Infection Genetics and Evolution最新文献

{"title":"Duplex PCR-Nanopore sequencing assay for Cryptosporidium species and subtype determination","authors":"Gustav Killander ,&nbsp;Georgina Isak ,&nbsp;Anna-Malin Linde ,&nbsp;Abdolreza Advani ,&nbsp;Caroline Rönnberg ,&nbsp;Ioana Bujila","doi":"10.1016/j.meegid.2025.105727","DOIUrl":"10.1016/j.meegid.2025.105727","url":null,"abstract":"<div><div>The protozoan parasite <em>Cryptosporidium</em> is a global cause of gastrointestinal disease and cryptosporidiosis outbreaks are common. Current widely used methods for <em>Cryptosporidium</em> species and subtype determination, i.e., analysis of the small subunit ribosomal RNA (<em>ssu RNA</em>) and the 60 kDa glycoprotein (<em>gp60</em>) using Sanger sequencing, are complex and labor intensive. As such, developing a more rapid, accurate, automated and cost-effective method for species and subtype determination is desired. In this study, we describe the design of a new method for rapid simultaneous PCR-amplification of the <em>ssu rRNA</em> and <em>gp60</em> loci followed by Nanopore sequencing.</div><div>Species and subtypes assessed by Sanger sequencing, were successfully detected using Nanopore sequencing with 95 % concordance. Further, sequence similarity was assessed by comparing <em>ssu rRNA</em> and <em>gp60</em> sequences attained from the two methods. Minor differences between the two methods in regards to <em>ssu rRNA</em> sequences were detected, however these differences did not affect species determination. In regards to the <em>gp60</em> gene, all sequences were identical.</div><div>Overall, duplex PCR followed by Nanopore sequencing correlated well with Sanger sequencing, which is commonly used for <em>Cryptosporidium</em> species and subtype determination. As such, this newly developed method will replace Sanger sequencing at the Public Health Agency of Sweden.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105727"},"PeriodicalIF":2.6,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143437550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotoxic risks in patients with COVID-19","authors":"Nurşen Başaran ,&nbsp;Olga Szewczyk-Roszczenko ,&nbsp;Piotr Roszczenko ,&nbsp;Yegor Vassetzky ,&nbsp;Nikolajs Sjakste","doi":"10.1016/j.meegid.2025.105728","DOIUrl":"10.1016/j.meegid.2025.105728","url":null,"abstract":"<div><div>The COVID-19 pandemic has caused numerous deaths worldwide. Despite the mitigation of infection manifestations in recent months, the possible consequences of the epidemic remain difficult to predict. Genotoxicity and subsequent development of neoplasms are possible outcomes. This review summarises the data on these questions. Studies from several countries have reported increased levels of DNA damage in nucleated blood cells of patients with severe forms of COVID-19 infection. The level of DNA damage can be used as a prognostic factor for the disease outcome. It is considered that SARS-CoV-2 spike proteins play a crucial role in DNA damage; however, the virus also inhibits the DNA repair system. Co-morbidities and use of antiviral drugs may also contribute to DNA damage in patients with COVID-19.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105728"},"PeriodicalIF":2.6,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative phylogenetic and sequence identity analysis of internal transcribed spacer 2 and cytochrome c oxidase subunit I as DNA barcode markers for the most common equine Strongylidae species","authors":"Irina Diekmann ,&nbsp;Jürgen Krücken ,&nbsp;Tetiana A. Kuzmina ,&nbsp;Christina M. Bredtmann ,&nbsp;Mariana Louro ,&nbsp;Vitaliy A. Kharchenko ,&nbsp;Thomas Tzelos ,&nbsp;Jacqueline B. Matthews ,&nbsp;Luís M. Madeira de Carvalho ,&nbsp;Georg von Samson-Himmelstjerna","doi":"10.1016/j.meegid.2025.105729","DOIUrl":"10.1016/j.meegid.2025.105729","url":null,"abstract":"<div><div>Morphologically, 64 strongylid species have been described in equines. Co-infections are common, with up to 29 species reported in a single horse. Morphological identification of these species is time consuming and requires expert knowledge due to their similar appearance. Therefore, non-invasive identification methods are needed. DNA barcoding offers a rapid and reliable tool for species identification and the discovery of cryptic species for these most