{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,10]],"date-time":"2026-11-10T04:04:04Z","timestamp":1794283444120,"version":"4.9.0"},"reference-count":123,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T00:00:00Z","timestamp":1720569600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T00:00:00Z","timestamp":1720569600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Extraintestinal Pathogenic\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains. Additionally, 49 strains harbor toxins typical of enteric\n                    <jats:italic>E. coli<\/jats:italic>\n                    pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring\n                    <jats:italic>fosA3<\/jats:italic>\n                    ,\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M-14<\/jats:sub>\n                    , and\n                    <jats:italic>mcr-1<\/jats:italic>\n                    genes between swine ExPEC and human-origin\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.\n                  <\/jats:p>","DOI":"10.1038\/s41467-024-50268-2","type":"journal-article","created":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T15:02:12Z","timestamp":1720623732000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China"],"prefix":"10.1038","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0524-6128","authenticated-orcid":false,"given":"Xudong","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5543-8390","authenticated-orcid":false,"given":"Huifeng","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongwei","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taiquan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youlan","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0191-1378","authenticated-orcid":false,"given":"Xiangru","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5249-328X","authenticated-orcid":false,"given":"Zhong","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5465-5983","authenticated-orcid":false,"given":"Ming","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanchun","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0147-5900","authenticated-orcid":false,"given":"Jinshui","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4622-4483","authenticated-orcid":false,"given":"Chen","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,10]]},"reference":[{"key":"50268_CR1","doi-asserted-by":"publisher","first-page":"00135","DOI":"10.1128\/CMR.00135-18","volume":"32","author":"AR Manges","year":"2019","unstructured":"Manges, A. R. et al. Global extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Clin. Microbiol. Rev. 32, 00135\u201318 (2019).","journal-title":"Clin. Microbiol. Rev."},{"key":"50268_CR2","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1067\/mlc.2002.121550","volume":"139","author":"JR Johnson","year":"2002","unstructured":"Johnson, J. R. & Russo, T. A. Extraintestinal pathogenic Escherichia coli:\u201cthe other bad E coli\u201d. J. Lab. Clin. Med. 139, 155\u2013162 (2002).","journal-title":"J. Lab. Clin. Med."},{"key":"50268_CR3","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1056\/NEJMoa022139","volume":"348","author":"GS Martin","year":"2003","unstructured":"Martin, G. S., Mannino, D. M., Eaton, S. & Moss, M. The epidemiology of sepsis in the United States from 1979 through 2000. N. Engl. J. Med. 348, 1546\u20131554 (2003).","journal-title":"N. Engl. J. Med."},{"key":"50268_CR4","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.mib.2011.12.004","volume":"15","author":"CJ Alteri","year":"2012","unstructured":"Alteri, C. J. & Mobley, H. L. Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments. Curr. Opin. Microbiol. 15, 3\u20139 (2012).","journal-title":"Curr. Opin. Microbiol."},{"key":"50268_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-018-3449-2","volume":"18","author":"B-A Lindstedt","year":"2018","unstructured":"Lindstedt, B.-A., Finton, M. D., Porcellato, D. & Brandal, L. T. High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples. BMC Infect. Dis. 18, 1\u201312 (2018).","journal-title":"BMC Infect. Dis."},{"key":"50268_CR6","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1016\/j.jinf.2015.09.009","volume":"71","author":"AP Dale","year":"2015","unstructured":"Dale, A. P. & Woodford, N. Extra-intestinal pathogenic Escherichia coli (ExPEC): disease, carriage and clones. J. Infect. 