrial minor pilin subunit Biofilm Type 3 fimbriae mrkH Transcriptional activator Biofilm Type 3 fimbriae mrkJ Phosphodiesterase Biofilm Alginate mucD Serine protease mucD precursor Biofilm PNAG pgaA Poly-beta-1,6 N-acetyl-D-glucosamine export porin Effector delivery system T6SS clpB Type VI secretion system Effector delivery system T6SS clpV/tssH Type VI secretion system Effector delivery system HIS-1 clpV1 Type VI secretion system AAA + family Effector delivery system Exe T2SS exeD General secretion pathway protein Effector delivery system Exe T2SS exeE General secretion pathway protein Effector delivery system Exe T2SS exeF General secretion pathway protein Effector delivery system Exe T2SS exeG General secretion pathway protein Effector delivery system Exolysin exlA Hemolysin Effector delivery system T2SS gspE General secretion pathway protein Effector delivery system T2SS gspG General secretion pathway protein Effector delivery system T6SS icmF/tssM Type VI secretion protein Effector delivery system T6SS impA/tssA Type VI secretion system protein Effector delivery system HIS-2 PA1663 Transcriptional regulator Effector delivery system HIS-3 PA2359 Transcriptional regulator Effector delivery system T6SS tssF Type VI secretion system baseplate subunit Effector delivery system T6SS tssG Type VI secretion system baseplate subunit Effector delivery system HIS-2 tssH Type VI secretion system Effector delivery system T6SS-1 tssH-5/clpV Clp-type chaperone protein Effector delivery system HIS-2 tssM Type VI secretion system membrane subunit Effector delivery system T6SS vasE/tssK Type VI secretion system baseplate subunit Effector delivery system T6SS vasH Sigma-54 dependent transcriptional regulator Effector delivery system T6SS vgrG/tssI Type VI secretion system tip protein Effector delivery system T6SS vipB/tssC Type VI secretion system contractile sheath large subunit Effector delivery system Xcp secretion xcpR General secretion pathway protein Effector delivery system Yst1 T2SS yst1E Type II secretion system Exotoxin Cya cyaB Cyclolysin secretion ATP-binding protein Exotoxin RtxA rtxB RTX toxin transporter Immune modulation Capsule galF Galu regulator Immune modulation LOS gmhA/lpcA Phosphoheptose isomerase Immune modulation LPS KP1_RS17220 Glycosyltransferase Immune modulation LPS KP1_RS17230 Glycosyltransferase Immune modulation LPS KP1_RS17240 DUF4422 domain-containing protein Immune modulation Capsule KP1_RS17345 Capsule assembly Wzi family protein Immune modulation LOS rfaD ADP-L-glycero-D-mannoheptose-6-epimerase Immune modulation LPS rfaJ Alpha-1,6 Glc transferase Immune modulation LPS rfbA O-antigen export ABC transporter permease Immune modulation LPS rfbB O-antigen export ABC transporter ATP-binding protein Immune modulation LPS rfbD UDP-galactopyranose mutase Immune modulation Capsule rfbK1 O9 family phosphomannomutase Immune modulation LOS rffG Dtdp-glucose 46-dehydratase Immune modulation LPS waaA Lipopolysaccharide core biosynthesis protein Immune modulation LPS waaC 3-deoxy-D-manno-octulosonic-acid (KDO) transferase Immune modulation LPS waaF Heptosyltransferase I Invasion Ibes ibeB Cu(+)/Ag(+) efflux RND transporter outer membrane channel Invasion ompA ompA Outer membrane protein Motility Flagella flrA Sigma-54 dependent transcriptional activator Motility Polar flagella flmH Short chain dehydrogenase/reductase family oxidoreductase Motility Polar flagella nueA Neua protein Nutritional/Metabolic factor Ent entA 2,3-dihydroxybenzoate-2,3-dehydrogenase Nutritional/Metabolic factor Ent entC Isochorismate synthase Nutritional/Metabolic factor Ent entE Enterobactin synthase subunit Nutritional/Metabolic factor Ent entF Enterobactin synthase subunit Nutritional/Metabolic factor Ent entS Enterobactin exporter Nutritional/Metabolic factor FbpABC fbpC Iron(III) ABC transporter, ATP-binding protein Nutritional/Metabolic factor Enterobactin fepA Ferrienterobactin outer membrane transporter Nutritional/Metabolic factor Ent fepD Iron-enterobactin transporter membrane protein Nutritional/Metabolic factor Ent fes Enterobactin/ferric enterobactin esterase Nutritional/Metabolic factor Sal iroE Siderophore esterase iroe Nutritional/Metabolic factor Salmochelin siderophore iroN Salmochelin receptor Nutritional/Metabolic factor Aerobactin iutA Ferric aerobactin receptor Nutritional/Metabolic factor MgtBC mgtB Mg2 + transport protein Nutritional/Metabolic factor Pyochelin pchI ABC transporter ATP-binding protein Others Isocitrate lyase icl Isocitrate lyase Regulation CdpA cdpA Cyclic di-GMP phosphodiesterase Regulation PhoQ phoP Response regulator in two-component regulatory system with PhoQ Regulation PhoQ phoQ Sensor protein PhoQ Regulation SigA sigA/rpoV RNA polymerase sigma factor Regulation PmrAB pmrA Response regulator Regulation PmrAB pmrB Sensory kinase Regulation RelA relA Probable GTP pyrophosphokinase Mobile genetic elements, Plasmid and Phages There are a total of 23 insertion sequences (IS) classified into eight IS families: IS1, IS3, IS5, IS110, IS66, IS91, IS630, and ISNCY in the genome of strain Cow102. A comprehensive list of all identified IS, along with their corresponding CDS positions and terminal inverted repeats (TIR) is presented in Table S2 . The only plasmids found in the present genome were IncFIB(K)-1-Kpn3 and Col440I_1. These plasmids were respectively detected in 16 (67%) and 11 (46%) of 24 K. pneumoniae isolates from powdered milk from Germany [ 17 ]. Additionally, five bacteriophages were detected, of which three (Klebsi phiKO2, Escher 500465, Entero cdtI) were intact, one (Salmon 118970 sal3) was incomplete, and one (Escher RCS47) yielded inconclusive results. Figure S1 illustrates the positions of these bacteriophages within the CDS region of the Cow102 strain. Comparative genomics A first glance at the genomic comparison analysis between the current and 22 other strains of K. pneumoniae suggested a high level of sequence similarity with pairwise average nucleotide identity (ANI) ranging from 99.1–99.9% (Figure S3 ). It is worthy of note that the other strains were from various hosts (chicken, cow, human, pig) and sources (chicken faeces, open wound, blood, urine, vaginal swab, pork, cow milk). Pairwise whole-genome alignments with CLC genomic workbench for all 22 assemblies against the cow102 strain revealed sequence alignment percentages of about 85% and 90% (Figure S3 ), despite the fact that huge differences were observed in assembly metrics such as N50 and GC content. A closer look at the variations between the genomes using DNAdiff found significant differences ( p < 0.05) in sequence inversions, insertions/deletions (indels), relocations and translocations between the assemblies and the examined strains (Table S3 ). The most common structural rearrangements discovered were translocations (x̄=105), which occurred between neighbouring 1-to-1 alignment blocks in different sequences. Additionally, there was an average of approximately nine breaks in the alignment where adjacent 1-to-1 alignment blocks were in the same sequence (relocations), and two somewhat unusual breaks where adjacent 1-to-1 alignment blocks were inverted with regard to each other (inversions). Furthermore, an average of 221 insertion events, three tandem duplication insertion events (TandemIns), 32995 Single Nucleotide Polymorphism (SNPs) and 2629 Single Nucleotide Materials and methods Bacterial isolation and growth conditions The current report stemmed from a 2019 study that sought to identify functional bacteria in animal milk [ 9 , 10 ]. A synopsis of the sample collection and bacterial isolation conducted is provided here. Cow milk samples (n = 20) were collected from dairy farms in Sokoto State, Nigeria, between May and June 2019. Each sample was subjected to six dilution series. Bacteria were isolated on De-Mann Rogosa Sharpe (MRS) agar plates supplemented with D-Sorbitol and incubation of inoculated plates was performed in anaerobic conditions at 37°C for 24 hours. Antimicrobial susceptibility testing and screening of the ESBL production Antimicrobial susceptibility testing (AST) was done using the agar diffusion method and the Clinical and Laboratory Standards Institute (CLSI) M100 guideline (31st edition) for drug selection and interpretation of result. Briefly, Mueller–Hinton agar plates (20ml) were overlaid with MacFarland standardized broth containing the Klebsiella pneumoniae subsp. pneumoniae strain Cow102. The plates were then treated with a selection of antibiotics from various classes: aminoglycosides (streptomycin [10 µg]) quinolones (ciprofloxacin [5 µg], nalidixic acid [30 µg]) beta-lactams (amoxicillin + clavulanic acid [20/10 µg], ampicillin [10 µg], cefotaxime [30 µg], ceftazidime [30 µg], piperacillin [100 µg]), folic acid synthesis inhibitor (trimethoprim/sulfamethoxazole [1.25/23.75 µg]), monobactams (aztreonam [30 µg]) and other antibiotics (fosfomycin [200 µg], tetracycline [30 µg]). Plates were incubated at 37°C for 24 hours under aerobic conditions, thereafter the diameters of the inhibition zones were measured. The strain was considered susceptible or resistant, using the breakpoints established