common parasitic nematodes of equines. In total, 269 cytochrome <em>c</em> oxidase subunit I (COI) gene and 312 internal transcribed spacer 2 (ITS-2) sequences from 27 equine Strongylidae species, including sequences from two uncharacterised species, <em>Coronocyclus sagittatus</em> and <em>Triodontophorus tenuicollis</em>, were generated and combined with COI and ITS-2 sequences data from six Cyathostominae species from previous studies. This study represents a comprehensive DNA barcoding analysis of 22 Cyathostominae and six Strongylinae species using mitochondrial COI gene and ITS-2 sequences. Maximum likelihood phylogenetic trees were constructed and the intra- and interspecific genetic distances for both markers were compared. Analysis revealed complex phylogenetic relationships. Para- and polyphyletic relationships were observed among most genera within Strongylinae and Cyathostominae. This challenges current morphological classifications. Although both markers showed overlapping pairwise identities in intra- and inter-species comparisons, COI had higher discriminatory power than ITS-2. Expanding the COI and ITS-2 reference database, including the first sequences for <em>Coronocyclus sagittatus</em> and <em>Triodontophorus tenuicollis,</em> improve a reliable species identification and advanced studies on Strongylinae and Cyathostominae diversity using barcoding and metabarcoding.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105729"},"PeriodicalIF":2.6,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylodynamic analysis of a prolonged meningococcal epidemic reveals multiple introductions and pre-epidemic expansion","authors":"Zuyu Yang ,&nbsp;Heather Davies ,&nbsp;Jane Clapham ,&nbsp;Liza Lopez ,&nbsp;Holly B. Bratcher ,&nbsp;Audrey Tiong ,&nbsp;Xavier Didelot ,&nbsp;Martin C.J. Maiden ,&nbsp;Philip E. Carter ,&nbsp;Xiaoyun Ren","doi":"10.1016/j.meegid.2025.105726","DOIUrl":"10.1016/j.meegid.2025.105726","url":null,"abstract":"<div><div><em>Neisseria meningitidis</em> is the causative agent of invasive meningococcal disease (IMD), a form of bacterial meningitis and septicaemia, leading to isolated cases, outbreaks, and epidemics worldwide. Between 1991 and 2008, Aotearoa/New Zealand (NZ) experienced a prolonged hyperendemic group B IMD outbreak caused by the NZMenB epidemic strain, belonging to clonal-complex 41/44 (cc41/44) and identified by the PorA variant P1.7–2,4 (B:4:P1.7–2,4:cc41/44). NZMenB continues to account for approximately one-quarter of group B meningococcal disease cases in NZ. To understand NZMenB origin and initiation we used phylodynamic tools to analyse approximately 97 % of all NZMenB isolates submitted to the NZ Meningococcal Reference Laboratory from 1990 to 2019. We found NZMenB can be divided into three major clades: clade41, clade154, and clade42, each with distinct origins and expansion patterns. Our evidence from molecular dating and clonal expansion analysis suggests that NZMenB was circulating and had expanded before the epidemic. Comparison with international data showed multiple importations and re-introductions of NZMenB into NZ, while not suggesting close relationships with international variants. The recent COVID-19 health emergency and differing governmental responses have brought societal and environmental contributions to epidemics and pandemics into focus. We propose the NZMenB epidemic may have been triggered by increasing societal inequality and household crowding resulting from government policies at the time.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105726"},"PeriodicalIF":2.6,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diamonds in the rif: Alignment-free comparative genomics analysis reveals strain-transcendent Plasmodium falciparum antigens amidst extensive genetic diversity","authors":"Jonathan G. Lawton ,&nbsp;Albert E. Zhou ,&nbsp;Emily M. Stucke ,&nbsp;Shannon Takala-Harrison ,&nbsp;Joana C. Silva ,&nbsp;Mark A. Travassos","doi":"10.1016/j.meegid.2025.105725","DOIUrl":"10.1016/j.meegid.2025.105725","url":null,"abstract":"<div><div>The repetitive interspersed family (<em>rif</em>) and subtelomeric variable open reading frames (<em>stevor</em>) are highly diverse multi-gene families in the malaria parasite <em>Plasmodium falciparum</em>. Embedded on the surface of infected erythrocytes, RIFIN