Characterization and Comparative Genomic Analysis of Yersinia enterocolitica strains Isolated from Poultry and Red Meat in South Korea

Characterization and Comparative Genomic Analysis of Yersinia enterocolitica strains Isolated from Poultry and Red Meat in South Korea | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Characterization and Comparative Genomic Analysis of Yersinia enterocolitica strains Isolated from Poultry and Red Meat in South Korea Dabin Kim, Sumin Ryu, Yeeun Kim, Jaehyun Choi, Min Jung Lee, Yonghoon Kim, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8676138/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 13 You are reading this latest preprint version Abstract Background Yersinia enterocolitica is a psychrotrophic foodborne bacterium capable of growing at refrigeration temperatures and is frequently associated with animal-source foods, raising concerns for food safety and public health. Despite its relevance and the increasing use of whole-genome sequencing (WGS) for bacterial surveillance, genomic studies on Y. enterocolitica isolates from South Korea are limited. In this study, we analyzed 157 Y. enterocolitica isolates obtained from pork, beef, chicken, and duck collected nationwide using WGS to elucidate their genomic diversity and adaptive features. Results Phylogenomic analysis classified all isolates as biotype 1A (sub-biotype 1Aa) and revealed considerable genetic heterogeneity, comprising 40 sequence types (STs) and 66 core-genome types (CTs). No clear segregation by source was observed, suggesting cross-source circulation within livestock production and processing environments. Pan-genome analysis identified 23,110 gene clusters, revealing an open pan-genome enriched in genes associated with metabolism, defense mechanisms, and stress responses, reflecting high genomic flexibility. Although the canonical virulence plasmid pYV was absent, we identified a conserved set of chromosomal virulence-associated genes linked to adhesion ( inv , yapE ), secretion, and enterotoxicity ( ystB ), suggesting enhanced potential for persistence rather than pronounced pathogenicity. Antimicrobial resistance (AMR) genes were predominantly intrinsic, including blaA (β-lactamase) and vat(F) (streptogramin resistance), which were universally detected, whereas acquired AMR genes such as tet(C) and ant(3'')-Ia were sporadically observed. Furthermore, approximately one-third of isolates harbored Col- and Inc-type plasmid replicons, supporting the occurrence of horizontal gene exchange and environmental adaptation. Conclusions Y. enterocolitica from animal-source foods in South Korea represents a genetically diverse and environmentally resilient population with limited virulence and predominantly intrinsic AMR determinants. These findings establish a genomic framework for understanding the ecology of Y. enterocolitica in animal-source foods and underscore the need for ongoing genomic surveillance to detect emerging variants that may influence food safety and public health. Yersinia enterocolitica comparative genomics whole-genome sequencing (WGS) genome surveillance food safety Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Background Yersinia enterocolitica is a psychrotrophic zoonotic bacterium responsible for foodborne yersiniosis, a gastrointestinal infection characterized by diarrhea, fever, and mesenteric lymphadenitis, and occasionally associated with systemic complications such as sepsis and reactive arthritis [ 1 , 2 ]. In the European Union, yersiniosis consistently ranks among the top three reported zoonoses, with the majority of cases attributed to Y. enterocolitica [ 3 ]. Transmission typically occurs through the consumption of contaminated animal-source foods, particularly pork, which is recognized as the primary reservoir for pathogenic Y. enterocolitica [ 4 , 5 ]. Contamination has also been reported in other animal-derived foods, including beef, chicken, and duck, reflecting the persistence of this pathogen in slaughter and processing environments [ 6 , 7 ]. Its ability to survive and grow at refrigeration temperatures underscores its relevance to food safety and highlights the need for continued monitoring throughout livestock production and cold-chain systems [ 8 – 10 ]. Traditionally, Y. enterocolitica has been divided into six biotypes (1A, 1B, and 2–5) that differ in pathogenic potential [ 11 ]. Biotype 1B is highly virulent and responsible for most human yersiniosis cases, whereas biotypes 2–5 display moderate pathogenicity [ 12 ]. Biotype 1A has generally been regarded as nonpathogenic because it typically lacks the virulence plasmid (pYV) and chromosomal markers such as ail and ystA [ 13 ]. Nonetheless, genomic and epidemiological studies have demonstrated that biotype 1A is genetically diverse and may harbor loci associated with adhesion or enterotoxicity, including ystB , inv , and yaxA / B [ 14 , 15 ]. These findings suggest that certain 1A lineages may adapt to environmental niches and exhibit limited pathogenic potential under favorable conditions [ 16 ]. Beyond the traditional biotyping framework, advances in whole-genome sequencing (WGS) have enabled high-resolution characterization of Y. enterocolitica , including biotype prediction, sequence typing, and in silico detection of virulence factors, antimicrobial resistance (AMR) genes, and plasmid-associated elements [ 17 – 19 ]. WGS-based approaches have increasingly been applied for population structure analysis, outbreak investigations, and evolutionary studies of Y. enterocolitica in multiple countries [ 20 – 22 ]. Such genomic data provide critical insights into the population structure, virulence potential, and antimicrobial resistance profiles of strains circulating in food-associated environments. However, despite South Korea’s advanced livestock production and distribution systems, comprehensive genome-based investigations of Y. enterocolitica from animal-source foods limited. In this study, we conducted a comprehensive genomic analysis of Y. enterocolitica isolates recovered from animal-source foods, including pork, beef, chicken, and duck, collected across South Korea. By integrating whole-genome-based comparative and phylogenomic analyses, we assessed the genetic diversity, population structure, and adaptive traits underlying the ecology of Y. enterocolitica within the animal-source food chain. This work provides a genomic framework for understanding the evolutionary and functional characteristics of this species in food-related environments and represents the first WGS-based investigation of Y. enterocolitica from animal-source foods in South Korea. Methods Bacterial strains Y. enterocolitica strains (n = 157) were obtained from animal-source foods, including beef, pork, chicken, and duck, in South Korea and were provided by the Korean Culture Collection for Foodborne Pathogens (Ministry of Food and Drug Safety, Cheongju, Republic of Korea). An overview of the isolates is presented in Table 1 , and detailed metadata for each isolate are available in Supplementary Table S1 . Strain identification was performed using a VITEK MS system (BioMérieux Inc., Marcy-l’Etoile, France). Table 1 Overview of isolates and genotyping results. Category Description Isolates (country) 157 (South Korea) Sources, n (%) Pork 68 (43.3), Beef 49 (31.2), Chicken 31 (19.7), Duck 9 (0.06) Regions, n (%) Gyeonggi 14 (8.9), Gangwon 1 (0.6), Chungcheong 38 (24.2), Jeolla 86 (54.8), Gyeongsang 18 (11.04) Biotype / Sub-biotype 1A / 1Aa Sequence types (STs) 40 STs (13 unclassified) Core-genome types (CTs) 66 CTs Major STs (n > 2) ST134 (38), ST179 (19), ST150 (9), ST246 (9), ST470 (7), ST248 (5), ST200 (4), ST426 (4), ST220 (3), ST568 (3), ST1125 (3), ST138 (2), ST232 (2), ST234 (2), ST319 (2), ST322 (2), ST367 (2), ST484 (2), ST538 (2), ST724 (2), ST845 (2), ST848 (2) Major CTs (n > 2) CT3053 (26), CT2534 (8), CT2483 (7), CT480 (5), CT1548 (5), CT2546 (5), CT488 (4), CT2315 (4), CT2567 (4), CT150 (3), CT484 (3), CT486 (3), CT531 (3), CT542 (3), CT1420 (3), CT2676 (3), CT3063 (3), CT3096 (3), CT537 (2), CT1284 (2), CT1331 (2), CT1339 (2), CT1346 (2), CT1373 (2), CT1433 (2), CT1555 (2), CT1642 (2), CT1663 (2), CT1690 (2), CT2342 (2), CT2539 (2), CT2668 (2), CT3799 (2) Whole genome sequencing (WGS) DNA was extracted from 157 isolates using the Qiagen Dneasy Blood & Tissue kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. DNA concentration was estimated using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were prepared using the Illumina DNA prep kit (Illumina, San Diego, CA, USA) and sequenced on a NextSeq 1000/2000 platform (Illumina) producing 300 base pair (bp) paired-end reads. The reads were assembled de novo with the default k-mer size using the CLC Genomics Workbench v. 12.0 (Qiagen). In silico genotyping In silico genotyping was conducted for multilocus sequence typing (MLST) and core-genome MLST (cgMLST). MLST and cgMLST profiles of Y. enterocolitica were assigned using the EnteroBase platform ( https://enterobase.warwick.ac.uk/ ). The MLST scheme followed the Achtman 7-gene scheme ( adk , argA , aroA , glnA , thrA , tmk , and trpE ). cgMLST allele profiles were based on 1,553 loci defined in the EnteroBase Yersinia cgMLST scheme. Pairwise allelic distances were calculated using cgmlst-dists ( https://github.com/achtman-lab/cgmlst-dists ). Pan-genome analysis and functional annotation Pan-genome analysis was performed using the Bacterial Pan Genome Analysis tool (BPGA v1.3; default parameters). Orthologous gene clustering was conducted with USEARCH, using 95% sequence identity as the cut-off value. The pan-genome profile of the Y. enterocolitica isolates was characterized by calculating the number of core, accessory, and unique gene. In addition, a binary presence/absence matrix of orthologous gene clusters was constructed using a pan-genome analysis pipeline and visualized as a hierarchically clustered heatmap to illustrate the distribution of core, accessory, and unique gene families across the isolates. The functional classification of orthologous clusters was based on COG (Clusters of Orthologous Groups) categories. Biotype prediction Publicly available Y. enterocolitica genomes with known biotypes were retrieved from previous studies for biotype prediction [ 18 ] (Table S2 ) and analyzed together with the isolates in the pan-genome framework. Core gene alignments were used to construct a phylogenetic tree, and isolates clustering with reference genomes of known biotypes were assigned accordingly. The phylogenetic tree was constructed using the neighbor-joining method and visualized in iTOL v6. Genome features of Y. enterocolitica Genome features of the Y. enterocolitica were characterized with a focus on virulence factors, AMR genes, and plasmid replicons. These features were identified using ABRicate v1.0.1 ( https://github.com/tseemann/abricate ) with standard filtering parameters. Screening was performed against three databases: the Virulence Factor Database (VFDB, accessed 2025-09), ResFinder (accessed 2025-09), and PlasmidFinder (accessed 2025-09). For AMR genes, additional confirmation of gene family and predicted resistance phenotype was based on ResFinder annotations. The presence of plasmid replicons was used to infer potential plasmid carriage. Results Isolates A total of 157 Y. enterocolitica strains isolated from animal-source foods, including pork (68/157), beef (49/157), chicken (31/157), and duck (9/157), collected across different regions of South Korea were included (Table 1 , Table S1 ). The isolates represented a broad geographic distribution, with samples originating from Gyeonggi (14/157), Gangwon (1/157), Chungcheong (38/157), Jeolla (86/157), and Gyeongsang (18/157) provinces. Biotyping Phylogenetic analysis based on pan-genome protein sequences was used to predict the biotypes of the 157 isolates (Fig. 1 ). In the phylogeny, reference strains of each biotype consistently clustered together, supporting the reliability of the biotype predictions. All isolates were classified as biotype 1A (100%). To further resolve intra-biotype variation, the 157 isolates were compared with reference genomes representing the sub-biotypes 1Aa and 1Ab. These isolates clustered with the 1Aa references, confirming that all isolates analyzed in this study are sub-biotype 1Aa. Sequence types diversity The Y. enterocolitica isolates recovered from animal-source foods were assigned to 40 distinct sequence types (STs), and 66 core-genome types (CTs), while 13 additional isolates remained unclassified (unknown STs) (Table 1 , Fig. 2 ). Among them, ST134 was predominant, accounting for 38 of 157 isolates (24.2%), followed by ST179 (19 isolates, 12.1%), ST150 (9 isolates, 5.7%), and ST246 (9 isolates, 5.7.%). Overall, the MLST results revealed a genetically diverse population structure, with a few dominant STs and numerous rare ones, consistent with ongoing diversification within animal-source food associated Y. enterocolitica populations in South Korea. Among the predominant ST134 isolates, multiple distinct CTs were identified, indicating considerable genomic heterogeneity within this lineage. Specifically, ST134 isolates from pork were assigned to CT480, CT1548, and CT3053; those from chicken to CT522, CT1420, and CT3053; from beef to CT3053; and from duck also to CT3053. Notably, CT3053 was shared across all four animal sources, suggesting the presence of a widely distributed sublineage that circulates throughout the animal-source food production chain. This finding suggestests both the genomic diversification and cross-source persistence of Y. enterocolitica ST134 within animal-source foods. Allelic relationships among isolates were visualized using a cgMLST allele-distance heatmap (Fig. 3 ), which showed overall genomic similarity and no clear segregation by food source. Several isolates displayed zero allelic differences despite originating from different food categories, suggesting that genetically related Y. enterocolitica lineages circulate among multiple animal-source foods. Overall, Y. enterocolitica isolates from animal-source foods in South Korea form a largely homogeneous population across animal sources, implying the circulation of common lineages within food production and processing environments. Pan-genome and COG analysis Pan-genome analysis of the isolates identified 23,110 gene clusters, comprising 3,045 core (13%), 10,903 accessory (40%), and 9,162 unique (47%) genes (Fig. 4 A–C). Each isolate exhibited a distinct presence/absence profile and pan-/core-genome accumulation curves showed a continuously expanding pan-genome with a stable core, indicating an open pan-genome structure. This genomic openness may facilitate adaptation to diverse ecological niches. Functional annotation of orthologous clusters according to COG categories demonstrated that accessory and unique genes were broadly distributed across diverse functional classes, including metabolism, cellular processes, and information storage and processing (Fig. 4 D, Table S3 ). Accessory and unique genes were enriched in functional categories related to metabolism (e.g., carbohydrate, amino acid, and lipid metabolism), cellular processes (e.g., signal transduction and defense mechanisms), and information storage and processing (e.g., replication and repair). By contrast, core genes were mainly associated with essential housekeeping functions, including translation, energy production, and nucleotide metabolism. Collectively, these findings indicate that Y. enterocolitica isolates from animal-source foods possess an extensive genetic repertoire and functional diversity while maintaining a conserved genomic backbone. This combination of genomic stability and accessory variability may contribute to their environmental adaptability and persistence within the food production chain. Genomic features: virulence factors, AMR genes and plasmids Virulence factors By screening the 157 Y. enterocolitica isolates, we identified 105 virulence-associated genes grouped into eight functional categories (Fig. 5 , Table S4 ). More than 90% of these genes were shared among isolates, indicating a largely conserved virulence-gene repertoire within the population. All isolates carried multiple adhesion-related determinants. The psa locus showed variable distribution, with psaC present in all isolates and psaF and psaE detected in 83.4% and 30.6%, respectively. All isolates also carried yapE , whereas type IV pilus–associated genes (e.g., pilL , pilQ , and pilV ) were detected only sporadically (1–2%). Adherence- and capsule-related genes displayed greater variability among isolates, whereas enterotoxin-associated genes such as ystB and its secretion pathway components were almost universally conserved. The invasion-related genes inv and pla were found in all isolates, indicating a conserved potential for host cell entry. Enterotoxin-associated genes, including ystB and its secretion-related components ( yst1C – G , yst1J , yst1K , and yst1O ), were detected in more than 97% of isolates, demonstrating that enterotoxin functions are widely conserved. Capsule-related genes were more variable than other virulence categories, particularly those within the rfb cluster (2–45%). Exotoxin-associated genes ( yplA , yaxA , and yaxB ) were present in all isolates. Flagellar and chemotaxis genes were universally present, indicating that motility and environmental-sensing systems are genetically stable across this population. All isolates contained tolC , the outer-membrane channel of the type I secretion system (T1SS), and multiple type III secretion system (T3SS) genes ( sctD , sctI , sctJ , sctL , and sctR ), while the SPI-2–like ssaG gene was present in 95% of isolates. These results show that the major secretion systems are conserved among the isolates. Overall, adhesion and motility systems exhibited greater genetic variability than toxin and secretion systems, indicating differential evolutionary constraints among virulence categories. Collectively, these findings indicate that Y. enterocolitica isolates from animal-source foods harbor a conserved set of virulence genes encompassing adhesion, invasion, enterotoxicity, and secretion functions, reflecting a stable genomic backbone with latent pathogenic potential and a possible capacity for persistence within food-related environments. AMR genes All isolates carried the chromosomally encoded blaA (intrinsic β-lactam resistance) and vat(F) (streptogramin inactivation) genes indicating a conserved baseline resistance profile among isolates (Fig. 5 , Table S5 ). The detected AMR genes were categorized into two primary mechanisms: antibiotic inactivation and antibiotic efflux. Antibiotic inactivation, mediated by β-lactamase ( blaA ) and aminoglycoside-modifying enzymes such as ant(3'')-Ia , represented the predominant mechanism, whereas efflux-based resistance, mainly associated with tet(C) , was less frequently observed. These findings indicate that enzymatic inactivation is the major mechanism underlying AMR among the examined Y. enterocolitica isolates. Four isolates were classified as multidrug-resistant (MDR), each carrying acquired AMR genes conferring resistance to three antimicrobial classes. Two isolates (MFDS1030554 and MFDS2015999) carried the aminoglycoside resistance gene ant(3'')-Ia , whereas two others (MFDS1019044 and MFDS2016015) possessed the tetracycline resistance gene tet(C). Overall, the AMR genes identified among the isolates were primarily associated with resistance to β-lactams, aminoglycosides, tetracyclines, and streptogramins, reflecting the dominance of intrinsic resistance with sporadic acquisition of additional determinants. Plasmids Plasmid replicon analysis revealed that 36.9% (58/157) of the isolates carried at least one plasmid (Fig. 5 ). Among plasmid-positive isolates, multiple replicon types were identified with varying frequencies. The most prevalent replicon was ColRNAI, detected in 29.3% of plasmid-bearing isolates, followed by pYE854 (19.0%), Col440II (13.8%), and Col(Ye4449), ColE10, and IncN, each detected in 12.1% of isolates. Other replicon types occurred at lower frequencies, including Col440I (10.3%), IncN3 (5.2%), ColpVC (5.2%), pIP31758(p153) (3.4%), pIP31758(p59) (3.4%), and IncX5 (3.4%). Several additional replicons were detected as single occurrences (1.7% each), including Col(YF27601), ColpVC_1, IncFII(p14), IncFII(pCRY), IncFII(pKP91), IncX7, and pENTAS02. None of the isolates carried the classical pYV virulence plasmid, which is typically associated with pathogenic Y. enterocolitica strains. The predominance of Col- and Inc-type replicons indicates that diverse, likely mobilizable plasmids, rather than large virulence-associated plasmids, circulate among Y. enterocolitica isolates in animal-source foods in South Korea, potentially facilitating horizontal gene transfer within the food production environment. Discussion This study provides the first comprehensive genomic characterization of Y. enterocolitica isolates recovered from animal-source foods in South Korea. All 157 isolates were classified as biotype 1A (sub-biotype 1Aa), a lineage traditionally regarded as nonpathogenic. However, phylogenomic and sequence-typing analyses revealed extensive heterogeneity, comprising 40 STs and 66 CTs. The lack of source-specific clustering and the detection of shared cgMLST types across pork, beef, chicken, and duck suggest that common Y. enterocolitica lineages circulate within the livestock production and processing continuum. Similar population structures have been reported in previous studies from Europe and China, where biotype 1A predominated among food-derived isolates and exhibited high sequence-type diversity [ 22 , 23 ]. Nevertheless, the dominant