by CLSI. ESBL-production was suspected due to reduced susceptibility to Ceftazidime (30 µg) and Cefotaxime (30 µg) in the AST. The Combination Disc Test (CDT), as recommended by the CLSI, was employed to confirm the production of ESBL. In summary, clavulanic acid (10 µg) was combined with each of cefotaxime (30 µg) and ceftazidime (30 µg). The test was considered positive when an increase in the growth-inhibitory zone around either the ceftazidime or the cefotaxime disk with clavulanic acid was ≥ 5 mm the diameter around the disk containing ceftazidime or cefotaxime alone. Haemolysis test Haemolytic phenotype was tested on blood agar plates (Blood Agar Base number 2; Oxoid, Basingstoke, UK) containing defibrinated sheep erythrocytes 5% v/v. Production of haemolysis was read after overnight incubation at 37°C DNA extraction and sequencing High-quality genomic DNA was extracted from pure pellets of K. pneumoniae subsp. pneumoniae Cow102 using the Quick-DNA fungal/bacterial miniprep kit (Zymo Research) and sent to South Africa Novogene Bioinformatics Technology Co. Ltd. for genome sequencing using the Illumina NovaSeq 6000 instrument. Illumina library was constructed (300-cycle v1.5 kit) and its quality was assessed on the Qubit 2.0 Fluorometer (Thermo Scientific). Genome assembly, annotation, and alignment The quality of sequence reads was determined using FastQC Version 0.12.0 [ 18 ]. Adapter trimming, quality filtering, and per-read quality pruning was performed using fastp software [ 19 ]. The sequence reads were merged using PEAR v0.9.6 [ 20 ]. The filtered paired-end reads were de novo assembled using SPAdes v3.15.3 [ 21 ]. Genome quality and completeness was evaluated using CheckM v1.0.18 [ 22 ] while quality assessment of the assembled sequence was done using QUality ASsessment Tool (QUAST) v5.2.0 [ 23 ]. Genome annotation was performed using the RASTk version 1.073 [ 24 ]. Taxonomic assignment, Multilocus Sequence typing (MLST) and capsular typing Taxonomic classification of the strain was done using kraken2 v2.1.3 [ 25 ] and the Genome Database Taxonomy (GTDB-Tk) v2.3.2 [ 26 ]. High quality genomes from The National Center for Biotechnology Information (NCBI) Reference sequence (RefSeq) database [ 27 ] were retrieved for the calculation of evolutionary distances. Reference genomes closely similar to the cow102 strain were identified by Mash/MinHash algorithm [ 28 ], protein families were identified using Protein Families for the Microbial Genomes database (PATtyFam) [ 29 ]. The protein sequences were aligned using MUSCLE v5 [ 30 ] and the nucleotides for each of those sequences mapped to the protein alignment. The resulting alignments were concatenated into a data matrix for phylogenetic analysis using RaxML v8.2.12 [ 31 ]. Multilocus sequence typing (MLST) of seven housekeeping genes (gapA, infB, mdh, pgi, phoE, rpoB and tonB) was performed by querying the Pasteur Institute ( http://bigsdb.pasteur.fr/klebsiella/klebsiella.html ) [ 32 ] using the MLST v2.220 software [ 33 ]. The Kaptive tool v2.0.4 [ 34 ] was used to determine capsular type (K-type and O-type). Identification of resistance determinants, virulence factors, phages and mobile genetic elements The staramr tool v0.10 [ 35 ] was used to query the current genome against the ResFinder database v4.4.2 [ 36 ] for profiling of AMR genes and drug classes, the plasmidfinder database [ 37 ] for identification of plasmids. Using ABRicate v1.0.1 [ 38 ], virulence determinants were investigated by aligning the reads to the Virulence Factors Database (VFDB) [ 39 ]. ISEScan tool V1.7.2.3 [ 40 ] was used to identify IS elements on the ISFinder database [ 41 ]. Insertion sequence elements shorter than 400 base pairs or single copy IS elements without perfect terminal inverted repeats were not considered. Phages were identified using the PHASTER (PHAge Search Tool Enhanced Release) web tool ( https://phaster.ca/ ) [ 42 ]. Default parameters were used for all tools except otherwise stated. Comparative genome Twenty quality genomes of K. pneumoniae strains of different sequence types isolated from various hosts (chicken, human, pig) and different sources (chicken faeces, open wound, blood, urine, vaginal swab, pork) in Nigeria, one reference genome from the RefSeq database, and one strain that was chosen at random to serve as an outgroup were all obtained from the NCBI database. Description of selected strains is presented in supplementary table S3 . Sequence alignment, pairwise average nucleotide identity (ANI) and sequence alignment percentages was performed using the CLC genomic workbench software v24.0. Thereafter, genome-wide variants were identified using MUMmer4’s DNAdiff tool v4.0 [ 43 ] using the Klebsiella pneumoniae subsp. pneumoniae cow102 assemblies against each NCBI assembly. Structural relocations, translocations, and inversions were identified alongside total and aligned bases. Prior to running the DNAdiff tool, each assembly was filtered to remove contigs of < 1kb in length to prevent short sequences from exaggerating structural variations between assemblies. Ethical clearance According to the Animal Use and Care Committee (AUCC) of the National Veterinary Research Institute (NVRI), Nigeria, the approach used for milk sample was non-invasive and did not cause pain or suffering to the animals, hence no ethical approval was necessary. Quality assurance The genomic DNA used for sequencing was isolated from a single colony of the bacteria. The 16S rDNA gene was extracted from the genome using extractseq version 5.0.0 [ 44 ]. The assessment of potential contamination of the genomic library by allochthonous microorganisms was achieved through BLAST annotation against NCBI microbial 16S database. Declarations Author Contribution MOA: Conceptualization, Data curation, Data analysis and visualization, Methodology, Writing original draft; OAO: Writing original draft; MSK: Data curation, Review and editing; BAO: Resources, Review and editing; RAA: Resources, Review and editing; CNE: Conceptualization, Resources, Methodology, Review and editing. References Akram F, Imtiaz M, Haq Iul. Emergent crisis of antibiotic resistance: A silent pandemic threat to 21st century. Microb Pathog. 2023;174:105923. Padmini N, Ajilda AAK, Sivakumar N, Selvakumar G. Extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae: critical tools for antibiotic resistance pattern. J Basic Microbiol. 2017;57:460–70. Yang Y, Higgins CH, Rehman I, Galvao KN, Brito IL, Bicalho ML, Song J, Wang H, Bicalho RC. Genomic diversity, virulence, and antimicrobial resistance of Klebsiella pneumoniae strains from cows and humans. 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Curr Opin Microbiol. 2018;45:131–9. Akinyemi MO, Ogunremi OR, Adeleke RA, Ezekiel CN. Probiotic Potentials of Lactic Acid Bacteria and Yeasts from Raw Goat Milk in Nigeria. Probiotics Antimicrob Proteins. 2022. https://doi.org/10.1007/S12602-022-10022-W . Akinyemi MO, Ezeokoli OT, Mthiyane DMN, Adeleke RA, Ezekiel CN. Bacterial and yeast communities in raw milk from three dairy animal species in Nigeria. Lett Appl Microbiol. 2023. https://doi.org/10.1093/LAMBIO/OVAC010 . Diancourt L, Passet V, Verhoef J, Grimont PAD, Brisse S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol. 2005;43:4178–82. Brisse S, Passet V, Haugaard AB, Babosan A, Kassis-Chikhani N, Struve C, Decre D. wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains. J Clin Microbiol. 2013;51:4073–8. Tsakali E, Tsantes AG, Houhoula D, Laliotis GP, Batrinou A, Halvatsiotis P, Tsantes AE. The Detection of Bacterial Pathogens, including Emerging Klebsiella pneumoniae, Associated with Mastitis in the Milk of Ruminant Species. Appl Sci. 2023;13:11484. Amosun E, Olatoye I, Adetosoye A. (2012) Antimicrobial Resistance in Escherichia Coli, Klebsiella pneumoniae and Pseudomonas Aeruginosa Isolated from Milk of Dairy Cows in Three Nigerian Cities. Niger Vet J 33. Adekanye UO, Ekiri AB, Galipó E, et al. Knowledge, attitudes and practices of veterinarians towards antimicrobial resistance and stewardship in Nigeria. Antibiotics. 2020;9:1–16. Ogwuche A, Ekiri AB, Endacott I, Maikai BV, Idoga ES, Alafiatayo R, Cook AJC. Antibiotic use practices of veterinarians and para-veterinarians and the implications for antibiotic stewardship in Nigeria. J S Afr Vet Assoc. 2021;92:1–14. Wareth G, Linde J, Hammer P, Pletz MW, Neubauer H, Sprague LD. (2022) WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany. Microorganisms. https://doi.org/10.3390/MICROORGANISMS10030564 . Andrews S. (2010) FastQC: A Quality Control Tool for High Throughput Sequence. In: Data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ . http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90. Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20. Bankevich A, Nurk S, Antipov D, et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol. 2012;19:455–77. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55. Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018;34:i142–50. Brettin T, Davis JJ, Disz T, et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5:8365. Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. (2022) Metagenome analysis using the Kraken software suite. Nature Protocols 2022 17:12 17:2815–2839. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics. 2022;38:5315–6. O’Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733–45. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: Fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:1–14. Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H. PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. Front Microbiol. 2016;7:118. Edgar RC. (2022) High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. bioRxiv 2021.06.20.449169. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3. Jolley KA, Maiden MCJ. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:1–11. Seemann TMLST. GitHub - tseemann/mlst::id: Scan contig files against PubMLST typing schemes. https://github.com/tseemann/mlst?tab=readme-ov-file . Accessed 4 Mar 2024. Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom. 2016;2:e000102. Bharat A, Petkau A, Avery BP et al. (2022) Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr. Microorganisms 2022, Vol 10, Page 292 10:292. Florensa AF, Kaas RS, Clausen PTLC, Aytan-Aktug D, Aarestrup FM. ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom. 2022. https://doi.org/10.1099/MGEN.0.000748 . Carattoli A, Zankari E, Garciá-Fernández A, Larsen MV, Lund O, Villa L, Aarestrup FM, Hasman H. In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing. Antimicrob Agents Chemother. 2014;58:3895. Seemann TABR. GitHub - tseemann/abricate::mag_right: Mass screening of contigs for antimicrobial and virulence genes. https://github.com/tseemann/abricate . Accessed 4 Mar 2024. Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022;50:D912–7. Xie Z, Tang H. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics. 2017;33:3340–7. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34:D32–6. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16–21. Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol. 2018;14:e1005944. Rice P, Longden L, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000;16:276–7. Additional Declarations No competing interests reported. Supplementary Files FigureS1.tif FigureS2.jpg TableS1.xlsx TableS2.xlsx TableS3.xlsx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version 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. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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One of such examples involve the rising incidence of various species, especially strains of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e, acquiring the capability to synthesize extended-spectrum β-Lactamase (ESBL) enzymes that confer resistance to a broad range of β-lactam antibiotics [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Members of the \u003cem\u003eKlebsiella\u003c/em\u003e genus, a Gram-negative non-motile, encapsulated, facultative anaerobic bacterium, within the family Enterobacteriaceae cause a wide range of infections in both humans and animals. \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e is a versatile bacterium that can be found in various environments, including the oral cavity, skin, and gastrointestinal tracts of different mammals [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. While normally present as a part of the human microbiota, this bacterium can also act as an opportunistic pathogen, leading to a range of infections such as pneumonia, septicaemia, urinary tract infections, and soft tissue infections, among others [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eBeta-lactam antibiotics, e.g., penicillins, cephalosporins, monobactams, and carbapenems, which are widely used as therapeutic agents to combat bacterial infections, exert their antimicrobial effects by cleaving to the penicillin-binding protein [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. This binding prevents the biosynthesis of the bacterial cell membrane, ultimately inhibiting the growth and survival of the bacteria [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. However, the presence of ESBLs considerably reduces the efficacy of beta-lactam antibiotics, creating a serious problem in the treatment of infection by ESBL-producing bacteria.\u003c/p\u003e \u003cp\u003eIn recent years, the World Health Organization (WHO) has recognized \u003cem\u003eK. pneumoniae\u003c/em\u003e as being among the top priority pathogens due to the significant morbidity and mortality rates associated with its infections and status as a major worldwide reservoir and vector for antibiotic resistance [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. As a result, there is a growing demand for genotyping this important pathogen to better understand its genetic characteristics and transmission patterns. One of the molecular methods commonly employed for this purpose is multilocus sequence typing (MLST) based on housekeeping genes, this allows for the characterization of the genetic relationship between different bacterial strains. \u003cem\u003eKlebsiella\u003c/em\u003e strains are largely oligoclonal [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e], which means they can be assigned into several unique sequence types (STs). This method of classification provides unambiguous and reliable data, which allows researchers and healthcare professionals gain valuable insights into the genetic diversity and transmission patterns of this pathogen.\u003c/p\u003e \u003cp\u003eIn Nigeria, a significant proportion of the available data that employed molecular techniques to identify \u003cem\u003eKlebsiella\u003c/em\u003e strain is predominantly derived from studies conducted in healthcare facilities and medical settings [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Studying the genomic characteristics of ESBL-producing \u003cem\u003eK. pneumoniae\u003c/em\u003e isolated from alternative sources, such as animal milk, could offer fresh perspectives on the transmission of these opportunistic pathogens across different niches in Nigeria. Moreover, genome typing of \u003cem\u003eKlebsiella\u003c/em\u003e strains from various sources will provide resources for bio-surveillance. This research also contributes to understanding antibiotic resistance dissemination as well as the development of targeted interventions and preventive measures to mitigate the spread of \u003cem\u003eK. pneumoniae\u003c/em\u003e in both animal and human populations.\u003c/p\u003e"},{"header":"Results and discussion","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eAntimicrobial susceptibility profile\u003c/h2\u003e \u003cp\u003e \u003cem\u003eKlebsiella\u003c/em\u003e species are major global reservoirs and conduit of drug resistance genes between various bacterial niches [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. We report the draft genome sequence of an ESBL-producing \u003cem\u003eK. pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e strain Cow102 previously isolated from cow milk [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. The phenotypic antimicrobial susceptibility profile of strain cow102 showed resistance to cephalosporins, carbapenem, and drugs from different classes of antibiotics including aminoglycosides (streptomycin), quinolone (ciprofloxacin, nalidixic acid), beta-lactams (amoxicillin\u0026thinsp;+\u0026thinsp;clavulanic acid, ampicillin, cefotaxime, ceftazidime, piperacillin), folic acid synthesis inhibitor (trimethoprim/sulfamethoxazole), monobactams (aztreonam), fosfomycin, and tetracycline. The strain was identified as an ESBL producer due to its resistance to aztreonam, cefotaxime, ceftazidime, and ceftriaxone, which are commonly used as indicators for ESBL production.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eHaemolysis test\u003c/h2\u003e \u003cp\u003eThe strain reported in this study was non-hemolytic on blood agar and lacked the genes hlyA and cnf-1 that code for this function.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eGeneral genome features\u003c/h2\u003e \u003cp\u003eIllumina sequencing of the genomic DNA of strain cow102 generated 12,005,232 total read pairs (2 \u0026times; 150 bp) giving approximately 336 \u0026times; coverage. The assembly genome totalled 5,359,907 bp with 70 contigs, an N50 value of 376,296 bp, and a GC content of 57.35%. The assembly was characterized using CheckM as 100% complete with, 0.1% contamination, 99.4% and 97.8% coarse and fine consistencies, respectively. Genome annotation performed using RASTk identified, a total of 5,244 protein coding sequences (CDS), 72 transfer RNA (tRNA) genes, and 5 ribosomal RNA (rRNA) genes. There were 4,605 proteins with functional assignments and 639 hypothetical proteins in the annotation. Among the proteins with functional assignments, 1,457 possessed Enzyme Commission (EC) numbers, 1,208 had Gene Ontology (GO) assignments, and 1,065 contained KEGG pathway mappings. Also, about 31% of the CDS was mapped to a subsystem. Genes responsible for amino acids and derivatives (417 ORFs), protein metabolism (227 ORFs), and cofactors, vitamins, prosthetic groups, and pigments (196 ORFs) were abundant among the SEED subsystem categories. An overview of the subsystem categories and feature counts is shown in Fig.