71, 615\u2013626 (2015).","journal-title":"J. Infect."},{"key":"50268_CR7","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1101\/gr.216606.116","volume":"27","author":"T Kallonen","year":"2017","unstructured":"Kallonen, T. et al. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Res. 27, 1437\u20131449 (2017).","journal-title":"Genome Res"},{"key":"50268_CR8","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1101\/gr.180190.114","volume":"25","author":"SJ Salipante","year":"2015","unstructured":"Salipante, S. J. et al. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains. Genome Res 25, 119\u2013128 (2015).","journal-title":"Genome Res"},{"key":"50268_CR9","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1128\/AEM.06663-11","volume":"78","author":"SJ Weissman","year":"2012","unstructured":"Weissman, S. J. et al. High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli. Appl. Environ. Microbiol. 78, 1353\u20131360 (2012).","journal-title":"Appl. Environ. Microbiol."},{"key":"50268_CR10","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1016\/j.ijmm.2011.09.006","volume":"301","author":"C-D K\u00f6hler","year":"2011","unstructured":"K\u00f6hler, C.-D. & Dobrindt, U. What defines extraintestinal pathogenic Escherichia coli? Int. J. Med. Microbiol. 301, 642\u2013647 (2011).","journal-title":"Int. J. Med. Microbiol."},{"key":"50268_CR11","doi-asserted-by":"publisher","first-page":"F1000 Faculty R","DOI":"10.12688\/f1000research.10609.1","volume":"6","author":"JD Pitout","year":"2017","unstructured":"Pitout, J. D. & DeVinney, R. Escherichia coli ST131: a multidrug-resistant clone primed for global domination. F1000Research 6, F1000 Faculty Rev\u2013F1000 Faculty 195 (2017).","journal-title":"F1000Research"},{"key":"50268_CR12","doi-asserted-by":"publisher","first-page":"e02146","DOI":"10.1128\/AAC.02146-21","volume":"66","author":"M-D Phan","year":"2022","unstructured":"Phan, M.-D. et al. Plasmid-mediated ciprofloxacin resistance imparts a selective advantage on Escherichia coli ST131. Antimicrob. Agents Chemother. 66, e02146\u201321 (2022).","journal-title":"Antimicrob. Agents Chemother."},{"key":"50268_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13568-018-0646-8","volume":"8","author":"L Chen","year":"2018","unstructured":"Chen, L. et al. Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swine. AMB Express 8, 1\u201311 (2018).","journal-title":"AMB Express"},{"key":"50268_CR14","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.vetmic.2014.03.027","volume":"171","author":"L Osugui","year":"2014","unstructured":"Osugui, L., de Castro, A. P., Iovine, R., Irino, K. & Carvalho, V. Virulence genotypes, antibiotic resistance and the phylogenetic background of extraintestinal pathogenic Escherichia coli isolated from urinary tract infections of dogs and cats in Brazil. Vet. Microbiol. 171, 242\u2013247 (2014).","journal-title":"Vet. Microbiol."},{"key":"50268_CR15","doi-asserted-by":"publisher","first-page":"1049391","DOI":"10.3389\/fmicb.2022.1049391","volume":"13","author":"J Hu","year":"2022","unstructured":"Hu, J. et al. Characteristics, pathogenic mechanism, zoonotic potential, drug resistance, and prevention of avian pathogenic Escherichia coli (APEC). Front. Microbiol. 13, 1049391 (2022).","journal-title":"Front. Microbiol."},{"key":"50268_CR16","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1146\/annurev-publhealth-031912-114426","volume":"34","author":"P Rabinowitz","year":"2013","unstructured":"Rabinowitz, P. & Conti, L. Links among human health, animal health, and ecosystem health. Annu. Rev. Public Health 34, 189\u2013204 (2013).","journal-title":"Annu. Rev. Public Health"},{"key":"50268_CR17","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1038\/s41564-023-01351-9","volume":"8","author":"D Larsson","year":"2023","unstructured":"Larsson, D., Gaze, W., Laxminarayan, R. & Topp, E. AMR, One Health and the environment. Nat. Microbiol. 8, 754\u2013755 (2023).","journal-title":"Nat. Microbiol."},{"key":"50268_CR18","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1016\/j.tvjl.2011.06.038","volume":"192","author":"C Tan","year":"2012","unstructured":"Tan, C. et al. Serotypes and virulence genes of extraintestinal pathogenic Escherichia coli isolates from diseased pigs in China. Vet. J. 192, 483\u2013488 (2012).","journal-title":"Vet. J."