sequence types differed by region. For example, a study of 158 Y. enterocolitica isolates from England identified ST18 as the most prevalent lineage, whereas ST134 was detected only sporadically [ 23 ]. In contrast, ST134 was the predominant lineage in the present study, accounting for 24.2% of all isolates, suggesting possible regional differences in the distribution and ecological adaptation of biotype 1A populations [ 23 ]. These findings collectively suggest that Y. enterocolitica biotype 1A in South Korea forms a genetically heterogeneous yet ecologically cohesive population capable of persisting across diverse food-associated ecosystems. Pan-genome analysis further demonstrated the remarkable genomic flexibility of these isolates. Among 23,110 identified gene clusters, only 13% constituted the core genome, confirming an open pan-genome structure. The large accessory and unique gene pools, which were enriched in metabolic, defense, and stress-response functions, highlight the organism’s capacity for functional diversification and persistence under variable conditions. Such genomic plasticity likely facilitates survival under cold storage, nutrient limitation, or antimicrobial pressure, all of which are common in food-processing and distribution settings. Collectively, the phylogenomic and pan-genomic findings indicate that biotype 1A Y. enterocolitica represents a genetically diverse yet evolutionarily cohesive population capable of long-term maintenance within the food production chain. Although the canonical virulence plasmid pYV was absent, all isolates retained a highly conserved set of chromosomal virulence-associated genes related to adhesion ( yapE , psaC ), invasion ( inv , pla ), secretion systems, and enterotoxicity ( ystB ). These genes do not necessarily confer high pathogenicity but may facilitate colonization and persistence on food-contact surfaces or within processing environments [ 24 ]. The absence of pYV, combined with the consistent presence of ystB and other enterotoxin-related genes, reflects the typical genetic background of biotype 1A while suggesting that certain strains may retain low-level virulence potential under favorable conditions [ 15 , 24 ]. AMR determinants were primarily intrinsic, with blaA (β-lactamase) and vat(F) (streptogramin resistance) universally detected. Only a few isolates carried additional acquired genes conferring resistance to aminoglycosides or tetracyclines, suggesting that antimicrobial exposure in the food production environment is low and that horizontal gene acquisition occurs only sporadically. Approximately one-third of the isolates carried plasmids, and among them, a few isolates possessed the pYE854 plasmid, which has previously been detected only in pathogenic Y. enterocolitica isolates [ 19 ]. The predominant plasmid groups were Col- and Inc-type replicons, which are mainly associated with mobilization and stress adaptation rather than virulence [ 25 , 26 ]. Their presence suggests a latent potential for horizontal gene transfer among food-associated microbial communities [ 25 , 26 ]. Taken together, Y. enterocolitica isolates from animal-source foods in South Korea represent a genetically diverse yet environmentally resilient population. Although all isolates belong to biotype 1A and are not considered highly pathogenic, their conserved virulence-associated genes, intrinsic AMR, and plasmid-mediated adaptability highlight their capacity for persistence within food-related environments. These characteristics suggest that biotype 1A strains may act as long-term contaminants in food processing and distribution systems, thereby contributing to the maintenance of microbial reservoirs that could compromise food hygiene. From a food safety perspective, continuous genomic surveillance of Y. enterocolitica in animal-source foods and processing facilities is essential for tracking genetic evolution, understanding contamination dynamics, and implementing effective control strategies to minimize potential risks to consumers. Conclusions In this study, we present the first large-scale genomic characterization of Y. enterocolitica isolates obtained from animal-source foods in South Korea. Whole-genome sequencing revealed that all isolates belonged to biotype 1A but exhibited substantial genomic heterogeneity, an open and flexible pan-genome, and a conserved chromosomal backbone. Despite the absence of the classical virulence plasmid pYV, the isolates harbored multiple virulence-associated genes and intrinsic antimicrobial resistance determinants, reflecting both evolutionary stability and ecological adaptability. The frequent detection of small Col- and Inc-type plasmids further suggests a capacity for horizontal gene transfer within food-associated microbial communities. Overall, these findings indicate that Y. enterocolitica populations from animal-source foods are genetically diverse yet environmentally resilient, capable of persisting under cold and nutrient-limited conditions commonly encountered in the food chain. From a food safety perspective, these traits may allow biotype 1A strains to act as long-term contaminants in processing or distribution environments, emphasizing the importance of sustained genomic surveillance and hygiene management practices. Continued monitoring of Y. enterocolitica is essential to detect emerging variants that could impact food quality and consumer health. Abbreviations Antimicrobial resistance (AMR) Bacterial Pan Genome Analysis tool (BPGA) core genome multilocus sequence typing (cgMLST) Clusters of Orthologous Groups (COG) core genome type (CT) multilocus sequence typing (MLST) sequence type (ST) virulence factor (VF) whole genome sequencing (WGS). Declarations Ethics approval and consent to participate Not applicable Consent for publication Not applicable Competing interests The authors declare no conflicts of interest. Funding This study was funded by the Ministry of Food and Drug Safety (grant number 25191MFDS002). The findings and conclusions of this study are our own, and do not necessarily represent the views of the Ministry of Food and Drug Safety. Author Contribution DK, ML, YK, IJ and WJ conceived and designed the study.DK, SR, YK and JC performed the experiments and analyzed the sequence data.DK, SR, YK and JC conducted data curation and bioinformatic analyses.DK and WJ prepared the initial draft of the manuscript.DK, ML, YK, IJ and WJ reviewed and edited the manuscript.All authors read and approved the final manuscript. Acknowledgements Not applicable Data Availability Sequence data were submitted to publicly accessible NCBI archives, including GenBank, under the accession numbers listed in Table S1. References Bancerz-Kisiel A, Szweda W. Yersiniosis–zoonotic foodborne disease of relevance to public health. Ann Agric Environ Med. 2015;22:397–402. Rosner BM, Stark K, Werber D. Epidemiology of reported Yersinia enterocolitica infections in Germany, 2001–2008. BMC Public Health. 2010;10:337. European Food Safety Authority (EFSA). European Centre for Disease Prevention and Control (ECDC). 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Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid. 2022;123–4:102650. Additional Declarations No competing interests reported. Supplementary Files TableS2.xlsx TableS5.xlsx TableS4.xlsx TableS1.xlsx Figure1.pdf Figure3.pdf Figure2.pdf Figure5.pdf Figure4.pdf TableS3.xlsx Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 23 Mar, 2026 Reviews received at journal 04 Mar, 2026 Reviews received at journal 02 Mar, 2026 Reviews received at journal 23 Feb, 2026 Reviewers agreed at journal 11 Feb, 2026 Reviewers agreed at journal 11 Feb, 2026 Reviewers agreed at journal 10 Feb, 2026 Reviewers agreed at journal 10 Feb, 2026 Reviewers invited by journal 09 Feb, 2026 Editor invited by journal 27 Jan, 2026 Editor assigned by journal 24 Jan, 2026 Submission checks completed at journal 24 Jan, 2026 First submitted to journal 23 Jan, 2026 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. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8676138","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":581324403,"identity":"abe3a697-2d76-448e-a731-2c8d3ae58459","order_by":0,"name":"Dabin Kim","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Dabin","middleName":"","lastName":"Kim","suffix":""},{"id":581324404,"identity":"8b3968ea-4c56-4426-8452-87bb77e09a52","order_by":1,"name":"Sumin Ryu","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Sumin","middleName":"","lastName":"Ryu","suffix":""},{"id":581324405,"identity":"c6c3d4e2-b575-4f28-9df9-5d7b80746516","order_by":2,"name":"Yeeun Kim","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Yeeun","middleName":"","lastName":"Kim","suffix":""},{"id":581324406,"identity":"dce59d7b-af91-433f-9c5e-51b557b1abc7","order_by":3,"name":"Jaehyun Choi","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Jaehyun","middleName":"","lastName":"Choi","suffix":""},{"id":581324407,"identity":"bc863efb-7afe-4a2b-bf7b-888740b44a1a","order_by":4,"name":"Min Jung Lee","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Min","middleName":"Jung","lastName":"Lee","suffix":""},{"id":581324408,"identity":"45d2b078-ef05-4036-b153-949353dedd2d","order_by":5,"name":"Yonghoon Kim","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Yonghoon","middleName":"","lastName":"Kim","suffix":""},{"id":581324409,"identity":"5830ab73-1bd2-4b97-8623-790a088f351a","order_by":6,"name":"Insun Joo","email":"","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":false,"prefix":"","firstName":"Insun","middleName":"","lastName":"Joo","suffix":""},{"id":581324410,"identity":"7fd10621-a876-4a87-9420-278fd789a368","order_by":7,"name":"Woojung Lee","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA60lEQVRIiWNgGAWjYJACAyCWYWDg//jgwwGwADNRWniA2NhwBrFaGKBazKR5iNFicLz5QDHvjloegxsJadI2Z2zy+dkPMBtX4NNy5liCMe+Z4yAth61zbqRZzuxJYE48g0eL2Y0cA2PetmM8BmcONt7O+XDYwOBAAvPBBuK0HGaQtgBqsT//gCgtNTwGx9uYpBluAG2RADoMnxZ7oF8M57Yd4JE83sNs2HMmzUDixsNmQ3xaJNubjxm8bauT4zvMw/jgxzEbA/7+5MOS+LQAARswKg8jCzAS0ACMuAcMDHWEFI2CUTAKRsFIBgAonVDdgs7uGwAAAABJRU5ErkJggg==","orcid":"","institution":"Ministry of Food and Drug Safety","correspondingAuthor":true,"prefix":"","firstName":"Woojung","middleName":"","lastName":"Lee","suffix":""}],"badges":[],"createdAt":"2026-01-23 07:24:07","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8676138/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8676138/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":101316606,"identity":"ce102d36-c768-433c-a618-897945eb7f45","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":467823,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic relationships of \u003cem\u003eY. enterocolitica\u003c/em\u003eisolates based on pan-genome protein sequences. A neighbor-joining phylogenetic tree was constructed from pan-genome protein sequences of 157 \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates collected in South Korea, together with reference genomes representing known biotypes (1A, 1B, 2, 3, 4, and 5) and sub-biotypes (1Aa, 1Ab). Colored outer rings indicate biotype and sub-biotype classification, and reference genomes are marked with navy circles. The tree was visualized using iTOL v6.