\u0026nbsp;1A while the genome annotation can be viewed on Figshare.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003ePhylogenetic analysis, Multilocus Sequence typing (MLST) and capsular typing\u003c/h2\u003e \u003cp\u003eThe whole-genome phylogenetic analysis showed that strain Cow102 is closely related to \u003cem\u003eK. pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e strains IS39, DSM30104, ISC21, and DSM30104, all of which belong to the HS11286 group (Fig.\u0026nbsp;1B).\u003c/p\u003e \u003cp\u003eMultilocus Sequence typing analysis revealed that the current isolate had a new allelic profile [(gapA (2), infB (3), mdh (70) pgi (1) phoE (275), rpoB (44) and tonB (39)], assigned as sequence type 6914 based on the standard 7-gene MLST scheme, initially defined by Diancourt \u003cem\u003eet al\u003c/em\u003e [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. eBURST analyses showed that ST6914 clustered closely with ST494, ST4138, ST4139 and ST6476 (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eA). The current strain, ST6914 is a triple-locus variant to all closely clustered ST, differing at the phoE, rpoB and tonB loci. The serotyping of ST6914 revealed a 99.96% match with K locus 122 with an unknown K type (KL122) for the capsular (K typing) antigen (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eB) using the wzi sequencing K-typing method [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e], and a 98.51% match with O locus O1/O2v2 with type O2afg for the lipopolysaccharide (O typing) antigen (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eC).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003eAntimicrobial resistance genes\u003c/h2\u003e \u003cp\u003eSeveral studies in Nigeria reported drug-resistant \u003cem\u003eKlebsiella\u003c/em\u003e strains in raw animal milk and milk products; however, genomic data and serotypes of the reported strains are rare [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. Molecular characterization of the resistance factors associated with strain Cow102 revealed the presence of 38 Antibiotic Resistance Genes (ARGs) (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e and Fig.\u0026nbsp;2), out of which 24 genes were fully concordant with the phenotypically derived resistance profile. The resistance genes identified in strain Cow102 include core chromosomal resistance genes belonging to the \u003cem\u003ebla\u003c/em\u003e\u003csub\u003eSHV\u003c/sub\u003e family, which transfer resistance to beta-lactam antibiotics. In addition, acquired genes such as aadA2, an aminoglycoside nucleotidyltransferase gene; catA2 and catII, which confer resistance by enzymatic inactivation of amphenicol antibiotics; TEM families, which transfer resistance through similar mechanisms as \u003cem\u003ebla\u003c/em\u003e\u003csub\u003eSHV\u003c/sub\u003e family; and \u003cem\u003eEscherichia coli\u003c/em\u003e FosA and oqxAB gene conferring resistance to fosfomycin and quinolones, respectively, were found. Furthermore, the presence of the efflux pump gene, Tet (D), which provides resistance to tetracycline, was expected (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e and Fig.\u0026nbsp;2). This is likely due to the common practice among veterinary and para-veterinary professionals in Nigeria to prescribe oxytetracycline for treating diseases [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eAntimicrobial resistance genes identified in \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e strain Cow102 and conferring resistance to tested antibiotics\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eResistance gene\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAntibiotic Class\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAntibiotic (phenotype observed)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eaadA2b\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eaminoglycoside\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eStreptomycin (resistant)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-1\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\" morerows=\"13\" rowspan=\"14\"\u003e \u003cp\u003ebeta-lactam\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAmoxicillin (resistant) \u003csup\u003ea,b,c,d,f,g,n\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-11\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAmoxicillin\u0026thinsp;+\u0026thinsp;clavulanic acid (resistant)\u003csup\u003ed\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-13\u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAmpicillin(resistant) \u003csup\u003ea,b,c,d,f,g,n\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-26\u003csup\u003ed\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAmpicillin\u0026thinsp;+\u0026thinsp;clavulanic acid (resistant)\u003csup\u003ed\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-70\u003csup\u003ee\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAztreonam (resistant)\u003csup\u003ec,e,g\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-78\u003csup\u003ef\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eCefotaxime (resistant) \u003csup\u003ec,e,g\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-98\u003csup\u003eg\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eCeftazidime (resistant) \u003csup\u003ec,e,g\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-145\u003csup\u003eh\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eCeftriaxone (resistant) \u003csup\u003ec,e,g\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-161\u003csup\u003ei\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ePiperacillin (resistant) \u003csup\u003ea,b,c,d,f,g,n\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-179\u003csup\u003ej\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-185\u003csup\u003ek\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-194\u003csup\u003el\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaSHV-199\u003csup\u003em\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eblaTEM-1B\u003csup\u003en\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ecatA2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eamphenicol\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eChloramphenicol (intermediate)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003edfrA16\u003csup\u003eq\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003efolic acid synthesis inhibitor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etrimethoprim\u003csup\u003eo,q\u003c/sup\u003e/sulfamethoxazole\u003csup\u003ep\u003c/sup\u003e (resistant)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003efosA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003efosfomycin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eFosfomycin (intermediate)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003efosA5\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003efosA6\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOqxA\u003csup\u003eo\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eQuinolone and folic acid synthesis inhibitor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eCiprofloxacin (intermediate)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOqxB\u003csup\u003eo\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNalidixic acid (resistant)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003esul1\u003csup\u003ep\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003efolic acid synthesis inhibitor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSul2\u003csup\u003ep\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTet(D)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003etetracycline\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTetracyclin (resistant)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"3\"\u003eKey: Superscripts represent combination of resistance gene conferring resistance to an antibiotic\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe genome as shown in Fig.\u0026nbsp;2 includes several additional genes associated with antimicrobial resistance that were not phenotypically tested, and their presence alone does not confirm resistance. These include KatG gene and operons MarA, MarB, and MarR, which are involved in enzymatic catalysis of antibiotics. The BcrC gene serves as a protective protein for antibiotic targets. GdpD and PgsA genes are involved in altering the charge of the cell wall, while OccD6/OprQ and OprB modulate antibiotic permeability. The presence of AcrAB-TolC, EmrAB-TolC, H-NS, and OxyR suggests the role of regulatory factors in modulating the expression of antibiotic resistance genes. Additionally, the genome harbours other ARGs that were acquired through horizontal gene transfer such as the \u003cem\u003eE. coli\u003c/em\u003e UhpT gene, which carries a mutation conferring resistance to fosfomycin, mdfA gene, an efflux pump, and multidrug transporter, as well as the \u003cem\u003eHaemophilus influenzae\u003c/em\u003e PBP3 gene which confers resistance to beta-lactam antibiotics (Fig.