},{"key":"50268_CR19","doi-asserted-by":"publisher","first-page":"2005","DOI":"10.1111\/tbed.13848","volume":"68","author":"J Ma","year":"2021","unstructured":"Ma, J. et al. Screening virulence factors of porcine extraintestinal pathogenic Escherichia coli (an emerging pathotype) required for optimal growth in swine blood. Transbound. Emerg. Dis. 68, 2005\u20132016 (2021).","journal-title":"Transbound. Emerg. Dis."},{"key":"50268_CR20","doi-asserted-by":"publisher","first-page":"28","DOI":"10.3389\/fmicb.2015.00028","volume":"6","author":"RS Singer","year":"2015","unstructured":"Singer, R. S. Urinary tract infections attributed to diverse ExPEC strains in food animals: evidence and data gaps. Front. Microbiol. 6, 28 (2015).","journal-title":"Front. Microbiol."},{"key":"50268_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1574-695X.2011.00797.x","volume":"62","author":"L B\u00e9langer","year":"2011","unstructured":"B\u00e9langer, L. et al. Escherichia coli from animal reservoirs as a potential source of human extraintestinal pathogenic E. coli. FEMS Immunol. Med. Microbiol. 62, 1\u201310 (2011).","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"50268_CR22","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.vetmic.2013.08.007","volume":"167","author":"A Mora","year":"2013","unstructured":"Mora, A. et al. Poultry as reservoir for extraintestinal pathogenic Escherichia coli O45: K1: H7-B2-ST95 in humans. Vet. Microbiol. 167, 506\u2013512 (2013).","journal-title":"Vet. Microbiol."},{"key":"50268_CR23","doi-asserted-by":"publisher","first-page":"415","DOI":"10.3201\/eid1803.111099","volume":"18","author":"CR Bergeron","year":"2012","unstructured":"Bergeron, C. R. et al. Chicken as reservoir for extraintestinal pathogenic Escherichia coli in humans. Can. Emerg. Infect. Dis. 18, 415 (2012).","journal-title":"Can. Emerg. Infect. Dis."},{"key":"50268_CR24","doi-asserted-by":"publisher","DOI":"10.1016\/j.onehlt.2023.100558","volume":"16","author":"V Garc\u00eda","year":"2023","unstructured":"Garc\u00eda, V. et al. 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. One Health 16, 100558 (2023).","journal-title":"One Health"},{"key":"50268_CR25","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1111\/tbed.13755","volume":"68","author":"X Zhuge","year":"2021","unstructured":"Zhuge, X. et al. Chicken\u2010source Escherichia coli within phylogroup F shares virulence genotypes and is closely related to extraintestinal pathogenic E. coli causing human infections. Transbound. Emerg. Dis. 68, 880\u2013895 (2021).","journal-title":"Transbound. Emerg. Dis."},{"key":"50268_CR26","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1146\/annurev-food-032519-051618","volume":"11","author":"LW Riley","year":"2020","unstructured":"Riley, L. W. Extraintestinal foodborne pathogens. Annu. Rev. Food Sci. Technol. 11, 275\u2013294 (2020).","journal-title":"Annu. Rev. Food Sci. Technol."},{"key":"50268_CR27","doi-asserted-by":"publisher","first-page":"107713","DOI":"10.1016\/j.foodcont.2020.107713","volume":"123","author":"D D\u00edaz-Jim\u00e9nez","year":"2021","unstructured":"D\u00edaz-Jim\u00e9nez, D., Garc\u00eda-Meni\u00f1o, I., Herrera, A., Lest\u00f3n, L. & Mora, A. Microbiological risk assessment of Turkey and chicken meat for consumer: Significant differences regarding multidrug resistance, mcr or presence of hybrid aEPEC\/ExPEC pathotypes of E. coli. Food Control 123, 107713 (2021).","journal-title":"Food Control"},{"key":"50268_CR28","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1038\/s41564-019-0496-4","volume":"4","author":"J Sun","year":"2019","unstructured":"Sun, J. et al. Plasmid-encoded tet (X) genes that confer high-level tigecycline resistance in Escherichia coli. Nat. Microbiol. 4, 1457\u20131464 (2019).","journal-title":"Nat. Microbiol."},{"key":"50268_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28750-6","volume":"13","author":"Z Peng","year":"2022","unstructured":"Peng, Z. et al. Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China. Nat. Commun. 13, 1116 (2022).","journal-title":"Nat. Commun."