{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:55:00Z","timestamp":1792641300301,"version":"4.5.0"},"reference-count":68,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T00:00:00Z","timestamp":1747267200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences","award":["25-LZIHPS-03"],"award-info":[{"award-number":["25-LZIHPS-03"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives: Livestock species, particularly dairy animals, can serve as important reservoirs of E. coli, carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we performed the pathogenomic analysis of seven multidrug resistant (MDR) E. coli strains carrying efflux-associated and virulence genes from the dairy farm environment in Xinjiang Province, China. Methods: First, we processed the samples using standard microbiological techniques followed by species identification with MALDI-TOF MS. Then, we performed whole genome sequencing (WGS) on the Illumina NovaSeq PE150 platform and conducted pathogenomic analysis using multiple bioinformatics tools.\u00a0Results: WGS analysis revealed that the E. coli strains harbored diverse antibiotic efflux-associated genes, including conferring resistance to fluoroquinolones, aminoglycosides, aminocoumarins, macrolides, peptides, phosphonic acid, nitroimidazole, tetracyclines, disinfectants\/antiseptics, and multidrug resistance. The phylogenetic analysis classified seven E. coli strains into B1 (n = 4), C (n = 2), and F (n = 1) phylogroups. PathogenFinder predicted all E. coli strains as potential human pathogens belonging to distinct serotypes and carrying broad virulence genes (ranging from 12 to 27), including the Shiga toxin-producing gene (stx1, n = 1). However, we found that a few of the virulence genes were associated with prophages and genomic islands in the E. coli strains. Moreover, all E. coli strains carried a diverse bacterial secretion systems and biofilm-associated genes. Conclusions: The present study highlights the need for large-scale genomic surveillance of antibiotic-resistant bacteria in dairy farm environments to identify AMR reservoir spillover and pathogenic risks to humans and design targeted interventions to further stop their spread under a One Health framework.<\/jats:p>","DOI":"10.3390\/antibiotics14050511","type":"journal-article","created":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T09:58:27Z","timestamp":1747303107000},"page":"511","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Pathogenomic Characterization of Multidrug-Resistant Escherichia coli Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China"],"prefix":"10.3390","volume":"14","author":[{"given":"Muhammad","family":"Shoaib","sequence":"first","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"},{"name":"Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9135-5709","authenticated-orcid":false,"given":"Sehrish","family":"Gul","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University of Agriculture, Faisalabad 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sana","family":"Majeed","sequence":"additional","affiliation":[{"name":"Laboratory of Aquatic Animal Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuolin","family":"He","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3420-6299","authenticated-orcid":false,"given":"Baocheng","family":"Hao","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minjia","family":"Tang","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xunjing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongyong","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5195-5059","authenticated-orcid":false,"given":"Shengyi","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4607-5855","authenticated-orcid":false,"given":"Wanxia","family":"Pu","sequence":"additional","affiliation":[{"name":"Key Laboratory of New Animal Drug Project Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Shoaib, M., He, Z., Geng, X., Tang, M., Hao, R., Wang, S., Shang, R., Wang, X., Zhang, H., and Pu, W. (2023). The Emergence of Multidrug Resistant and Virulence Gene Carrying Escherichia coli Strains in the Dairy Environment: A Rising Threat to the Environment, Animal, and Public Health. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1197579"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1038\/s41538-021-00097-0","article-title":"Genomic analysis of Shiga toxin-producing Escherichia coli O157:H7 from cattle and pork-production related environments","volume":"5","author":"Zhang","year":"2021","journal-title":"npj Sci. Food"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Ray, R., and Singh, P. (2022). Prevalence and Implications of Shiga Toxin-Producing E. coli in Farm and Wild Ruminants. Pathogens, 11.","DOI":"10.3390\/pathogens11111332"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e02185-21","DOI":"10.1128\/aem.02185-21","article-title":"Genetic Characteristics of the Transmissible Locus of Stress Tolerance (TLST) and TLST Harboring Escherichia coli as Revealed by Large-Scale Genomic Analysis","volume":"88","author":"Zhang","year":"2022","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.1099\/mic.0.000367","article-title":"Phylogenetic Diversity, Antimicrobial Susceptibility and Virulence Characteristics of Phylogroup F Escherichia coli in Australia","volume":"162","author":"Vangchhia","year":"2016","journal-title":"Microbiology"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Carlos, C., Pires, M.M., Stoppe, N.C., Hachich, E.M., Sato, M.I.Z., Gomes, T.A.T., Amaral, L.A., and Ottoboni, L.M.M. (2010). Escherichia coli Phylogenetic Group Determination and Its Application in the Identification of the Major Animal Source of Fecal Contamination. BMC Microbiol., 10.","DOI":"10.1186\/1471-2180-10-161"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Benedict, K.M., Gow, S.P., McAllister, T.A., Booker, C.W., Hannon, S.J., Checkley, S.L., Noyes, N.R., and Morley, P.S. (2015). Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Cattle and Associations with Antimicrobial Use. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0143995"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Wepking, C., Avera, B., Badgley, B., Barrett, J.E., Franklin, J., Knowlton, K.F., Ray, P.P., Smitherman, C., and Strickland, M.S. (2017). Exposure to Dairy Manure Leads to Greater Antibiotic Resistance and Increased Mass-Specific Respiration in Soil Microbial Communities. Proc. R. Soc. B Biol. Sci., 284.","DOI":"10.1098\/rspb.2016.2233"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3526395","DOI":"10.1155\/2024\/3526395","article-title":"Genomic Characterization of Extended-Spectrum \u03b2-Lactamase (ESBL) Producing E. coli Harboring blaOXA\u22121-catB3-arr-3 Genes Isolated from Dairy Farm Environment in China","volume":"2024","author":"Shoaib","year":"2024","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"70","DOI":"10.3201\/eid1401.070704","article-title":"Dissemination of Multidrug-Resistant Bacteria into the Arctic","volume":"14","author":"Bonnedahl","year":"2008","journal-title":"Emerg. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"13754","DOI":"10.1007\/s11356-016-6457-z","article-title":"Environmental Application of Nanotechnology: Air, Soil, and Water","volume":"23","author":"Ibrahim","year":"2016","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13756-015-0100-5","article-title":"Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli O157 and Non-O157 Recovered from Domestic Farm Animals in Rural Communities in Northwestern Mexico","volume":"5","author":"Lee","year":"2016","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Manyi-Loh, C., Mamphweli, S., Meyer, E., and Okoh, A. (2018). Antibiotic Use in Agriculture and Its Consequential Resistance in Environmental Sources: Potential Public Health Implications. Molecules, 23.","DOI":"10.3390\/molecules23040795"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Rehman, M.A., Yin, X., Lepp, D., Laing, C., Ziebell, K., Talbot, G., Topp, E., and Diarra, M.S. (2017). Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure. Vet. Sci., 4.","DOI":"10.3390\/vetsci4040057"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Naidoo, N., and Zishiri, O.T. (2023). Comparative Genomics Analysis and Characterization of Shiga Toxin-Producing Escherichia coli O157:H7 Strains Reveal Virulence Genes, Resistance Genes, Prophages and Plasmids. BMC Genom., 24.","DOI":"10.1186\/s12864-023-09902-4"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1128\/AAC.00669-09","article-title":"Bacteriophage Cocktail for the Prevention of Biofilm Formation by Pseudomonas Aeruginosa on Catheters in an in Vitro Model System","volume":"54","author":"Fu","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1080\/09593330.2020.1829084","article-title":"Metagenomic Insights into Quorum Sensing in Membrane-Aerated Biofilm Reactors for Phenolic Wastewater Treatment","volume":"43","author":"Hu","year":"2022","journal-title":"Environ. Technol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Yang, X., Wang, H., Hrycauk, S., Holman, D.B., and Ells, T.C. (2023). Microbial Dynamics in Mixed-Culture Biofilms of Salmonella Typhimurium and Escherichia coli O157:H7 and Bacteria Surviving Sanitation of Conveyor Belts of Meat Processing Plants. Microorganisms, 11.","DOI":"10.3390\/microorganisms11020421"},{"key":"ref_19","first-page":"496","article-title":"Class I Integrons: Prevalence and Impact on Antibiotic Susceptibility in 278 Consecutive Unrelated