\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/e5873cb7df5b598503fe8bb2.png"},{"id":101397734,"identity":"41ead341-a241-458e-a632-cd3284751478","added_by":"auto","created_at":"2026-01-29 09:36:13","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":319367,"visible":true,"origin":"","legend":"\u003cp\u003eDistribution of multilocus sequence types (STs) and isolation sources of \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates. Bar plots show the number of isolates that were positive for each sequence type (ST), colored according to the animal-source food commodity from which they were isolated. Colors correspond to different animal-source food categories as indicated in the legend (pork, beef, chicken and duck).\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/57fb2bbb5d276444b75555eb.png"},{"id":101316607,"identity":"c16b24e4-5140-4476-a64f-aa559f66bb85","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":365979,"visible":true,"origin":"","legend":"\u003cp\u003eAllelic distance heatmap of \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates based on core-genome multilocus sequence typing (cgMLST). Pairwise allelic distances among 157 \u003cem\u003eY. enterocolitica\u003c/em\u003eisolates were calculated using the EnteroBase cgMLST scheme (1,553 loci). The heatmap illustrates genomic relatedness between isolates, with red indicating high similarity (low allelic distance) and blue representing greater divergence.\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/dddb70046a1a45ec2bb39c38.png"},{"id":101398449,"identity":"4f00ddc5-46df-42f9-a7ce-07ed76f883ef","added_by":"auto","created_at":"2026-01-29 09:41:36","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1142936,"visible":true,"origin":"","legend":"\u003cp\u003ePan-genome analysis and functional classification of \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates collected in South Korea. (a) Gene presence/absence matrix of 23,110 gene clusters among 157 isolates, aligned with a hierarchical tree showing their genetic relationships. (b) Pan- and core-genome accumulation curves illustrating the increase in total gene clusters and the plateauing of core genes with the addition of new genomes. (c) Proportional composition of core (13%), accessory (40%), and unique (47%) genes in the pan-genome. (d) Functional classification of core, accessory, and unique genes based on Clusters of Orthologous Groups (COG) categories.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/6f71c681177ec3aecce8a38a.png"},{"id":101316615,"identity":"9983c074-15b8-43a4-bb3e-e013c4935079","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":3177430,"visible":true,"origin":"","legend":"\u003cp\u003eDistribution of virulence factors (VFs), antimicrobial resistance (AMR) genes, and plasmid replicons among \u003cem\u003eY. enterocolitica\u003c/em\u003eisolates. The heatmap summarizes the genomic features identified across isolates, including virulence-associated genes (blue), AMR genes (green), and plasmid replicons (yellow). Each column represents a gene, and each row represents an isolate. The presence and absence of genes are indicated by colored and blank cells, respectively. Metadata columns on the left display the source of isolation, biotype, multilocus sequence type (ST), and core-genome type (CT). Virulence genes are grouped by functional categories (adherence, capsule, enterotoxin, exotoxin, flagella, invasion, type I secretion system and type III secretion system). AMR genes include multidrug-resistant (MDR) determinants, and plasmid replicons are color-coded according to their presence or absence.\u003c/p\u003e","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/7d9da8c71c059aab9a747b50.png"},{"id":101399924,"identity":"2966d265-bb11-4c93-9629-e6cd50b26e6d","added_by":"auto","created_at":"2026-01-29 09:55:45","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":6255771,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/ce83b583-c552-40c4-88b4-c2098910050f.pdf"},{"id":101398070,"identity":"1e5d8e71-814e-4d27-bae4-9902834cb2dc","added_by":"auto","created_at":"2026-01-29 09:39:26","extension":"xlsx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":14420,"visible":true,"origin":"","legend":"","description":"","filename":"TableS2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/a2ad032a498e656c0350cff9.xlsx"},{"id":101397891,"identity":"721d8179-ca6f-43f4-b4d3-ce53e9ec07b0","added_by":"auto","created_at":"2026-01-29 09:37:57","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":11340,"visible":true,"origin":"","legend":"","description":"","filename":"TableS5.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/f1c3b659007877761f8519e1.xlsx"},{"id":101398153,"identity":"f659fddb-091c-4aa8-9029-6fcb388e37c7","added_by":"auto","created_at":"2026-01-29 09:39:53","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":16208,"visible":true,"origin":"","legend":"","description":"","filename":"TableS4.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/07c733748a419e7ffbc699d0.xlsx"},{"id":101316609,"identity":"bcd87c09-134f-4850-ac68-e85c494d4a64","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":20672,"visible":true,"origin":"","legend":"","description":"","filename":"TableS1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/d863bf3d358d47a3b3cb3378.xlsx"},{"id":101316621,"identity":"aedffbca-d2cf-4f3d-a6b8-7e623bb933b7","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":330454,"visible":true,"origin":"","legend":"","description":"","filename":"Figure1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/57be4411877a608700c18f20.pdf"},{"id":101316620,"identity":"ce40a713-3bf1-486b-afa3-599b79a73e14","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":143298,"visible":true,"origin":"","legend":"","description":"","filename":"Figure3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/a242a07d7ffab5d87b140e10.pdf"},{"id":101316612,"identity":"e5f9c7c1-e677-4c02-84ca-ec1a9899cd47","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"pdf","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":69772,"visible":true,"origin":"","legend":"","description":"","filename":"Figure2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/bc045cde337e0ecfbda08d21.pdf"},{"id":101316619,"identity":"5242ef91-86c0-495d-8bec-84609c9abbc9","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"pdf","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":129291,"visible":true,"origin":"","legend":"","description":"","filename":"Figure5.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/14604ee8a2a4939d454295ea.pdf"},{"id":101316616,"identity":"2514b860-acc9-425d-9a86-5bbfcef045ef","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"pdf","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":390495,"visible":true,"origin":"","legend":"","description":"","filename":"Figure4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/060cd2c961079beb0052920b.pdf"},{"id":101316614,"identity":"420e037f-39be-4754-bd0e-0c58d5a8cf7f","added_by":"auto","created_at":"2026-01-28 12:07:43","extension":"xlsx","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":12113,"visible":true,"origin":"","legend":"","description":"","filename":"TableS3.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8676138/v1/bd928bc6cdc2832a40b308d5.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Characterization and Comparative Genomic Analysis of Yersinia enterocolitica strains Isolated from Poultry and Red Meat in South Korea","fulltext":[{"header":"Background","content":"\u003cp\u003e \u003cem\u003eYersinia enterocolitica\u003c/em\u003e is a psychrotrophic zoonotic bacterium responsible for foodborne yersiniosis, a gastrointestinal infection characterized by diarrhea, fever, and mesenteric lymphadenitis, and occasionally associated with systemic complications such as sepsis and reactive arthritis [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. In the European Union, yersiniosis consistently ranks among the top three reported zoonoses, with the majority of cases attributed to \u003cem\u003eY. enterocolitica\u003c/em\u003e [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. Transmission typically occurs through the consumption of contaminated animal-source foods, particularly pork, which is recognized as the primary reservoir for pathogenic \u003cem\u003eY. enterocolitica\u003c/em\u003e [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Contamination has also been reported in other animal-derived foods, including beef, chicken, and duck, reflecting the persistence of this pathogen in slaughter and processing environments [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Its ability to survive and grow at refrigeration temperatures underscores its relevance to food safety and highlights the need for continued monitoring throughout livestock production and cold-chain systems [\u003cspan additionalcitationids=\"CR9\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eTraditionally, \u003cem\u003eY. enterocolitica\u003c/em\u003e has been divided into six biotypes (1A, 1B, and 2\u0026ndash;5) that differ in pathogenic potential [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. Biotype 1B is highly virulent and responsible for most human yersiniosis cases, whereas biotypes 2\u0026ndash;5 display moderate pathogenicity [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Biotype 1A has generally been regarded as nonpathogenic because it typically lacks the virulence plasmid (pYV) and chromosomal markers such as \u003cem\u003eail\u003c/em\u003e and \u003cem\u003eystA\u003c/em\u003e [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. Nonetheless, genomic and epidemiological studies have demonstrated that biotype 1A is genetically diverse and may harbor loci associated with adhesion or enterotoxicity, including \u003cem\u003eystB\u003c/em\u003e, \u003cem\u003einv\u003c/em\u003e, and \u003cem\u003eyaxA\u003c/em\u003e/\u003cem\u003eB\u003c/em\u003e [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e, \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. These findings suggest that certain 1A lineages may adapt to environmental niches and exhibit limited pathogenic potential under favorable conditions [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eBeyond the traditional biotyping framework, advances in whole-genome sequencing (WGS) have enabled high-resolution characterization of \u003cem\u003eY. enterocolitica\u003c/em\u003e, including biotype prediction, sequence typing, and \u003cem\u003ein silico\u003c/em\u003e detection of virulence factors, antimicrobial resistance (AMR) genes, and plasmid-associated elements [\u003cspan additionalcitationids=\"CR18\" citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. WGS-based approaches have increasingly been applied for population structure analysis, outbreak investigations, and evolutionary studies of \u003cem\u003eY. enterocolitica\u003c/em\u003e in multiple countries [\u003cspan additionalcitationids=\"CR21\" citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. Such genomic data provide critical insights into the population structure, virulence potential, and antimicrobial resistance profiles of strains circulating in food-associated environments. However, despite South Korea\u0026rsquo;s advanced livestock production and distribution systems, comprehensive genome-based investigations of \u003cem\u003eY. enterocolitica\u003c/em\u003e from animal-source foods limited.