},{"key":"50268_CR30","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1007\/s40121-023-00791-4","volume":"12","author":"JD Pitout","year":"2023","unstructured":"Pitout, J. D. & Chen, L. The significance of epidemic plasmids in the success of multidrug-resistant drug pandemic extraintestinal pathogenic Escherichia coli. Infect. Dis. Ther. 12, 1029\u20131041 (2023).","journal-title":"Infect. Dis. Ther."},{"key":"50268_CR31","doi-asserted-by":"publisher","first-page":"E238","DOI":"10.1111\/1469-0691.12128","volume":"19","author":"M Accogli","year":"2013","unstructured":"Accogli, M. et al. IncI1 plasmids associated with the spread of CMY\u20102, CTX\u2010M\u20101 and SHV\u201012 in Escherichia coli of animal and human origin. Clin. Microbiol. Infect. 19, E238\u2013E240 (2013).","journal-title":"Clin. Microbiol. Infect."},{"key":"50268_CR32","doi-asserted-by":"publisher","first-page":"102291","DOI":"10.1016\/j.mib.2023.102291","volume":"73","author":"M Despotovic","year":"2023","unstructured":"Despotovic, M., de Nies, L., Busi, S. B. & Wilmes, P. Reservoirs of antimicrobial resistance in the context of One Health. Curr. Opin. Microbiol. 73, 102291 (2023).","journal-title":"Curr. Opin. Microbiol."},{"key":"50268_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1746-6148-8-140","volume":"8","author":"Y Ding","year":"2012","unstructured":"Ding, Y. et al. Clonal analysis and virulent traits of pathogenic extraintestinal Escherichia coli isolates from swine in China. BMC Vet. Res. 8, 1\u20137 (2012).","journal-title":"BMC Vet. Res."},{"key":"50268_CR34","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1080\/21505594.2019.1573491","volume":"10","author":"B Zong","year":"2019","unstructured":"Zong, B. et al. Characterization of multiple type-VI secretion system (T6SS) VgrG proteins in the pathogenicity and antibacterial activity of porcine extra-intestinal pathogenic Escherichia coli. Virulence 10, 118\u2013132 (2019).","journal-title":"Virulence"},{"key":"50268_CR35","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1080\/01652176.2018.1519321","volume":"38","author":"MG Spindola","year":"2018","unstructured":"Spindola, M. G. et al. Genetic diversity, virulence genotype and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from sows. Vet. Q. 38, 79\u201387 (2018).","journal-title":"Vet. Q."},{"key":"50268_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12917-017-0975-x","volume":"13","author":"Y Zhu","year":"2017","unstructured":"Zhu, Y. et al. Characterization and virulence clustering analysis of extraintestinal pathogenic Escherichia coli isolated from swine in China. BMC Vet. Res. 13, 1\u201310 (2017).","journal-title":"BMC Vet. Res."},{"key":"50268_CR37","doi-asserted-by":"publisher","first-page":"158749","DOI":"10.1016\/j.scitotenv.2022.158749","volume":"853","author":"DA Holcomb","year":"2022","unstructured":"Holcomb, D. A., Quist, A. J. & Engel, L. S. Exposure to industrial hog and poultry operations and urinary tract infections in North Carolina. Usa. Sci. Total Environ. 853, 158749 (2022).","journal-title":"Usa. Sci. Total Environ."},{"key":"50268_CR38","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1002\/fee.1505","volume":"15","author":"BJ Koch","year":"2017","unstructured":"Koch, B. J., Hungate, B. A. & Price, L. B. Food\u2010animal production and the spread of antibiotic resistance: the role of ecology. Front. Ecol. Environ. 15, 309\u2013318 (2017).","journal-title":"Front. Ecol. Environ."},{"key":"50268_CR39","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.tvjl.2009.10.017","volume":"187","author":"H-X Jiang","year":"2011","unstructured":"Jiang, H.-X. et al. High prevalence and widespread distribution of multi-resistant Escherichia coli isolates in pigs and poultry in China. Vet. J. 187, 99\u2013103 (2011).","journal-title":"Vet. J."},{"key":"50268_CR40","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/nrmicro818","volume":"2","author":"JB Kaper","year":"2004","unstructured":"Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123\u2013140 (2004).","journal-title":"Nat. Rev. Microbiol."