\u0026nbsp;2). Comprehensive details of ARGs, their orientation and genomic location is presented in Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eVirulence factors\u003c/h2\u003e \u003cp\u003eProfiling of virulence features in the current strain revealed the presence of 98 virulence factors (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e) classified into 12 categories: adherence (15 genes), antimicrobial activity/competitive advantage (3 genes), biofilm formation (10 genes), effector delivery system (25 genes), exotoxins (2 genes), immune modulation (16 genes), invasion (2 genes), motility (3 genes), nutritional/metabolic factors (14 genes), regulation (7 genes), and other (1 gene).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eVirulence genes of \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e strain Cow102.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVirulence factor\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCategory\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eRelated Gene\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eProduct\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType I fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efimC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePeriplasmic chaperone\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType I fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efimD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eOuter membrane usher protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType I fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efimH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType 1 fimbrial adhesin precursor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType I fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efimK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTranscriptional regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlagella\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efleQ\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTranscriptional regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHsp60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehtpB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eHsp60, heat shock protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eChiRP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epilB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType IV-A pilus assembly\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType IV pili\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epilR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTwo-component response regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType IV pili\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epilT\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTwitching motility protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType IV pili\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erpoN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eRNA polymerase factor sigma-54\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType IV pili\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erpoS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eRNA polymerase sigma factor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType IV pili\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etapT\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTwitching\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEF-Tu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etufA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eElongation factor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType IV pili\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003evfr\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCamp-regulatory protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAdherence\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eECP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eyagX/ecpC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eE. coli common pilus usher\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAntimicrobial activity/ Competitive advantage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMtrCDE\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emtrD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eMultiple transferable resistance system protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAntimicrobial activity/ Competitive advantage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAcrAB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eacrA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAcriflavine resistance protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAntimicrobial activity/ Competitive advantage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAcrAB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eacrB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAcriflavine resistance protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAlginate\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ealgW\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAlgw protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAI-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eluxS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eS-ribosylhomocysteinase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType 3 fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emrkB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eFimbrial chaperone protein mrkB precursor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType 3 fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emrkC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eFimbrial biogenesis outer membrane usher protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType 3 fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emrkD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eFimbrial adhesin protein precursor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType 3 fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emrkF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType 3 fimbrial minor pilin subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType 3 fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emrkH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTranscriptional activator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType 3 fimbriae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emrkJ\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePhosphodiesterase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAlginate\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emucD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSerine protease mucD precursor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiofilm\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePNAG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epgaA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePoly-beta-1,6 N-acetyl-D-glucosamine export porin\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eclpB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eclpV/tssH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIS-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eclpV1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system AAA\u0026thinsp;+\u0026thinsp;family\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eExe T2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eexeD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eExe T2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eexeE\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eExe T2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eexeF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eExe T2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eexeG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eExolysin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eexlA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eHemolysin\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003egspE\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003egspG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eicmF/tssM\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eimpA/tssA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIS-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ePA1663\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTranscriptional regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIS-3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ePA2359\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTranscriptional regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etssF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system baseplate subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etssG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system baseplate subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIS-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etssH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etssH-5/clpV\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eClp-type chaperone protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIS-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003etssM\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system membrane subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003evasE/tssK\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system baseplate subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003evasH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSigma-54 dependent transcriptional regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003evgrG/tssI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system tip protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eT6SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003evipB/tssC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType VI secretion system contractile sheath large subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eXcp secretion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003excpR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGeneral secretion pathway protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEffector delivery system\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eYst1 T2SS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eyst1E\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eType II secretion system\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eExotoxin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCya\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ecyaB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCyclolysin secretion ATP-binding protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eExotoxin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eRtxA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ertxB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eRTX toxin transporter\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCapsule\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003egalF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGalu regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLOS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003egmhA/lpcA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePhosphoheptose isomerase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKP1_RS17220\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGlycosyltransferase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKP1_RS17230\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eGlycosyltransferase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKP1_RS17240\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eDUF4422 domain-containing protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCapsule\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKP1_RS17345\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCapsule assembly Wzi family protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLOS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erfaD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eADP-L-glycero-D-mannoheptose-6-epimerase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erfaJ\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAlpha-1,6 Glc transferase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erfbA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eO-antigen export ABC transporter permease\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erfbB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eO-antigen export ABC transporter ATP-binding protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erfbD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eUDP-galactopyranose mutase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCapsule\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erfbK1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eO9 family phosphomannomutase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLOS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erffG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eDtdp-glucose 46-dehydratase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ewaaA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLipopolysaccharide core biosynthesis protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ewaaC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3-deoxy-D-manno-octulosonic-acid (KDO) transferase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eImmune modulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eLPS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ewaaF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eHeptosyltransferase I\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eInvasion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eIbes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eibeB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCu(+)/Ag(+) efflux RND transporter outer membrane channel\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eInvasion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eompA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eompA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eOuter membrane protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMotility\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlagella\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eflrA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSigma-54 dependent transcriptional activator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMotility\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePolar flagella\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eflmH\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eShort chain dehydrogenase/reductase family oxidoreductase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMotility\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePolar flagella\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003enueA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNeua protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eentA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2,3-dihydroxybenzoate-2,3-dehydrogenase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eentC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIsochorismate synthase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eentE\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEnterobactin synthase subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eentF\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEnterobactin synthase subunit\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eentS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEnterobactin exporter\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFbpABC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efbpC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIron(III) ABC transporter, ATP-binding protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnterobactin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efepA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eFerrienterobactin outer membrane transporter\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efepD\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIron-enterobactin transporter membrane protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEnt\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003efes\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEnterobactin/ferric enterobactin esterase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSal\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eiroE\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSiderophore esterase iroe\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSalmochelin siderophore\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eiroN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSalmochelin receptor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAerobactin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eiutA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eFerric aerobactin receptor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMgtBC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003emgtB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eMg2\u0026thinsp;+\u0026thinsp;transport protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNutritional/Metabolic factor\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePyochelin\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epchI\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eABC transporter ATP-binding protein\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOthers\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eIsocitrate lyase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eicl\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIsocitrate lyase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCdpA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ecdpA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCyclic di-GMP phosphodiesterase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePhoQ\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ephoP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eResponse regulator in two-component regulatory system with PhoQ\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePhoQ\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ephoQ\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSensor protein PhoQ\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSigA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003esigA/rpoV\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eRNA polymerase sigma factor\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePmrAB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epmrA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eResponse regulator\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePmrAB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003epmrB\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSensory kinase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eRelA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003erelA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eProbable GTP pyrophosphokinase\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003eMobile genetic elements, Plasmid and Phages\u003c/h2\u003e \u003cp\u003eThere are a total of 23 insertion sequences (IS) classified into eight IS families: IS1, IS3, IS5, IS110, IS66, IS91, IS630, and ISNCY in the genome of strain Cow102. A comprehensive list of all identified IS, along with their corresponding CDS positions and terminal inverted repeats (TIR) is presented in Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e. The only plasmids found in the present genome were IncFIB(K)-1-Kpn3 and Col440I_1. These plasmids were respectively detected in 16 (67%) and 11 (46%) of 24 \u003cem\u003eK. pneumoniae\u003c/em\u003e isolates from powdered milk from Germany [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. Additionally, five bacteriophages were detected, of which three (Klebsi phiKO2, Escher 500465, Entero cdtI) were intact, one (Salmon 118970 sal3) was incomplete, and one (Escher RCS47) yielded inconclusive results. Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e illustrates the positions of these bacteriophages within the CDS region of the Cow102 strain.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eComparative genomics\u003c/h2\u003e \u003cp\u003eA first glance at the genomic comparison analysis between the current and 22 other strains of \u003cem\u003eK. pneumoniae\u003c/em\u003e suggested a high level of sequence similarity with pairwise average nucleotide identity (ANI) ranging from 99.1\u0026ndash;99.9% (Figure \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). It is worthy of note that the other strains were from various hosts (chicken, cow, human, pig) and sources (chicken faeces, open wound, blood, urine, vaginal swab, pork, cow milk). Pairwise whole-genome alignments with CLC genomic workbench for all 22 assemblies against the cow102 strain revealed sequence alignment percentages of about 85% and 90% (Figure \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e), despite the fact that huge differences were observed in assembly metrics such as N50 and GC content. A closer look at the variations between the genomes using DNAdiff found significant differences (\u003cem\u003ep\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05) in sequence inversions, insertions/deletions (indels), relocations and translocations between the assemblies and the examined strains (Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). The most common structural rearrangements discovered were translocations (x̄=105), which occurred between neighbouring 1-to-1 alignment blocks in different sequences. Additionally, there was an average of approximately nine breaks in the alignment where adjacent 1-to-1 alignment blocks were in the same sequence (relocations), and two somewhat unusual breaks where adjacent 1-to-1 alignment blocks were inverted with regard to each other (inversions). Furthermore, an average of 221 insertion events, three tandem duplication insertion events (TandemIns), 32995 Single Nucleotide Polymorphism (SNPs) and 2629 Single Nucleotide\u003c/p\u003e \u003c/div\u003e"},{"header":"Materials and methods","content":"\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eBacterial isolation and growth conditions\u003c/h2\u003e \u003cp\u003eThe current report stemmed from a 2019 study that sought to identify functional bacteria in animal milk [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. A synopsis of the sample collection and bacterial isolation conducted is provided here. Cow milk samples (n\u0026thinsp;=\u0026thinsp;20) were collected from dairy farms in Sokoto State, Nigeria, between May and June 2019. Each sample was subjected to six dilution series. Bacteria were isolated on De-Mann Rogosa Sharpe (MRS) agar plates supplemented with D-Sorbitol and incubation of inoculated plates was performed in anaerobic conditions at 37\u0026deg;C for 24 hours.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eAntimicrobial susceptibility testing and screening of the ESBL production\u003c/h2\u003e \u003cp\u003eAntimicrobial susceptibility testing (AST) was done using the agar diffusion method and the Clinical and Laboratory Standards Institute (CLSI) M100 guideline (31st edition) for drug selection and interpretation of result. Briefly, Mueller\u0026ndash;Hinton agar plates (20ml) were overlaid with MacFarland standardized broth containing the \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e strain Cow102. The plates were then treated with a selection of antibiotics from various classes: aminoglycosides (streptomycin [10 \u0026micro;g]) quinolones (ciprofloxacin [5 \u0026micro;g], nalidixic acid [30 \u0026micro;g]) beta-lactams (amoxicillin\u0026thinsp;+\u0026thinsp;clavulanic acid [20/10 \u0026micro;g], ampicillin [10 \u0026micro;g], cefotaxime [30 \u0026micro;g], ceftazidime [30 \u0026micro;g], piperacillin [100 \u0026micro;g]), folic acid synthesis inhibitor (trimethoprim/sulfamethoxazole [1.25/23.75 \u0026micro;g]), monobactams (aztreonam [30 \u0026micro;g]) and other antibiotics (fosfomycin [200 \u0026micro;g], tetracycline [30 \u0026micro;g]). Plates were incubated at 37\u0026deg;C for 24 hours under aerobic conditions, thereafter the diameters of the inhibition zones were measured. The strain was considered susceptible or resistant, using the breakpoints established by CLSI.\u003c/p\u003e \u003cp\u003eESBL-production was suspected due to reduced susceptibility to Ceftazidime (30 \u0026micro;g) and Cefotaxime (30 \u0026micro;g) in the AST. The Combination Disc Test (CDT), as recommended by the CLSI, was employed to confirm the production of ESBL. In summary, clavulanic acid (10 \u0026micro;g) was combined with each of cefotaxime (30 \u0026micro;g) and ceftazidime (30 \u0026micro;g). The test was considered positive when an increase in the growth-inhibitory zone around either the ceftazidime or the cefotaxime disk with clavulanic acid was \u0026ge;\u0026thinsp;5 mm the diameter around the disk containing ceftazidime or cefotaxime alone.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eHaemolysis test\u003c/h2\u003e \u003cp\u003eHaemolytic phenotype was tested on blood agar plates (Blood Agar Base number 2; Oxoid, Basingstoke, UK) containing defibrinated sheep erythrocytes 5% v/v. Production of haemolysis was read after overnight incubation at 37\u0026deg;C\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003eDNA extraction and sequencing\u003c/h2\u003e \u003cp\u003eHigh-quality genomic DNA was extracted from pure pellets of \u003cem\u003eK. pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e Cow102 using the Quick-DNA fungal/bacterial miniprep kit (Zymo Research) and sent to South Africa Novogene Bioinformatics Technology Co. Ltd. for genome sequencing using the Illumina NovaSeq 6000 instrument. Illumina library was constructed (300-cycle v1.5 kit) and its quality was assessed on the Qubit 2.0 Fluorometer (Thermo Scientific).