\u003c/p\u003e \u003cp\u003eIn this study, we conducted a comprehensive genomic analysis of \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates recovered from animal-source foods, including pork, beef, chicken, and duck, collected across South Korea. By integrating whole-genome-based comparative and phylogenomic analyses, we assessed the genetic diversity, population structure, and adaptive traits underlying the ecology of \u003cem\u003eY. enterocolitica\u003c/em\u003e within the animal-source food chain. This work provides a genomic framework for understanding the evolutionary and functional characteristics of this species in food-related environments and represents the first WGS-based investigation of \u003cem\u003eY. enterocolitica\u003c/em\u003e from animal-source foods in South Korea.\u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eBacterial strains\u003c/h2\u003e \u003cp\u003e \u003cem\u003eY. enterocolitica\u003c/em\u003e strains (n\u0026thinsp;=\u0026thinsp;157) were obtained from animal-source foods, including beef, pork, chicken, and duck, in South Korea and were provided by the Korean Culture Collection for Foodborne Pathogens (Ministry of Food and Drug Safety, Cheongju, Republic of Korea). An overview of the isolates is presented in Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, and detailed metadata for each isolate are available in Supplementary Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e. Strain identification was performed using a VITEK MS system (BioM\u0026eacute;rieux Inc., Marcy-l\u0026rsquo;Etoile, France).\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\u003eOverview of isolates and genotyping results.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\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 \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCategory\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eDescription\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eIsolates (country)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e157 (South Korea)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSources, n (%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePork 68 (43.3), Beef 49 (31.2), Chicken 31 (19.7), Duck 9 (0.06)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegions, n (%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGyeonggi 14 (8.9), Gangwon 1 (0.6), Chungcheong 38 (24.2), Jeolla 86 (54.8), Gyeongsang 18 (11.04)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiotype / Sub-biotype\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1A / 1Aa\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSequence types (STs)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e40 STs (13 unclassified)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCore-genome types (CTs)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e66 CTs\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMajor STs (n\u0026thinsp;\u0026gt;\u0026thinsp;2)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eST134 (38), ST179 (19), ST150 (9), ST246 (9), ST470 (7), ST248 (5), ST200 (4), ST426 (4), ST220 (3), ST568 (3), ST1125 (3), ST138 (2), ST232 (2), ST234 (2), ST319 (2), ST322 (2), ST367 (2), ST484 (2), ST538 (2), ST724 (2), ST845 (2), ST848 (2)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMajor CTs (n\u0026thinsp;\u0026gt;\u0026thinsp;2)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCT3053 (26), CT2534 (8), CT2483 (7), CT480 (5), CT1548 (5), CT2546 (5), CT488 (4), CT2315 (4), CT2567 (4), CT150 (3), CT484 (3), CT486 (3), CT531 (3), CT542 (3), CT1420 (3), CT2676 (3), CT3063 (3), CT3096 (3), CT537 (2), CT1284 (2), CT1331 (2), CT1339 (2), CT1346 (2), CT1373 (2), CT1433 (2), CT1555 (2), CT1642 (2), CT1663 (2), CT1690 (2), CT2342 (2), CT2539 (2), CT2668 (2), CT3799 (2)\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\n\u003ch3\u003eWhole genome sequencing (WGS)\u003c/h3\u003e\n\u003cp\u003eDNA was extracted from 157 isolates using the Qiagen Dneasy Blood \u0026amp; Tissue kit (Qiagen, Hilden, Germany) following the manufacturer\u0026rsquo;s instructions. DNA concentration was estimated using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).\u003c/p\u003e \u003cp\u003eLibraries were prepared using the Illumina DNA prep kit (Illumina, San Diego, CA, USA) and sequenced on a NextSeq 1000/2000 platform (Illumina) producing 300 base pair (bp) paired-end reads. The reads were assembled \u003cem\u003ede novo\u003c/em\u003e with the default k-mer size using the CLC Genomics Workbench v. 12.0 (Qiagen).\u003c/p\u003e\n\u003ch3\u003eIn silico genotyping\u003c/h3\u003e\n\u003cp\u003e \u003cem\u003eIn silico\u003c/em\u003e genotyping was conducted for multilocus sequence typing (MLST) and core-genome MLST (cgMLST). MLST and cgMLST profiles of \u003cem\u003eY. enterocolitica\u003c/em\u003e were assigned using the EnteroBase platform (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://enterobase.warwick.ac.uk/\u003c/span\u003e\u003cspan address=\"https://enterobase.warwick.ac.uk/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). The MLST scheme followed the Achtman 7-gene scheme (\u003cem\u003eadk\u003c/em\u003e, \u003cem\u003eargA\u003c/em\u003e, \u003cem\u003earoA\u003c/em\u003e, \u003cem\u003eglnA\u003c/em\u003e, \u003cem\u003ethrA\u003c/em\u003e, \u003cem\u003etmk\u003c/em\u003e, and \u003cem\u003etrpE\u003c/em\u003e). cgMLST allele profiles were based on 1,553 loci defined in the EnteroBase Yersinia cgMLST scheme. Pairwise allelic distances were calculated using cgmlst-dists (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/achtman-lab/cgmlst-dists\u003c/span\u003e\u003cspan address=\"https://github.com/achtman-lab/cgmlst-dists\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e).\u003c/p\u003e\n\u003ch3\u003ePan-genome analysis and functional annotation\u003c/h3\u003e\n\u003cp\u003ePan-genome analysis was performed using the Bacterial Pan Genome Analysis tool (BPGA v1.3; default parameters). Orthologous gene clustering was conducted with USEARCH, using 95% sequence identity as the cut-off value. The pan-genome profile of the \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates was characterized by calculating the number of core, accessory, and unique gene. In addition, a binary presence/absence matrix of orthologous gene clusters was constructed using a pan-genome analysis pipeline and visualized as a hierarchically clustered heatmap to illustrate the distribution of core, accessory, and unique gene families across the isolates. The functional classification of orthologous clusters was based on COG (Clusters of Orthologous Groups) categories.\u003c/p\u003e\n\u003ch3\u003eBiotype prediction\u003c/h3\u003e\n\u003cp\u003ePublicly available \u003cem\u003eY. enterocolitica\u003c/em\u003e genomes with known biotypes were retrieved from previous studies for biotype prediction [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e] (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e) and analyzed together with the isolates in the pan-genome framework. Core gene alignments were used to construct a phylogenetic tree, and isolates clustering with reference genomes of known biotypes were assigned accordingly. The phylogenetic tree was constructed using the neighbor-joining method and visualized in iTOL v6.\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eGenome features of Y. enterocolitica\u003c/h2\u003e \u003cp\u003eGenome features of the \u003cem\u003eY. enterocolitica\u003c/em\u003e were characterized with a focus on virulence factors, AMR genes, and plasmid replicons. These features were identified using ABRicate v1.0.1 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/tseemann/abricate\u003c/span\u003e\u003cspan address=\"https://github.com/tseemann/abricate\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) with standard filtering parameters. Screening was performed against three databases: the Virulence Factor Database (VFDB, accessed 2025-09), ResFinder (accessed 2025-09), and PlasmidFinder (accessed 2025-09). For AMR genes, additional confirmation of gene family and predicted resistance phenotype was based on ResFinder annotations. The presence of plasmid replicons was used to infer potential plasmid carriage.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eIsolates\u003c/h2\u003e \u003cp\u003eA total of 157 \u003cem\u003eY. enterocolitica\u003c/em\u003e strains isolated from animal-source foods, including pork (68/157), beef (49/157), chicken (31/157), and duck (9/157), collected across different regions of South Korea were included (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). The isolates represented a broad geographic distribution, with samples originating from Gyeonggi (14/157), Gangwon (1/157), Chungcheong (38/157), Jeolla (86/157), and Gyeongsang (18/157) provinces.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eBiotyping\u003c/h2\u003e \u003cp\u003ePhylogenetic analysis based on pan-genome protein sequences was used to predict the biotypes of the 157 isolates (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). In the phylogeny, reference strains of each biotype consistently clustered together, supporting the reliability of the biotype predictions. All isolates were classified as biotype 1A (100%). To further resolve intra-biotype variation, the 157 isolates were compared with reference genomes representing the sub-biotypes 1Aa and 1Ab. These isolates clustered with the 1Aa references, confirming that all isolates analyzed in this study are sub-biotype 1Aa.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eSequence types diversity\u003c/h2\u003e \u003cp\u003eThe \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates recovered from animal-source foods were assigned to 40 distinct sequence types (STs), and 66 core-genome types (CTs), while 13 additional isolates remained unclassified (unknown STs) (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Among them, ST134 was predominant, accounting for 38 of 157 isolates (24.2%), followed by ST179 (19 isolates, 12.1%), ST150 (9 isolates, 5.7%), and ST246 (9 isolates, 5.7.