},{"key":"50268_CR41","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.3390\/pathogens10111355","volume":"10","author":"VM Sora","year":"2021","unstructured":"Sora, V. M. et al. Extraintestinal pathogenic Escherichia coli: Virulence factors and antibiotic resistance. Pathogens 10, 1355 (2021).","journal-title":"Pathogens"},{"key":"50268_CR42","doi-asserted-by":"publisher","first-page":"149205","DOI":"10.1016\/j.scitotenv.2021.149205","volume":"798","author":"Y Shao","year":"2021","unstructured":"Shao, Y., Wang, Y., Yuan, Y. & Xie, Y. A systematic review on antibiotics misuse in livestock and aquaculture and regulation implications in China. Sci. Total Environ. 798, 149205 (2021).","journal-title":"Sci. Total Environ."},{"key":"50268_CR43","doi-asserted-by":"publisher","first-page":"e02015","DOI":"10.1128\/spectrum.02015-22","volume":"10","author":"J Ma","year":"2022","unstructured":"Ma, J. et al. Large-scale studies on antimicrobial resistance and molecular characterization of Escherichia coli from food animals in developed areas of eastern China. Microbiol. Spectr. 10, e02015\u2013e02022 (2022).","journal-title":"Microbiol. Spectr."},{"key":"50268_CR44","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.vetmic.2017.02.008","volume":"203","author":"P Zhang","year":"2017","unstructured":"Zhang, P. et al. Surveillance of antimicrobial resistance among Escherichia coli from chicken and swine, China, 2008\u20132015. Vet. Microbiol. 203, 49\u201355 (2017).","journal-title":"Vet. Microbiol."},{"key":"50268_CR45","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","volume":"18","author":"A-P Magiorakos","year":"2012","unstructured":"Magiorakos, A.-P. et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 18, 268\u2013281 (2012).","journal-title":"Clin. Microbiol. Infect."},{"key":"50268_CR46","doi-asserted-by":"publisher","first-page":"30","DOI":"10.4103\/0255-0857.148373","volume":"33","author":"M Krishnaraju","year":"2015","unstructured":"Krishnaraju, M. et al. Complete sequencing of an IncX3 plasmid carrying blaNDM-5 allele reveals an early stage in the dissemination of the blaNDM gene. Indian J. Med. Microbiol. 33, 30\u201338 (2015).","journal-title":"Indian J. Med. Microbiol."},{"key":"50268_CR47","doi-asserted-by":"publisher","first-page":"6973","DOI":"10.1128\/AAC.01457-16","volume":"60","author":"E Snesrud","year":"2016","unstructured":"Snesrud, E. et al. A model for transposition of the colistin resistance gene mcr-1 by ISApl1. Antimicrob. Agents Chemother. 60, 6973\u20136976 (2016).","journal-title":"Antimicrob. Agents Chemother."},{"key":"50268_CR48","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03205-z","volume":"9","author":"R Wang","year":"2018","unstructured":"Wang, R. et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat. Commun. 9, 1179 (2018).","journal-title":"Nat. Commun."},{"key":"50268_CR49","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.ebiom.2019.03.006","volume":"42","author":"X Lu","year":"2019","unstructured":"Lu, X. et al. Epidemiologic and genomic insights on mcr-1-harbouring Salmonella from diarrhoeal outpatients in Shanghai, China, 2006\u20132016. EBioMedicine 42, 133\u2013144 (2019).","journal-title":"EBioMedicine"},{"key":"50268_CR50","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1093\/jac\/dkz415","volume":"75","author":"Q Luo","year":"2020","unstructured":"Luo, Q. et al. MDR Salmonella enterica serovar Typhimurium ST34 carrying mcr-1 isolated from cases of bloodstream and intestinal infection in children in China. J. Antimicrob. Chemother. 75, 92\u201395 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"50268_CR51","doi-asserted-by":"publisher","first-page":"e00602","DOI":"10.1128\/mSphere.00602-19","volume":"4","author":"B Zheng","year":"2019","unstructured":"Zheng, B. et al. Occurrence and genomic characterization of two MCR-1-producing Escherichia coli isolates from the same mink farmer. mSphere 4, e00602\u2013e00619 (2019).","journal-title":"mSphere"},{"key":"50268_CR52","doi-asserted-by":"publisher","first-page":"00137","DOI":"10.1128\/mSphere.00137-18","volume":"3","author":"J Wang","year":"2018","unstructured":"Wang, J. et al. Evolution and comparative genomics of F33: A\u2212: B\u2212 plasmids carrying blaCTX-M-55 or blaCTX-M-65 in Escherichia coli and Klebsiella pneumoniae isolated from animals, food products, and humans in China. mSphere 3, 00137\u201318 (2018).","journal-title":"mSphere"},{"key":"50268_CR53","doi-asserted-by":"publisher","first-page":"4464","DOI":"10.1128\/AAC.00501-15","volume":"59","author":"L Liu","year":"2015","unstructured":"Liu, L. et al. blaCTX-M-1\/9\/1 hybrid genes may have been generated from blaCTX-M-15 on an IncI2 plasmid. Antimicrob. Agents Chemother. 