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eGenome assembly, annotation, and alignment\u003c/h2\u003e \u003cp\u003eThe quality of sequence reads was determined using FastQC Version 0.12.0 [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. Adapter trimming, quality filtering, and per-read quality pruning was performed using fastp software [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. The sequence reads were merged using PEAR v0.9.6 [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. The filtered paired-end reads were \u003cem\u003ede novo\u003c/em\u003e assembled using SPAdes v3.15.3 [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Genome quality and completeness was evaluated using CheckM v1.0.18 [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e] while quality assessment of the assembled sequence was done using QUality ASsessment Tool (QUAST) v5.2.0 [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Genome annotation was performed using the RASTk version 1.073 [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003eTaxonomic assignment, Multilocus Sequence typing (MLST) and capsular typing\u003c/h2\u003e \u003cp\u003eTaxonomic classification of the strain was done using kraken2 v2.1.3 [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e] and the Genome Database Taxonomy (GTDB-Tk) v2.3.2 [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. High quality genomes from The National Center for Biotechnology Information (NCBI) Reference sequence (RefSeq) database [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e] were retrieved for the calculation of evolutionary distances. Reference genomes closely similar to the cow102 strain were identified by Mash/MinHash algorithm [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e], protein families were identified using Protein Families for the Microbial Genomes database (PATtyFam) [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. The protein sequences were aligned using MUSCLE v5 [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e] and the nucleotides for each of those sequences mapped to the protein alignment. The resulting alignments were concatenated into a data matrix for phylogenetic analysis using RaxML v8.2.12 [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eMultilocus sequence typing (MLST) of seven housekeeping genes (gapA, infB, mdh, pgi, phoE, rpoB and tonB) was performed by querying the Pasteur Institute (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://bigsdb.pasteur.fr/klebsiella/klebsiella.html\u003c/span\u003e\u003cspan address=\"http://bigsdb.pasteur.fr/klebsiella/klebsiella.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e] using the MLST v2.220 software [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. The Kaptive tool v2.0.4 [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e] was used to determine capsular type (K-type and O-type).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section2\"\u003e \u003ch2\u003eIdentification of resistance determinants, virulence factors, phages and mobile genetic elements\u003c/h2\u003e \u003cp\u003eThe staramr tool v0.10 [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e] was used to query the current genome against the ResFinder database v4.4.2 [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e] for profiling of AMR genes and drug classes, the plasmidfinder database [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e] for identification of plasmids. Using ABRicate v1.0.1 [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e], virulence determinants were investigated by aligning the reads to the Virulence Factors Database (VFDB) [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]. ISEScan tool V1.7.2.3 [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e] was used to identify IS elements on the ISFinder database [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]. Insertion sequence elements shorter than 400 base pairs or single copy IS elements without perfect terminal inverted repeats were not considered. Phages were identified using the PHASTER (PHAge Search Tool Enhanced Release) web tool (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://phaster.ca/\u003c/span\u003e\u003cspan address=\"https://phaster.ca/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. Default parameters were used for all tools except otherwise stated.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec19\" class=\"Section2\"\u003e \u003ch2\u003eComparative genome\u003c/h2\u003e \u003cp\u003eTwenty quality genomes of \u003cem\u003eK. pneumoniae\u003c/em\u003e strains of different sequence types isolated from various hosts (chicken, human, pig) and different sources (chicken faeces, open wound, blood, urine, vaginal swab, pork) in Nigeria, one reference genome from the RefSeq database, and one strain that was chosen at random to serve as an outgroup were all obtained from the NCBI database. Description of selected strains is presented in supplementary table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e. Sequence alignment, pairwise average nucleotide identity (ANI) and sequence alignment percentages was performed using the CLC genomic workbench software v24.0. Thereafter, genome-wide variants were identified using MUMmer4\u0026rsquo;s DNAdiff tool v4.0 [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e] using the \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e cow102 assemblies against each NCBI assembly. Structural relocations, translocations, and inversions were identified alongside total and aligned bases. Prior to running the DNAdiff tool, each assembly was filtered to remove contigs of \u0026lt;\u0026thinsp;1kb in length to prevent short sequences from exaggerating structural variations between assemblies.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec20\" class=\"Section2\"\u003e \u003ch2\u003eEthical clearance\u003c/h2\u003e \u003cp\u003eAccording to the Animal Use and Care Committee (AUCC) of the National Veterinary Research Institute (NVRI), Nigeria, the approach used for milk sample was non-invasive and did not cause pain or suffering to the animals, hence no ethical approval was necessary.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec21\" class=\"Section2\"\u003e \u003ch2\u003eQuality assurance\u003c/h2\u003e \u003cp\u003eThe genomic DNA used for sequencing was isolated from a single colony of the bacteria. The 16S rDNA gene was extracted from the genome using extractseq version 5.0.0 [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. The assessment of potential contamination of the genomic library by allochthonous microorganisms was achieved through BLAST annotation against NCBI microbial 16S database.\u003c/p\u003e \u003c/div\u003e"},{"header":"Declarations","content":"\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eMOA: Conceptualization, Data curation, Data analysis and visualization, Methodology, Writing original draft; OAO: Writing original draft; MSK: Data curation, Review and editing; BAO: Resources, Review and editing; RAA: Resources, Review and editing; CNE: Conceptualization, Resources, Methodology, Review and editing.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eAkram F, Imtiaz M, Haq Iul. Emergent crisis of antibiotic resistance: A silent pandemic threat to 21st century. Microb Pathog. 2023;174:105923.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePadmini N, Ajilda AAK, Sivakumar N, Selvakumar G. 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Trends Genet. 2000;16:276\u0026ndash;7.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"animal milk, draft genome, Klebsiella pneumoniae subsp. pneumoniae, multidrug resistance","lastPublishedDoi":"10.21203/rs.3.rs-4123332/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4123332/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eCow milk which is sometimes consumed raw host a plethora of microorganisms of beneficial or food safety concern. The draft genome of an extended-spectrum β-Lactamase-producing \u003cem\u003eKlebsiella pneumoniae\u003c/em\u003e subsp. \u003cem\u003epneumoniae\u003c/em\u003e strain Cow102, isolated from cow milk used for production of traditional foods in Nigeria, is reported.\u003c/p\u003e\u003ch2\u003eResult\u003c/h2\u003e \u003cp\u003eThe genome has a total length of 5,359,907 bp with 70 contigs and GC content of 57.35%. A total of 5,244 protein coding sequences were detected with 31% mapped to a subsystem, and genes coding for amino acids and derivatives being the most prevalent. Multilocus sequence typing revealed that the strain had new allelic profile assigned to the novel 6914 sequence type possessing capsular and lipopolysaccharide antigen K locus 122 with an unknown K type (KL122) and O locus O1/O2v2 with type O2afg, respectively. A total of 28 resistance-related genes, 98 virulence-related genes, two plasmids and five phages were identified in the genome. Comparative analysis indicated translocation was the most common structural rearrangements in the genome.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eWhole-genome sequencing and bioinformatics analysis revealed new allelic profile, structural rearrangements, virulence and drug resistance factors in the genome, however, further studies are required to characterize the capsular K type oof Cow102.\u003c/p\u003e","manuscriptTitle":"Genomic characterisation of an extended-spectrum β-Lactamase- producing Klebsiella pneumoniae isolate assigned to a novel sequence type (6914)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-03-22 19:21:21","doi":"10.21203/rs.3.rs-4123332/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"25028fa1-7a9a-4052-a8fe-0d3b2ed787c7","owner":[],"postedDate":"March 22nd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-03-26T09:20:06+00:00","versionOfRecord":[],"versionCreatedAt":"2024-03-22 19:21:21","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4123332","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4123332","identity":"rs-4123332","version":["v1"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}