%). Overall, the MLST results revealed a genetically diverse population structure, with a few dominant STs and numerous rare ones, consistent with ongoing diversification within animal-source food associated \u003cem\u003eY. enterocolitica\u003c/em\u003e populations in South Korea. Among the predominant ST134 isolates, multiple distinct CTs were identified, indicating considerable genomic heterogeneity within this lineage. Specifically, ST134 isolates from pork were assigned to CT480, CT1548, and CT3053; those from chicken to CT522, CT1420, and CT3053; from beef to CT3053; and from duck also to CT3053. Notably, CT3053 was shared across all four animal sources, suggesting the presence of a widely distributed sublineage that circulates throughout the animal-source food production chain. This finding suggestests both the genomic diversification and cross-source persistence of \u003cem\u003eY. enterocolitica\u003c/em\u003e ST134 within animal-source foods.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eAllelic relationships among isolates were visualized using a cgMLST allele-distance heatmap (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e), which showed overall genomic similarity and no clear segregation by food source. Several isolates displayed zero allelic differences despite originating from different food categories, suggesting that genetically related \u003cem\u003eY. enterocolitica\u003c/em\u003e lineages circulate among multiple animal-source foods.\u003c/p\u003e \u003cp\u003eOverall, \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates from animal-source foods in South Korea form a largely homogeneous population across animal sources, implying the circulation of common lineages within food production and processing environments.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003ePan-genome and COG analysis\u003c/h2\u003e \u003cp\u003ePan-genome analysis of the isolates identified 23,110 gene clusters, comprising 3,045 core (13%), 10,903 accessory (40%), and 9,162 unique (47%) genes (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eA\u0026ndash;C). Each isolate exhibited a distinct presence/absence profile and pan-/core-genome accumulation curves showed a continuously expanding pan-genome with a stable core, indicating an open pan-genome structure. This genomic openness may facilitate adaptation to diverse ecological niches.\u003c/p\u003e \u003cp\u003eFunctional annotation of orthologous clusters according to COG categories demonstrated that accessory and unique genes were broadly distributed across diverse functional classes, including metabolism, cellular processes, and information storage and processing (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eD, Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e). Accessory and unique genes were enriched in functional categories related to metabolism (e.g., carbohydrate, amino acid, and lipid metabolism), cellular processes (e.g., signal transduction and defense mechanisms), and information storage and processing (e.g., replication and repair). By contrast, core genes were mainly associated with essential housekeeping functions, including translation, energy production, and nucleotide metabolism.\u003c/p\u003e \u003cp\u003eCollectively, these findings indicate that \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates from animal-source foods possess an extensive genetic repertoire and functional diversity while maintaining a conserved genomic backbone. This combination of genomic stability and accessory variability may contribute to their environmental adaptability and persistence within the food production chain.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eGenomic features: virulence factors, AMR genes and plasmids\u003c/h2\u003e \u003cdiv id=\"Sec15\" class=\"Section3\"\u003e \u003ch2\u003eVirulence factors\u003c/h2\u003e \u003cp\u003eBy screening the 157 \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates, we identified 105 virulence-associated genes grouped into eight functional categories (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Table \u003cspan refid=\"MOESM4\" class=\"InternalRef\"\u003eS4\u003c/span\u003e). More than 90% of these genes were shared among isolates, indicating a largely conserved virulence-gene repertoire within the population.\u003c/p\u003e \u003cp\u003eAll isolates carried multiple adhesion-related determinants. The \u003cem\u003epsa\u003c/em\u003e locus showed variable distribution, with \u003cem\u003epsaC\u003c/em\u003e present in all isolates and \u003cem\u003epsaF\u003c/em\u003e and \u003cem\u003epsaE\u003c/em\u003e detected in 83.4% and 30.6%, respectively. All isolates also carried \u003cem\u003eyapE\u003c/em\u003e, whereas type IV pilus\u0026ndash;associated genes (e.g., \u003cem\u003epilL\u003c/em\u003e, \u003cem\u003epilQ\u003c/em\u003e, and \u003cem\u003epilV\u003c/em\u003e) were detected only sporadically (1\u0026ndash;2%). Adherence- and capsule-related genes displayed greater variability among isolates, whereas enterotoxin-associated genes such as \u003cem\u003eystB\u003c/em\u003e and its secretion pathway components were almost universally conserved. The invasion-related genes \u003cem\u003einv\u003c/em\u003e and \u003cem\u003epla\u003c/em\u003e were found in all isolates, indicating a conserved potential for host cell entry. Enterotoxin-associated genes, including \u003cem\u003eystB\u003c/em\u003e and its secretion-related components (\u003cem\u003eyst1C\u003c/em\u003e\u0026ndash;\u003cem\u003eG\u003c/em\u003e, \u003cem\u003eyst1J\u003c/em\u003e, \u003cem\u003eyst1K\u003c/em\u003e, and \u003cem\u003eyst1O\u003c/em\u003e), were detected in more than 97% of isolates, demonstrating that enterotoxin functions are widely conserved. Capsule-related genes were more variable than other virulence categories, particularly those within the \u003cem\u003erfb\u003c/em\u003e cluster (2\u0026ndash;45%). Exotoxin-associated genes (\u003cem\u003eyplA\u003c/em\u003e, \u003cem\u003eyaxA\u003c/em\u003e, and \u003cem\u003eyaxB\u003c/em\u003e) were present in all isolates. Flagellar and chemotaxis genes were universally present, indicating that motility and environmental-sensing systems are genetically stable across this population. All isolates contained \u003cem\u003etolC\u003c/em\u003e, the outer-membrane channel of the type I secretion system (T1SS), and multiple type III secretion system (T3SS) genes (\u003cem\u003esctD\u003c/em\u003e, \u003cem\u003esctI\u003c/em\u003e, \u003cem\u003esctJ\u003c/em\u003e, \u003cem\u003esctL\u003c/em\u003e, and \u003cem\u003esctR\u003c/em\u003e), while the SPI-2\u0026ndash;like \u003cem\u003essaG\u003c/em\u003e gene was present in 95% of isolates. These results show that the major secretion systems are conserved among the isolates.\u003c/p\u003e \u003cp\u003eOverall, adhesion and motility systems exhibited greater genetic variability than toxin and secretion systems, indicating differential evolutionary constraints among virulence categories. Collectively, these findings indicate that \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates from animal-source foods harbor a conserved set of virulence genes encompassing adhesion, invasion, enterotoxicity, and secretion functions, reflecting a stable genomic backbone with latent pathogenic potential and a possible capacity for persistence within food-related environments.\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eAMR genes\u003c/h2\u003e \u003cp\u003eAll isolates carried the chromosomally encoded \u003cem\u003eblaA\u003c/em\u003e (intrinsic β-lactam resistance) and \u003cem\u003evat(F)\u003c/em\u003e (streptogramin inactivation) genes indicating a conserved baseline resistance profile among isolates (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Table \u003cspan refid=\"MOESM5\" class=\"InternalRef\"\u003eS5\u003c/span\u003e). The detected AMR genes were categorized into two primary mechanisms: antibiotic inactivation and antibiotic efflux. Antibiotic inactivation, mediated by β-lactamase (\u003cem\u003eblaA\u003c/em\u003e) and aminoglycoside-modifying enzymes such as \u003cem\u003eant(3'')-Ia\u003c/em\u003e, represented the predominant mechanism, whereas efflux-based resistance, mainly associated with \u003cem\u003etet(C)\u003c/em\u003e, was less frequently observed. These findings indicate that enzymatic inactivation is the major mechanism underlying AMR among the examined \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates.\u003c/p\u003e \u003cp\u003eFour isolates were classified as multidrug-resistant (MDR), each carrying acquired AMR genes conferring resistance to three antimicrobial classes. Two isolates (MFDS1030554 and MFDS2015999) carried the aminoglycoside resistance gene \u003cem\u003eant(3'')-Ia\u003c/em\u003e, whereas two others (MFDS1019044 and MFDS2016015) possessed the tetracycline resistance gene \u003cem\u003etet(C).\u003c/em\u003e\u003c/p\u003e \u003cp\u003eOverall, the AMR genes identified among the isolates were primarily associated with resistance to β-lactams, aminoglycosides, tetracyclines, and streptogramins, reflecting the dominance of intrinsic resistance with sporadic acquisition of additional determinants.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003ePlasmids\u003c/h2\u003e \u003cp\u003ePlasmid replicon analysis revealed that 36.9% (58/157) of the isolates carried at least one plasmid (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e). Among plasmid-positive isolates, multiple replicon types were identified with varying frequencies. The most prevalent replicon was ColRNAI, detected in 29.3% of plasmid-bearing isolates, followed by pYE854 (19.0%), Col440II (13.8%), and Col(Ye4449), ColE10, and IncN, each detected in 12.1% of isolates. Other replicon types occurred at lower frequencies, including Col440I (10.3%), IncN3 (5.2%), ColpVC (5.2%), pIP31758(p153) (3.4%), pIP31758(p59) (3.4%), and IncX5 (3.4%). Several additional replicons were detected as single occurrences (1.7% each), including Col(YF27601), ColpVC_1, IncFII(p14), IncFII(pCRY), IncFII(pKP91), IncX7, and pENTAS02.\u003c/p\u003e \u003cp\u003eNone of the isolates carried the classical pYV virulence plasmid, which is typically associated with pathogenic \u003cem\u003eY. enterocolitica\u003c/em\u003e strains. The predominance of Col- and Inc-type replicons indicates that diverse, likely mobilizable plasmids, rather than large virulence-associated plasmids, circulate among \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates in animal-source foods in South Korea, potentially facilitating horizontal gene transfer within the food production environment.