59, 4464\u20134470 (2015).","journal-title":"Antimicrob. Agents Chemother."},{"key":"50268_CR54","doi-asserted-by":"publisher","first-page":"366","DOI":"10.3390\/ijerph17010366","volume":"17","author":"E Bok","year":"2020","unstructured":"Bok, E., Ko\u017ca\u0144ska, A., Mazurek-Popczyk, J., Wojciech, M. & Baldy-Chudzik, K. Extended phylogeny and extraintestinal virulence potential of commensal Escherichia coli from piglets and sows. Int. J. Environ. Res. Public Health 17, 366 (2020).","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"50268_CR55","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000143","volume":"3","author":"CJ Reid","year":"2017","unstructured":"Reid, C. J. et al. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. Microb. Genomics 3, e000143 (2017).","journal-title":"Microb. Genomics"},{"key":"50268_CR56","doi-asserted-by":"publisher","first-page":"843","DOI":"10.3390\/microorganisms8060843","volume":"8","author":"T Zingali","year":"2020","unstructured":"Zingali, T. et al. Whole genome sequencing analysis of porcine faecal commensal Escherichia coli carrying class 1 integrons from sows and their offspring. Microorganisms 8, 843 (2020).","journal-title":"Microorganisms"},{"key":"50268_CR57","doi-asserted-by":"publisher","first-page":"861","DOI":"10.3389\/fmicb.2020.00861","volume":"11","author":"M AbuOun","year":"2020","unstructured":"AbuOun, M. et al. Characterizing antimicrobial resistant Escherichia coli and associated risk factors in a cross-sectional study of pig farms in Great Britain. Front. Microbiol. 11, 861 (2020).","journal-title":"Front. Microbiol."},{"key":"50268_CR58","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1038\/ng.3145","volume":"46","author":"A von Mentzer","year":"2014","unstructured":"von Mentzer, A. et al. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat. Genet. 46, 1321\u20131326 (2014).","journal-title":"Nat. Genet."},{"key":"50268_CR59","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/s41564-022-01079-y","volume":"7","author":"DM Muloi","year":"2022","unstructured":"Muloi, D. M. et al. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nat. Microbiol. 7, 581\u2013589 (2022).","journal-title":"Nat. Microbiol."},{"key":"50268_CR60","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/s41579-020-0416-x","volume":"19","author":"E Denamur","year":"2021","unstructured":"Denamur, E., Clermont, O., Bonacorsi, S. & Gordon, D. The population genetics of pathogenic Escherichia coli. Nat. Rev. Microbiol. 19, 37\u201354 (2021).","journal-title":"Nat. Rev. Microbiol."},{"key":"50268_CR61","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.aninu.2017.10.001","volume":"3","author":"Y Sun","year":"2017","unstructured":"Sun, Y. & Kim, S. W. Intestinal challenge with enterotoxigenic Escherichia coli in pigs, and nutritional intervention to prevent postweaning diarrhea. Anim. Nutr. 3, 322\u2013330 (2017).","journal-title":"Anim. Nutr."},{"key":"50268_CR62","doi-asserted-by":"publisher","first-page":"e01913","DOI":"10.1128\/AEM.01913-20","volume":"86","author":"V Garc\u00eda","year":"2020","unstructured":"Garc\u00eda, V. et al. F4-and F18-positive enterotoxigenic Escherichia coli isolates from diarrhea of postweaning pigs: genomic characterization. Appl. Environ. Microbiol. 86, e01913\u2013e01920 (2020).","journal-title":"Appl. Environ. Microbiol."},{"key":"50268_CR63","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1056\/NEJMoa1106920","volume":"365","author":"DA Rasko","year":"2011","unstructured":"Rasko, D. A. et al. Origins of the E. coli Strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 365, 709\u2013717 (2011).","journal-title":"N. Engl. J. Med."},{"key":"50268_CR64","doi-asserted-by":"publisher","first-page":"339","DOI":"10.3389\/fcimb.2020.00339","volume":"10","author":"ACDM Santos","year":"2020","unstructured":"Santos, A. C. D. M., Santos, F. F., Silva, R. M. & Gomes, T. A. T. Diversity of hybrid-and hetero-pathogenic Escherichia coli and their potential implication in more severe diseases. Front. Cell. Infect. Microbiol. 