and STEVOR proteins are involved in cytoadherence and immune evasion, but the extent of family-wide sequence diversity across strains has yet to be comprehensively investigated in light of improved resolution of the subtelomeric genome sequences. Using a <em>k-mer</em> frequency approach, we analyzed long-read genomic sequence data from 18 geographically diverse <em>P. falciparum</em> genome assemblies, including lab strains and clinical isolates. We hypothesized that <em>k-mer</em> sequence comparison can identify existing RIFIN and STEVOR subgroups, identify novel subgroups, and generate more robust and reliable estimates of family-wide sequence diversity. Full-length RIFIN and STEVOR proteins shared on average 49.5% and 61.1% amino acid <em>k-mer</em> similarity, respectively, which fell to 25.1% and 20% in the hypervariable regions alone. Despite this diversity, we identified 11 RIFINs and five STEVORs that were conserved across strains above expected thresholds. A subset of these strain-transcendent genes was similar and syntenic to genes in related <em>Plasmodium</em> species, suggesting an ancient origin. Additionally, <em>in silico</em> structural predictions from AlphaFold showed that three-dimensional structures of RIFIN receptor-binding regions were more conserved than their sequences suggested. Evolutionarily constrained RIFINs and STEVORs may have critical functions in parasite survival or pathogenesis. This study provides a framework for investigating diversity in highly variable multi-gene families and highlights the potential of strain-transcendent RIFIN and STEVOR proteins as vaccine candidates.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105725"},"PeriodicalIF":2.6,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular detection and phylogenetic analysis of microsporidia in stool specimens isolated from multiple sclerosis patients in the west of Iran","authors":"Hadi Abbasnia ,&nbsp;Taher Mohammadian ,&nbsp;Mohammadbagher Khademerfan ,&nbsp;Fares Bahrami ,&nbsp;Mansoureh Paknejadi","doi":"10.1016/j.meegid.2025.105720","DOIUrl":"10.1016/j.meegid.2025.105720","url":null,"abstract":"<div><h3>Background</h3><div>Intestinal microsporidiosis is an emerging opportunistic infection that primarily affects individuals with compromised immune systems. This study investigated intestinal microsporidia infections in individuals diagnosed with multiple sclerosis (MS) and elucidated the genetic diversity and evolutionary relationships of microsporidia.</div></div><div><h3>Methods</h3><div>A total of 116 stool samples were collected from individuals diagnosed with MS, including 54 men and 63 women, during 2022–2023 in Kurdistan Province, western Iran. The mean age of the participants was 38.28 ± 7.8 years. RNA extraction was performed, followed by amplification of the small subunit ribosomal RNA (SSU rRNA) to identify and characterize microsporidia and their associated genetic markers. A phylogenetic tree was constructed using MEGA X software to explore the evolutionary relationships among the isolates.</div></div><div><h3>Results</h3><div>PCR revealed <em>Enterocytozoon bieneusi</em> in 5 of 116 samples (4.3 %), whereas no positive cases of <em>Encephalitozoon</em> species were detected. Additionally, no statistically significant associations were observed between the presence of microsporidia and variables such as age, sex, or geographic region.</div></div><div><h3>Conclusion</h3><div>This study highlights the clinical significance of <em>Enterocytozoon bieneusi</em> in immunocompromised populations, particularly in patients with multiple sclerosis (MS). The findings underscore the potential role of zoonotic transmission and highlight the urgent need for enhanced diagnostic capabilities and preventive strategies to combat intestinal microsporidiosis in vulnerable groups, particularly in regions such as western Iran.