\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eThis study provides the first comprehensive genomic characterization of \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates recovered from animal-source foods in South Korea. All 157 isolates were classified as biotype 1A (sub-biotype 1Aa), a lineage traditionally regarded as nonpathogenic. However, phylogenomic and sequence-typing analyses revealed extensive heterogeneity, comprising 40 STs and 66 CTs. The lack of source-specific clustering and the detection of shared cgMLST types across pork, beef, chicken, and duck suggest that common \u003cem\u003eY. enterocolitica\u003c/em\u003e lineages circulate within the livestock production and processing continuum. Similar population structures have been reported in previous studies from Europe and China, where biotype 1A predominated among food-derived isolates and exhibited high sequence-type diversity [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e, \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Nevertheless, the dominant sequence types differed by region. For example, a study of 158 \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates from England identified ST18 as the most prevalent lineage, whereas ST134 was detected only sporadically [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. In contrast, ST134 was the predominant lineage in the present study, accounting for 24.2% of all isolates, suggesting possible regional differences in the distribution and ecological adaptation of biotype 1A populations [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. These findings collectively suggest that \u003cem\u003eY. enterocolitica\u003c/em\u003e biotype 1A in South Korea forms a genetically heterogeneous yet ecologically cohesive population capable of persisting across diverse food-associated ecosystems.\u003c/p\u003e \u003cp\u003ePan-genome analysis further demonstrated the remarkable genomic flexibility of these isolates. Among 23,110 identified gene clusters, only 13% constituted the core genome, confirming an open pan-genome structure. The large accessory and unique gene pools, which were enriched in metabolic, defense, and stress-response functions, highlight the organism\u0026rsquo;s capacity for functional diversification and persistence under variable conditions. Such genomic plasticity likely facilitates survival under cold storage, nutrient limitation, or antimicrobial pressure, all of which are common in food-processing and distribution settings. Collectively, the phylogenomic and pan-genomic findings indicate that biotype 1A \u003cem\u003eY. enterocolitica\u003c/em\u003e represents a genetically diverse yet evolutionarily cohesive population capable of long-term maintenance within the food production chain.\u003c/p\u003e \u003cp\u003eAlthough the canonical virulence plasmid pYV was absent, all isolates retained a highly conserved set of chromosomal virulence-associated genes related to adhesion (\u003cem\u003eyapE\u003c/em\u003e, \u003cem\u003epsaC\u003c/em\u003e), invasion (\u003cem\u003einv\u003c/em\u003e, \u003cem\u003epla\u003c/em\u003e), secretion systems, and enterotoxicity (\u003cem\u003eystB\u003c/em\u003e). These genes do not necessarily confer high pathogenicity but may facilitate colonization and persistence on food-contact surfaces or within processing environments [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]. The absence of pYV, combined with the consistent presence of \u003cem\u003eystB\u003c/em\u003e and other enterotoxin-related genes, reflects the typical genetic background of biotype 1A while suggesting that certain strains may retain low-level virulence potential under favorable conditions [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]. AMR determinants were primarily intrinsic, with \u003cem\u003eblaA\u003c/em\u003e (β-lactamase) and \u003cem\u003evat(F)\u003c/em\u003e (streptogramin resistance) universally detected. Only a few isolates carried additional acquired genes conferring resistance to aminoglycosides or tetracyclines, suggesting that antimicrobial exposure in the food production environment is low and that horizontal gene acquisition occurs only sporadically. Approximately one-third of the isolates carried plasmids, and among them, a few isolates possessed the pYE854 plasmid, which has previously been detected only in pathogenic \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. The predominant plasmid groups were Col- and Inc-type replicons, which are mainly associated with mobilization and stress adaptation rather than virulence [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. Their presence suggests a latent potential for horizontal gene transfer among food-associated microbial communities [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. Taken together, \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates from animal-source foods in South Korea represent a genetically diverse yet environmentally resilient population. Although all isolates belong to biotype 1A and are not considered highly pathogenic, their conserved virulence-associated genes, intrinsic AMR, and plasmid-mediated adaptability highlight their capacity for persistence within food-related environments. These characteristics suggest that biotype 1A strains may act as long-term contaminants in food processing and distribution systems, thereby contributing to the maintenance of microbial reservoirs that could compromise food hygiene. From a food safety perspective, continuous genomic surveillance of \u003cem\u003eY. enterocolitica\u003c/em\u003e in animal-source foods and processing facilities is essential for tracking genetic evolution, understanding contamination dynamics, and implementing effective control strategies to minimize potential risks to consumers.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eIn this study, we present the first large-scale genomic characterization of \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates obtained from animal-source foods in South Korea. Whole-genome sequencing revealed that all isolates belonged to biotype 1A but exhibited substantial genomic heterogeneity, an open and flexible pan-genome, and a conserved chromosomal backbone. Despite the absence of the classical virulence plasmid pYV, the isolates harbored multiple virulence-associated genes and intrinsic antimicrobial resistance determinants, reflecting both evolutionary stability and ecological adaptability. The frequent detection of small Col- and Inc-type plasmids further suggests a capacity for horizontal gene transfer within food-associated microbial communities. Overall, these findings indicate that \u003cem\u003eY. enterocolitica\u003c/em\u003e populations from animal-source foods are genetically diverse yet environmentally resilient, capable of persisting under cold and nutrient-limited conditions commonly encountered in the food chain. From a food safety perspective, these traits may allow biotype 1A strains to act as long-term contaminants in processing or distribution environments, emphasizing the importance of sustained genomic surveillance and hygiene management practices. Continued monitoring of \u003cem\u003eY. enterocolitica\u003c/em\u003e is essential to detect emerging variants that could impact food quality and consumer health.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cdiv class=\"DefinitionList\"\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eAntimicrobial resistance (AMR)\u003c/div\u003e \u003cdiv class=\"Description\"\u003e\u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eBacterial Pan Genome Analysis tool (BPGA)\u003c/div\u003e \u003cdiv class=\"Description\"\u003e\u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ecore\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003egenome multilocus sequence typing (cgMLST)\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eClusters of Orthologous Groups (COG)\u003c/div\u003e \u003cdiv class=\"Description\"\u003e\u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ecore\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003egenome type (CT)\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003emultilocus sequence typing (MLST)\u003c/div\u003e \u003cdiv class=\"Description\"\u003e\u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003esequence type (ST)\u003c/div\u003e \u003cdiv class=\"Description\"\u003e\u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003evirulence factor (VF)\u003c/div\u003e \u003cdiv class=\"Description\"\u003e\u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ewhole\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003egenome sequencing (WGS).\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003c/div\u003e"},{"header":"Declarations","content":" \u003cp\u003e \u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e \u003cp\u003eNot applicable\u003c/p\u003e \u003c/p\u003e \u003cp\u003e \u003cstrong\u003eConsent for publication\u003c/strong\u003e \u003cp\u003eNot applicable\u003c/p\u003e \u003c/p\u003e\u003cp\u003e \u003ch2\u003eCompeting interests\u003c/h2\u003e \u003cp\u003eThe authors declare no conflicts of interest.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eFunding\u003c/h2\u003e \u003cp\u003eThis study was funded by the Ministry of Food and Drug Safety (grant number 25191MFDS002). The findings and conclusions of this study are our own, and do not necessarily represent the views of the Ministry of Food and Drug Safety.\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eDK, ML, YK, IJ and WJ conceived and designed the study.DK, SR, YK and JC performed the experiments and analyzed the sequence data.DK, SR, YK and JC conducted data curation and bioinformatic analyses.DK and WJ prepared the initial draft of the manuscript.DK, ML, YK, IJ and WJ reviewed and edited the manuscript.All authors read and approved the final manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgements\u003c/h2\u003e \u003cp\u003eNot applicable\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e\u003cp\u003eSequence data were submitted to publicly accessible NCBI archives, including GenBank, under the accession numbers listed in Table S1.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eBancerz-Kisiel A, Szweda W. Yersiniosis\u0026ndash;zoonotic foodborne disease of relevance to public health. Ann Agric Environ Med. 2015;22:397\u0026ndash;402.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRosner BM, Stark K, Werber D. Epidemiology of reported \u003cem\u003eYersinia enterocolitica\u003c/em\u003e infections in Germany, 2001\u0026ndash;2008. BMC Public Health. 2010;10:337.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEuropean Food Safety Authority (EFSA). European Centre for Disease Prevention and Control (ECDC). The European Union one health 2022 zoonoses report. EFSA J. 2023;21:e8442.