10, 339 (2020).","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"50268_CR65","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-024-01882-y","volume":"17","author":"LE Kanje","year":"2024","unstructured":"Kanje, L. E. et al. Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania. BMC Med. Genomics 17, 110 (2024).","journal-title":"BMC Med. Genomics"},{"key":"50268_CR66","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-021-00892-0","volume":"13","author":"G Royer","year":"2021","unstructured":"Royer, G. et al. Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period. Genome Med. 13, 77 (2021).","journal-title":"Genome Med."},{"key":"50268_CR67","doi-asserted-by":"publisher","first-page":"420699","DOI":"10.3389\/fmicb.2018.02659","volume":"9","author":"I Garc\u00eda-Meni\u00f1o","year":"2018","unstructured":"Garc\u00eda-Meni\u00f1o, I. et al. Swine enteric colibacillosis in Spain: pathogenic potential of mcr-1 ST10 and ST131 E. coli isolates. Front. Microbiol. 9, 420699 (2018).","journal-title":"Front. Microbiol."},{"key":"50268_CR68","doi-asserted-by":"publisher","first-page":"00337","DOI":"10.1128\/mSphere.00337-18","volume":"3","author":"L Roer","year":"2018","unstructured":"Roer, L. et al. Escherichia coli sequence type 410 is causing new international high-risk clones. mSphere 3, 00337\u201318 (2018).","journal-title":"mSphere"},{"key":"50268_CR69","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1038\/s42003-019-0569-1","volume":"2","author":"Y Feng","year":"2019","unstructured":"Feng, Y. et al. Key evolutionary events in the emergence of a globally disseminated, carbapenem resistant clone in the Escherichia coli ST410 lineage. Commun. Biol. 2, 322 (2019).","journal-title":"Commun. Biol."},{"key":"50268_CR70","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1016\/j.micinf.2014.12.016","volume":"17","author":"S Guo","year":"2015","unstructured":"Guo, S. et al. Human-associated fluoroquinolone-resistant Escherichia coli clonal lineages, including ST354, isolated from canine feces and extraintestinal infections in Australia. Microbes Infect. 17, 266\u2013274 (2015).","journal-title":"Microbes Infect."},{"key":"50268_CR71","doi-asserted-by":"publisher","first-page":"3256","DOI":"10.1111\/tbed.14678","volume":"69","author":"F Xia","year":"2022","unstructured":"Xia, F. et al. Complete genomic analysis of ST117 lineage extraintestinal pathogenic Escherichia coli (ExPEC) to reveal multiple genetic determinants to drive its global transmission: ST117 E. coli as an emerging multidrug\u2010resistant foodborne ExPEC with zoonotic potential. Transbound. Emerg. Dis. 69, 3256\u20133273 (2022).","journal-title":"Transbound. Emerg. Dis."},{"key":"50268_CR72","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-45482-8","volume":"9","author":"B Zhang","year":"2019","unstructured":"Zhang, B. et al. Prevalence and antimicrobial susceptibilities of bacterial pathogens in Chinese pig farms from 2013 to 2017. Sci. Rep. 9, 9908 (2019).","journal-title":"Sci. Rep."},{"key":"50268_CR73","doi-asserted-by":"publisher","first-page":"52","DOI":"10.3390\/antibiotics9020052","volume":"9","author":"N Vidovic","year":"2020","unstructured":"Vidovic, N. & Vidovic, S. Antimicrobial resistance and food animals: Influence of livestock environment on the emergence and dissemination of antimicrobial resistance. Antibiotics 9, 52 (2020).","journal-title":"Antibiotics"},{"key":"50268_CR74","doi-asserted-by":"publisher","first-page":"e0185326","DOI":"10.1371\/journal.pone.0185326","volume":"12","author":"AK Yassin","year":"2017","unstructured":"Yassin, A. K. et al. Antimicrobial resistance in clinical Escherichia coli isolates from poultry and livestock, China. PLoS One 12, e0185326 (2017).","journal-title":"PLoS One"},{"key":"50268_CR75","unstructured":"Arumugham, V. B., Gujarathi, R. & Cascella, M. Third-Generation Cephalosporins. [Updated 2023 Jun 4]. In: StatPearls [Internet]. https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK549881\/ (2024)."},{"key":"50268_CR76","unstructured":"Bui, T. & Preuss, C. V. Cephalosporins. [Updated 2023 Mar 24]. In: StatPearls [Internet]. https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK551517\/ (2024)."},{"key":"50268_CR77","doi-asserted-by":"publisher","first-page":"360","DOI":"10.2471\/BLT.19.243501","volume":"98","author":"YJ Hu","year":"2020","unstructured":"Hu, Y. J. & Cowling, B. J. Reducing antibiotic use in livestock. China Bull. W. H. O. 98, 360 (2020).","journal-title":"China Bull. W. H. O."