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105720"},"PeriodicalIF":2.6,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143226891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of targeted next-generation sequencing for detecting respiratory pathogens in the sputum of patients with pulmonary infections","authors":"Hongting Da ,&nbsp;Tao Meng ,&nbsp;Yuanhong Xu","doi":"10.1016/j.meegid.2025.105722","DOIUrl":"10.1016/j.meegid.2025.105722","url":null,"abstract":"<div><div>Targeted next-generation sequencing (tNGS) might be valuable for identifying disease-causing pathogens. Herein, we assessed the utility of tNGS in diagnosing pulmonary infections using sputum samples. We gathered complete clinical information and tested the specimens using both conventional microbiological tests (CMTs) and tNGS. The goal was to compare the effectiveness of these two methods in detecting viral, bacterial, and fungal pathogens. Notably, tNGS demonstrated a higher pathogen detection rate compared to CMTs (80.26 % [122/152] vs. 33.55 % [51/152], <em>P</em> = 0.029). Specifically, tNGS was more effective in detecting viruses than CMTs (90.00 % vs. 28.07 %, <em>P</em> = 0.003). Moreover, tNGS detected certain fungi, such as <em>Candida albicans</em> and <em>Cryptococcus neoformans</em>, although the difference between the two assays was not statistically significant (<em>P</em> &gt; 0.05). Our findings reveal that tNGS offers significant advantages in detecting pathogens in patients with lung infections, particularly for bacteria and viruses, providing valuable information that complements CMTs.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105722"},"PeriodicalIF":2.6,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143226890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The σNS protein of NDRV antagonizes TRIM59-mediated antiviral innate immune response of Cherry Valley duck","authors":"Xiuyuan Wang ,&nbsp;Tingting Zhang ,&nbsp;Xiaoyu Lu ,&nbsp;Yirui Zhang ,&nbsp;Mingzhuo Tian ,&nbsp;Yujing Chen ,&nbsp;Yikun Wang ,&nbsp;Nan Liu ,&nbsp;Shuhan Li ,&nbsp;Jie Zhang ,&nbsp;Liangmeng Wei","doi":"10.1016/j.meegid.2025.105724","DOIUrl":"10.1016/j.meegid.2025.105724","url":null,"abstract":"<div><div>In recent years, outbreak of the novel duck reovirus (NDRV) disease has occurred frequently in duck populations. Due to its rapid spreading, absence of effective control methods, and high treatment costs, the NDRV disease has caused huge losses to waterfowl breeding in China. As reported, four non-structural (NS) proteins are encoded by the NDRV genome, among which the σNS protein is an RNA-binding protein that can improve the stability of bound RNA by forming oligomers (<span><span>Adams and Cory, 1998</span></span>). Nevertheless, the mechanism by which it facilitates reovirus replication remains ambiguous. According to previous studies, the NS protein 11 of the porcine reproductive and respiratory syndrome virus (PRRSV) can interact with tripartite motif-containing 59 (TRIM59) to regulate viral infection. However, the specific role of TRIM59 in NDRV infection remains unclear. This study focused on full-length amplification of duTRIM59, the mRNA distribution of duTRIM59 in Cherry Valley duck and successive biological examinations. The homology with <em>Anas platyrhynchos</em> TRIM59 was 98.6 %. The mRNA distribution level of duTRIM59 showed that duTRIM59 was widely expressed in bursae and thymus of the immune organs. Nevertheless, TRIM59 comprises three domains, including the transmembrane (TM), B-box (B), and RING-finger (R) domains. It also has the activity of ubiquitin-protein ligase (E3). It has been demonstrated that NDRV replication is inhibited by TRIM59 overexpression in duck embryonic fibroblasts (DEF) cells, particularly when the R domain is intact, suggesting that the R domain plays a key role in the spreading of the NDRV virus. In contrast, NDRV infection in DEF cells increased when TRIM59 was depleted by using small interfering RNA. Moreover, the σNS protein can be co-localized with duTRIM59 and stimulate NDRV replication in DEF cells in cases of NDRV infection. This study clarifies the correlation of NDRV infection and TRIM59-mediated antiviral innate immunity, and provides a sound theoretical basis for further understanding this disease.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105724"},"PeriodicalIF":2.