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDrummond N, Murphy BP, Ringwood T, Prentice MB, Buckley JF, Fanning S. \u003cem\u003eYersinia enterocolitica\u003c/em\u003e: a brief review of the issues relating to the zoonotic pathogen, public health challenges, and the pork production chain. Foodborne Pathog Dis. 2012;9:179\u0026ndash;89.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTerentjeva M, Ķibilds J, Gradovska S, Alksne L, Streikiša M, Meistere I, et al. Prevalence, virulence determinants, and genetic diversity in \u003cem\u003eYersinia enterocolitica\u003c/em\u003e isolated from slaughtered pigs and pig carcasses. Int J Food Microbiol. 2022;376:109756.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMancini ME, Beverelli M, Donatiello A, Didonna A, Dattoli L, Faleo S, et al. Isolation and characterization of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e from foods in Apulia and Basilicata regions (Italy) by conventional and modern methods. PLoS ONE. 2022;17:e0268706.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePeng Z, Zou M, Li M, Liu D, Guan W, Hao Q, et al. 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Food Microbiol. 1995;12:251\u0026ndash;7.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWauters G, Kandolo K, Janssens M. Revised biogrouping scheme of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e. Contrib Microbiol Immunol. 1987;9:14\u0026ndash;21.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBottone EJ. \u003cem\u003eYersinia enterocolitica\u003c/em\u003e: overview and epidemiologic correlates. Microbes Infect. 1999;1:323\u0026ndash;33.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePalau R, Bloomfield SJ, Jenkins C, Greig DR, Jorgensen F, Mather AE. \u003cem\u003eYersinia enterocolitica\u003c/em\u003e biovar 1A: an underappreciated potential pathogen in the food chain. Int J Food Microbiol. 2024;412:110554.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePlatt-Samoraj A, Syczyło K, Szczerba-Turek A, Bancerz-Kisiel A, Jabłoński A, Łabuć S, et al. Presence of \u003cem\u003eail\u003c/em\u003e and \u003cem\u003eystB\u003c/em\u003e genes in \u003cem\u003eYersinia enterocolitica\u003c/em\u003e biotype 1A isolates from game animals in Poland. Vet J. 2017;221:11\u0026ndash;3.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePlatt-Samoraj A. Toxigenic properties of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e biotype 1A. Toxins. 2022;14:118.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSabina Y, Rahman A, Ray RC, Montet D. \u003cem\u003eYersinia enterocolitica\u003c/em\u003e: mode of transmission, molecular insights of virulence, and pathogenesis of infection. J Pathog. 2011;2011:429069.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLe Guern AS, Savin C, Chereau F, Tessier S, Guglielmini J, Br\u0026eacute;mont S, et al. A novel cgMLST for genomic surveillance of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e infections in France allowed the detection and investigation of outbreaks in 2017\u0026ndash;2021. Microbiol Spectr. 2024;12:e0050424.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSavin C, Criscuolo A, Guglielmini J, Le Guern AS, Carniel E, Pizarro-Cerd\u0026aacute; J, et al. Genus-wide \u003cem\u003eYersinia\u003c/em\u003e core-genome multilocus sequence typing for species identification and strain characterization. Microb Genomics. 2019;5:e000301.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYue Y, Shen M, Liu X, Hao Q, Kang Y, Che Y, et al. Whole-genome sequencing-based prediction and analysis of antimicrobial resistance in \u003cem\u003eYersinia enterocolitica\u003c/em\u003e from Ningxia, China. Front Microbiol. 2022;13:936425.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMartins BTF, Meirelles JL, Omori WP, Oliveira RR, Yamatogi RS, Call DR, et al. Comparative genomics and antibiotic resistance of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e obtained from a pork production chain and human clinical cases in Brazil. Food Res Int. 2022;152:110917.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eStevens MJA, Horlbog JA, Diethelm A, Stephan R, N\u0026uuml;esch-Inderbinen M. Characteristics and comparative genome analysis of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e and related species associated with human infections in Switzerland 2019\u0026ndash;2023. Infect Genet Evol. 2024;123:105652.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFang L, Li S, Rong J, Li S, Zhang Y, Lou H, et al. Prevalence and genomic insights into \u003cem\u003eYersinia enterocolitica\u003c/em\u003e in Southeastern China (2008\u0026ndash;2022). Appl Microbiol Biotechnol. 2025;109:161.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHunter E, Greig DR, Schaefer U, Wright MJ, Dallman TJ, McNally A, et al. Identification and typing of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e and \u003cem\u003eYersinia pseudotuberculosis\u003c/em\u003e isolated from human clinical specimens in England between 2004 and 2018. J Med Microbiol. 2019;68:538\u0026ndash;48.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBancerz-Kisiel A, Pieczywek M, Łada P, Szweda W. The most important virulence markers of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e and their role during infection. Genes. 2018;9:235.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eStevens MJA, Barmettler K, Kelbert L, Stephan R, N\u0026uuml;esch-Inderbinen M. Genome based characterization of \u003cem\u003eYersinia enterocolitica\u003c/em\u003e from different food matrices in Switzerland in 2024. Infect Genet Evol. 2025;128:105719.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBalbuena-Alonso MG, Cort\u0026eacute;s-Cort\u0026eacute;s G, Kim JW, Lozano-Zarain P, Camps M, del Rocha-Gracia C. R. Genomic analysis of plasmid content in food isolates of \u003cem\u003eE. coli\u003c/em\u003e strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid. 2022;123\u0026ndash;4:102650.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"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":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Yersinia enterocolitica, comparative genomics, whole-genome sequencing (WGS), genome surveillance, food safety","lastPublishedDoi":"10.21203/rs.3.rs-8676138/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8676138/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003e \u003cem\u003eYersinia enterocolitica\u003c/em\u003e is a psychrotrophic foodborne bacterium capable of growing at refrigeration temperatures and is frequently associated with animal-source foods, raising concerns for food safety and public health. Despite its relevance and the increasing use of whole-genome sequencing (WGS) for bacterial surveillance, genomic studies on \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates from South Korea are limited. In this study, we analyzed 157 \u003cem\u003eY. enterocolitica\u003c/em\u003e isolates obtained from pork, beef, chicken, and duck collected nationwide using WGS to elucidate their genomic diversity and adaptive features.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003ePhylogenomic analysis classified all isolates as biotype 1A (sub-biotype 1Aa) and revealed considerable genetic heterogeneity, comprising 40 sequence types (STs) and 66 core-genome types (CTs). No clear segregation by source was observed, suggesting cross-source circulation within livestock production and processing environments. Pan-genome analysis identified 23,110 gene clusters, revealing an open pan-genome enriched in genes associated with metabolism, defense mechanisms, and stress responses, reflecting high genomic flexibility. Although the canonical virulence plasmid pYV was absent, we identified a conserved set of chromosomal virulence-associated genes linked to adhesion (\u003cem\u003einv\u003c/em\u003e, \u003cem\u003eyapE\u003c/em\u003e), secretion, and enterotoxicity (\u003cem\u003eystB\u003c/em\u003e), suggesting enhanced potential for persistence rather than pronounced pathogenicity. Antimicrobial resistance (AMR) genes were predominantly intrinsic, including \u003cem\u003eblaA\u003c/em\u003e (β-lactamase) and \u003cem\u003evat(F)\u003c/em\u003e (streptogramin resistance), which were universally detected, whereas acquired AMR genes such as \u003cem\u003etet(C)\u003c/em\u003e and \u003cem\u003eant(3'')-Ia\u003c/em\u003e were sporadically observed. Furthermore, approximately one-third of isolates harbored Col- and Inc-type plasmid replicons, supporting the occurrence of horizontal gene exchange and environmental adaptation.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003e \u003cem\u003eY. enterocolitica\u003c/em\u003e from animal-source foods in South Korea represents a genetically diverse and environmentally resilient population with limited virulence and predominantly intrinsic AMR determinants. These findings establish a genomic framework for understanding the ecology of \u003cem\u003eY. enterocolitica\u003c/em\u003e in animal-source foods and underscore the need for ongoing genomic surveillance to detect emerging variants that may influence food safety and public health.\u003c/p\u003e","manuscriptTitle":"Characterization and Comparative Genomic Analysis of Yersinia enterocolitica strains Isolated from Poultry and Red Meat in South Korea","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-28 12:07:38","doi":"10.21203/rs.3.rs-8676138/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-03-23T10:58:59+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-05T03:12:02+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-02T07:17:06+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-02-24T01:31:16+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"166251264217248530547557518144813857830","date":"2026-02-12T04:15:57+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"275564762965740767051825631036566067119","date":"2026-02-11T15:36:52+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"106427080619303892801304210434363545775","date":"2026-02-10T14:25:14+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"321326672951019109986898245658272169922","date":"2026-02-10T06:51:30+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-02-10T02:19:51+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-01-27T17:36:39+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-01-24T13:02:10+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-01-24T13:00:13+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2026-01-23T07:02:46+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"109737e6-67a6-4cea-b74d-2a137c4c1467","owner":[],"postedDate":"January 28th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2026-03-23T11:12:52+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-28 12:07:38","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8676138","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8676138","identity":"rs-8676138","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}