Gram-Negative Blood Isolates","volume":"5","author":"Schmitz","year":"1999","journal-title":"Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1128\/AEM.68.2.576-581.2002","article-title":"Antimicrobial Resistance of Escherichia coli O157 Isolated from Humans, Cattle, Swine, and Food","volume":"68","author":"Schroeder","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_21","first-page":"e000192","article-title":"ClermonTyping: An Easy-to-Use and Accurate in Silico Method for Escherichia Genus Strain Phylotyping","volume":"4","author":"Beghain","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"100385","DOI":"10.1016\/j.emcon.2024.100385","article-title":"Genomic insights into resistome, virulome, and mobilome as organic contaminants of ESKAPE pathogens and E. coli recovered from milk, farm workers, and environmental settings in Hainan, China","volume":"10","author":"Hao","year":"2024","journal-title":"Emerg. Contam."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1128\/AEM.01880-10","article-title":"Environmental Patterns Are Imposed on the Population Structure of Escherichia coli after Fecal Deposition","volume":"77","author":"Bergholz","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"120190","DOI":"10.1016\/j.envres.2024.120190","article-title":"Dairy Farm Waste: A Potential Reservoir of Diverse Antibiotic Resistance and Virulence Genes in Aminoglycoside- and Beta-Lactam-Resistant Escherichia coli in Gansu Province, China","volume":"263","author":"Shoaib","year":"2024","journal-title":"Environ. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1264\/jsme2.ME17030","article-title":"Distribution of Diverse Escherichia coli between Cattle and Pasture","volume":"32","author":"Nandakafle","year":"2017","journal-title":"Microbes Environ."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"258424","DOI":"10.1155\/2015\/258424","article-title":"Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples","volume":"2015","author":"Coura","year":"2015","journal-title":"Sci. World J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"7200","DOI":"10.1073\/pnas.1015622108","article-title":"Genome Sequencing of Environmental Escherichia coli Expands Understanding of the Ecology and Speciation of the Model Bacterial Species","volume":"108","author":"Luo","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/JB.00367-20","article-title":"The Evolutionary Conservation of Escherichia coli Drug Efflux Pumps Supports Physiological Functions","volume":"202","author":"Teelucksingh","year":"2020","journal-title":"J. Bacteriol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"326","DOI":"10.5483\/BMBRep.2023-0070","article-title":"AcrAB-TolC, a major efflux pump in Gram-negative bacteria: Toward understanding its operation mechanism","volume":"56","author":"Jang","year":"2023","journal-title":"BMB Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1111\/j.1365-2958.2008.06458.x","article-title":"GadX\/GadW-Dependent Regulation of the Escherichia coli Acid Fitness Island: Transcriptional Control at the GadY-GadW Divergent Promoters and Identification of Four Novel 42 Bp GadX\/GadW-Specific Binding Sites","volume":"70","author":"Tramonti","year":"2008","journal-title":"Mol. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"van Hung Le, V., Biggs, P.J., Wheeler, D., Davies, I.G., and Rakonjac, J. (2021). Novel Mechanisms of TolC-Independent Decreased Bile-Salt Susceptibility in Escherichia coli. FEMS Microbiol. Lett., 367.","DOI":"10.1093\/femsle\/fnaa083"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Manishimwe, R., Moncada, P.M., Musanayire, V., Shyaka, A., Morgan Scott, H., and Loneragan, G.H. (2021). Antibiotic-Resistant Escherichia coli and Salmonella from the Feces of Food Animals in the East Province of Rwanda. Animals, 11.","DOI":"10.3390\/ani11041013"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.prevetmed.2015.01.013","article-title":"Antimicrobial Resistance Risk Factors and Characterisation of Faecal E. coli Isolated from Healthy Labrador Retrievers in the United Kingdom","volume":"119","author":"Schmidt","year":"2015","journal-title":"Prev. Vet. Med."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1007\/s44337-024-00102-x","article-title":"Antibiotic resistance in toxigenic E. coli: A severe threat to global health","volume":"1","author":"Biswas","year":"2024","journal-title":"Discov. Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1089\/fpd.2023.0098","article-title":"Antibiotic Resistance and Genomic Analysis of Shiga Toxin-Producing Escherichia coli from Dairy Cattle, Raw Milk, and Farm Environment in Shaanxi Province, China","volume":"21","author":"Zhang","year":"2024","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Beutin, L., Delannoy, S., and Fach, P. (2016). Genetic Analysis and Detection of fliC H1 and fliC H12 Genes Coding for Serologically Closely Related Flagellar Antigens in Human and Animal Pathogenic Escherichia coli. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.00135"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"827","DOI":"10.3855\/jidc.15703","article-title":"Serogroups and Genetic Diversity of Diarrheagenic Strains of Escherichia coli: A Retrospective Study","volume":"16","author":"Mare","year":"2022","journal-title":"J. Infect. Dev. Ctries."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Alharbi, M.G., Al-Hindi, R.R., Esmael, A., Alotibi, I.A., Azhari, S.A., Alseghayer, M.S., and Teklemariam, A.D. (2022). The \u201cBig Six\u201d: Hidden Emerging Foodborne Bacterial Pathogens. Trop. Med. Infect. Dis., 7.","DOI":"10.3390\/tropicalmed7110356"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Wieczorek, K., and Osek, J. (2020). Identification and Molecular Characteristics of Verotoxin-Producing Escherichia coli (VTEC) from Bovine and Pig Carcasses Isolated in Poland during 2014\u20132018. Food Microbiol., 92.","DOI":"10.1016\/j.fm.2020.103587"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Brusa, V., Restovich, V., Galli, L., Teitelbaum, D., Signorini, M., Brasesco, H., Londero, A., Garc\u00eda, D., Padola, N.L., and Superno, V. (2017). Isolation and Characterization of Non-O157 Shiga Toxin-Producing Escherichia coli from Beef Carcasses, Cuts and Trimmings of Abattoirs in Argentina. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0183248"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Egerv\u00e4rn, M., and Flink, C. (2024). Shiga Toxin-Producing Escherichia coli (STEC) in Meat and Leafy Greens Available in the Swedish Retail Market\u2014Occurrence and Diversity of Stx Subtypes and Serotypes. Int. J. Food Microbiol., 408.","DOI":"10.1016\/j.ijfoodmicro.2023.110446"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Galarce, N., S\u00e1nchez, F., Escobar, B., Lapierre, L., Cornejo, J., Alegr\u00eda-Mor\u00e1n, R., Neira, V., Mart\u00ednez, V., Johnson, T., and Fuentes-Castillo, D. (2021). Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America. Animals, 11.","DOI":"10.3390\/ani11071845"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"van Overbeek, L.S., Wichers, J.H., van Amerongen, A., van Roermund, H.J.W., van der Zouwen, P., and Willemsen, P.T.J. (2020). Circulation of Shiga Toxin-Producing Escherichia coli Phylogenetic Group B1 Strains Between Calve Stable Manure and Pasture Land with Grazing Heifers. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01355"},{"key":"ref_44","first-page":"7180","article-title":"Detection of Acquired Antibiotic Resistance Determinants in the Intestinal Microbiota of Food Producing Animals in Hungary","volume":"Volume 64","author":"Libisch","year":"2022","journal-title":"Book of Abstracts, \u201cAntimicrobial Resistance: A Challenge for Public Health, Animal Health and Environment\u201d"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"100558","DOI":"10.1016\/j.onehlt.2023.100558","article-title":"Genomics, Biofilm Formation and Infection of Bladder Epithelial Cells in Potentially Uropathogenic Escherichia coli (UPEC) from Animal Sources and Human Urinary Tract Infections (UTIs) Further Support Food-Borne Transmission","volume":"16","author":"Parga","year":"2023","journal-title":"One Health"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e00124-24","DOI":"10.1128\/msphere.00124-24","article-title":"The yad and yeh fimbrial loci influence gene expression and virulence in Enterohemorrhagic Escherichia coli O157: H7","volume":"9","author":"Gonyar","year":"2024","journal-title":"Msphere"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Desvaux, M., Dalmasso, G., Beyrouthy, R., Barnich, N., Delmas, J., and Bonnet, R. (2020). Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.02065"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e0045221","DOI":"10.1128\/mSphere.00452-21","article-title":"Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens","volume":"6","author":"Kondo","year":"2021","journal-title":"mSphere"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.1038\/ismej.2016.79","article-title":"Prophages Mediate Defense against Phage Infection through Diverse Mechanisms","volume":"10","author":"Qian","year":"2016","journal-title":"ISME J."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Sv\u00e1b, D., Falgenhauer, L., Mag, T., Chakraborty, T., and T\u00f3th, I. (2022). Genomic Diversity, Virulence Gene, and Prophage Arrays of Bovine and Human Shiga Toxigenic and Enteropathogenic Escherichia coli Strains Isolated in Hungary. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.896296"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.9734\/jpri\/2020\/v32i2330783","article-title":"Identification of Antibiotic Resistance Pattern, and Detection of Virulence Genes Iss, and OmpT in Avian Pathogenic Escherichia coli from Broiler Chickens in Chitwan, Nepal","volume":"32","author":"Sankhi","year":"2020","journal-title":"J. Pharm. Res. Int."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Ovi, F., Zhang, L., Nabors, H., Jia, L., and Adhikari, P. (2023). A Compilation of Virulence-Associated Genes That Are Frequently Reported in Avian Pathogenic Escherichia coli (APEC) Compared to Other E. coli. J. Appl. Microbiol., 134.","DOI":"10.1093\/jambio\/lxad014"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Torres, A.N., Chamorro-Veloso, N., Costa, P., C\u00e1diz, L., Del Canto, F., Venegas, S.A., L\u00f3pez Nitsche, M., Coloma-Rivero, R.F., Montero, D.A., and Vidal, R.M. (2020). Deciphering Additional Roles for the EF-Tu, l-Asparaginase II and OmpT Proteins of Shiga Toxin-Producing Escherichia coli. Microorganisms, 8.","DOI":"10.3390\/microorganisms8081184"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"105861","DOI":"10.1016\/j.micpath.2022.105861","article-title":"Virulence-encoding genes related to extraintestinal pathogenic E. coli and multidrug resistant pattern of strains isolated from neonatal calves with different severity scores of umbilical infections","volume":"174","author":"Martins","year":"2023","journal-title":"Microb. Pathog."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Asadulghani, M., Ogura, Y., Ooka, T., Itoh, T., Sawaguchi, A., Iguchi, A., Nakayama, K., and Hayashi, T. (2009). The Defective Prophage Pool of Escherichia coli O157: Prophage-Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants. PLoS Pathog., 5.","DOI":"10.1371\/journal.ppat.1000408"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/nrmicro.2016.161","article-title":"Protein Export through the Bacterial Sec Pathway","volume":"15","author":"Tsirigotaki","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Green, E.R., and Mecsas, J. (2016). Bacterial Secretion Systems: An Overview. Microbiol. Spectr., 4.","DOI":"10.1128\/microbiolspec.VMBF-0012-2015"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1007\/s12223-021-00882-0","article-title":"Antibiotic-Mediated Expression Analysis of Shiga Toxin 1 and 2 in Multi-Drug-Resistant Shiga Toxigenic Escherichia coli","volume":"66","author":"Rehman","year":"2021","journal-title":"Folia Microbiol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Kempf, F., Slugocki, C., Blum, S.E., Leitner, G., and Germon, P. (2016). Genomic Comparative Study of Bovine Mastitis Escherichia coli. PLoS ONE., 11.","DOI":"10.1371\/journal.pone.0147954"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.meegid.2010.09.006","article-title":"Distribution of the Putative Type VI Secretion System Core Genes in Klebsiella spp.","volume":"11","author":"Sarris","year":"2011","journal-title":"Infect. Genet. Evol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1099\/mic.0.000947","article-title":"Novel Regulators of the CSGD Gene Encoding the Master Regulator of Biofilm Formation in Escherichia coli K-12","volume":"166","author":"Ogasawara","year":"2020","journal-title":"Microbiology"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1099\/jmm.0.080317-0","article-title":"Performance of the VITEK MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Rapid Bacterial Identification in Two Diagnostic Centres in China","volume":"64","author":"Luo","year":"2015","journal-title":"J. Med. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: A Self-Training Method for Prediction of Gene Starts in Microbial Genomes. Implications for Finding Sequence Motifs in Regulatory Regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/nar\/28.1.33","article-title":"The COG database: A tool for genome-scale analysis of protein functions and evolution","volume":"28","author":"Tatusov","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"D669","DOI":"10.1093\/nar\/gkv1269","article-title":"EffectiveDB\u2014Updates and Novel Features for a Better Annotation of Bacterial Secreted Proteins and Type III, IV, VI Secretion Systems","volume":"44","author":"Eichinger","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/5\/511\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:33:21Z","timestamp":1760031201000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/5\/511"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,15]]},"references-count":68,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["antibiotics14050511"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics14050511","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,15]]}}}