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Some novel field isolates belonging to lineage-1 of the genotype GI-avian infectious bronchitis virus (AIBV) show strong evidence of recombination with field/vaccinal strains","authors":"Abid Ullah Shah ,&nbsp;Lalitha Peddireddi ,&nbsp;Beverly Wood ,&nbsp;Maged Gomaa Hemida","doi":"10.1016/j.meegid.2025.105723","DOIUrl":"10.1016/j.meegid.2025.105723","url":null,"abstract":"<div><div>Avian infectious bronchitis virus (AIBV) infection remains one of the significant challenges for the poultry industry due to the high rates of morbidity, mortality, and poor production performance. The AIBV genome is prone to frequent changes due to the possibility of drift and recombination between various genotypes. Despite the massive administration of several types of vaccines, many outbreaks of AIBV continue to be reported worldwide. One of the major goals of this study was to monitor genetic changes in the viral genomes of some recent field isolates of the AIBV from broiler chickens. To achieve these goals, we tested several pools of tissue specimens (trachea and kidneys) from some suspected AIBV outbreaks in broiler chickens by quantitative real-time PCR (q-RT-PCR). We selected two samples, one from the trachea (IBV-4) and one from the kidney (AIBV-6), for the next-generation sequencing (NGS). The full-length genomes of these two isolates were deposited in the GenBank (Accession Numbers: PQ468962 and PQ468963). The viral genome size of AIBV-4 and AIBV-6 was 27,475 and 27,469 nucleotides in length. AIBV-4 have typical AIBV genome organization (5’UTR, ORF1a, ORF1b, S, 3a, 3b, E, M, 4b, 5a, 5b, N, and 3’UTR), while AIBV-6 lack 5b. These two AIBV isolates belong to sublineage-1 of the genotype GI-1 based on the phylogenetic using the full-length, the S, and the N protein sequences. The S1/S2 cleavage sites show polybasic amino acid sequences (RR-F-RR) as direct evidence of virulence of these isolates. The analysis shows multiple recombination events of these isolates with some natural and vaccine strains. The potential major parent for both AIBV-4 and AIBV-6 was AIBV Beaudette. Active and vigilant monitoring of the AIBV sequences of the currently circulating strains in chickens is highly encouraged to help develop novel vaccines and diagnostic assays that match the field circulating strains.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105723"},"PeriodicalIF":2.6,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome based characterization of Yersinia enterocolitica from different food matrices in Switzerland in 2024","authors":"Marc J.A. Stevens,&nbsp;Karen Barmettler,&nbsp;Lucien Kelbert,&nbsp;Roger Stephan,&nbsp;Magdalena Nüesch-Inderbinen","doi":"10.1016/j.meegid.2025.105719","DOIUrl":"10.1016/j.meegid.2025.105719","url":null,"abstract":"<div><div><em>Yersinia enterocolitica</em> causes food-borne gastroenteritis. However, little is known about the genetic diversity and pathogenic potential of <em>Y. enterocolitica</em> in different food commodities.</div><div>In this study, presumptive <em>Y. enterocolitica</em> strains were isolated from 32 of 100 pork samples, from 25 of 100 chicken meat samples, and from 22 of 97 produce samples (fresh herbs and salads), all collected at retail level in Switzerland in 2024. All isolates underwent whole-genome sequencing (WGS). One isolate was re-classified as <em>Y. hibernica</em>. Three strains belonged to biotype (BT) 4, all from pork, and 86 strains to BT 1A. The isolates belonged to 45 sequence types (STs). A total of 76 putative plasmids were detected. Each BT 4 isolate carried a pYV-like plasmid harbouring 44 virulence factors (VFs). Plasmids from the same type were identified in different ST, showing that genetic exchange between ST occurs. Twelve isolates from poultry meat carried plasmids harbouring the <em>msrAB</em> operon which is linked to oxidative stress tolerance. Nine isolates from pork and poultry meat contained plasmids carrying the <em>cag</em> pathogenicity island associated with cytotoxicity, and four isolates from produce carried plasmids harbouring a heat labile enterotoxin. None of the isolates harboured plasmid-mediated antimicrobial resistance (AMR) genes. <em>Y. enterocolitica</em> BT 4 (<em>n</em> = 3) and BT 1A (n = 3) were clonal to <em>Y. enterocolitica</em> previously isolated from Swiss human cases.</div><div>Our data provide valuable insights into the occurrence and genomic characteristics of <em>Y. enterocolitica</em> in food, their relatedness to human strains, and their adaptation to food matrices.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105719"},"PeriodicalIF":2.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}