},{"key":"50268_CR78","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13756-018-0426-x","volume":"8","author":"G Cheng","year":"2019","unstructured":"Cheng, G. et al. Selection and dissemination of antimicrobial resistance in Agri-food production. Antimicrobial Resistance Infect. Control 8, 1\u201313 (2019).","journal-title":"Antimicrobial Resistance Infect. Control"},{"key":"50268_CR79","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/j.jgar.2021.02.010","volume":"24","author":"H Sun","year":"2021","unstructured":"Sun, H. et al. Co-occurrence of plasmid-mediated resistance genes tet (X4) and blaNDM-5 in a multidrug-resistant Escherichia coli isolate recovered from chicken in China. J. Glob. Antimicrob. Resist. 24, 415\u2013417 (2021).","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"50268_CR80","doi-asserted-by":"publisher","first-page":"69","DOI":"10.3390\/antibiotics10010069","volume":"10","author":"N Puva\u010da","year":"2021","unstructured":"Puva\u010da, N. & de Llanos Frutos, R. Antimicrobial resistance in Escherichia coli strains isolated from humans and pet animals. Antibiotics 10, 69 (2021).","journal-title":"Antibiotics"},{"key":"50268_CR81","doi-asserted-by":"publisher","first-page":"e1004776","DOI":"10.1371\/journal.pgen.1004776","volume":"10","author":"M de Been","year":"2014","unstructured":"de Been, M. et al. Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages. PLoS Genet 10, e1004776 (2014).","journal-title":"PLoS Genet"},{"key":"50268_CR82","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1111\/jam.12099","volume":"114","author":"P Ho","year":"2013","unstructured":"Ho, P. et al. Dissemination of plasmid\u2010mediated fosfomycin resistance fosA3 among multidrug\u2010resistant Escherichia coli from livestock and other animals. J. Appl. Microbiol. 114, 695\u2013702 (2013).","journal-title":"J. Appl. Microbiol."},{"key":"50268_CR83","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","volume":"18","author":"E Tacconelli","year":"2018","unstructured":"Tacconelli, E. et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318\u2013327 (2018).","journal-title":"Lancet Infect. Dis."},{"key":"50268_CR84","doi-asserted-by":"publisher","first-page":"127249","DOI":"10.1016\/j.micres.2022.127249","volume":"266","author":"J Ma","year":"2022","unstructured":"Ma, J. et al. Global spread of carbapenem-resistant Enterobacteriaceae: Epidemiological features, resistance mechanisms, detection and therapy. Microbiol. Res. 266, 127249 (2022).","journal-title":"Microbiol. Res."},{"key":"50268_CR85","doi-asserted-by":"crossref","unstructured":"Sharma, J., Sharma, D., Singh, A. & Sunita, K. Colistin resistance and management of drug resistant infections. Can. J. Infect. Dis. Med. Microbiol. 2022 (2022).","DOI":"10.1155\/2022\/4315030"},{"key":"50268_CR86","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/S1473-3099(15)00424-7","volume":"16","author":"Y-Y Liu","year":"2016","unstructured":"Liu, Y.-Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161\u2013168 (2016).","journal-title":"Lancet Infect. Dis."},{"key":"50268_CR87","doi-asserted-by":"publisher","first-page":"1603","DOI":"10.1021\/acs.est.9b05919","volume":"54","author":"L Zhu","year":"2019","unstructured":"Zhu, L. et al. Comprehensive understanding of the plasmid-mediated colistin resistance gene mcr-1 in aquatic environments. Environ. Sci. Technol. 54, 1603\u20131613 (2019).","journal-title":"Environ. Sci. Technol."},{"key":"50268_CR88","doi-asserted-by":"publisher","first-page":"177","DOI":"10.3934\/microbiol.2023011","volume":"9","author":"R Abozahra","year":"2023","unstructured":"Abozahra, R., Gaballah, A. & Abdelhamid, S. M. Prevalence of the colistin resistance gene MCR-1 in colistin-resistant Klebsiella pneumoniae in Egypt. AIMS Microbiol 9, 177 (2023).","journal-title":"AIMS Microbiol"},{"key":"50268_CR89","doi-asserted-by":"publisher","first-page":"00404","DOI":"10.1128\/AAC.00404-18","volume":"62","author":"Y Shen","year":"2018","unstructured":"Shen, Y. et al. Prevalence and genetic analysis of mcr-3-positive Aeromonas species from humans, retail meat, and environmental water samples. Antimicrob. Agents Chemother. 62, 00404\u201300418 (2018).","journal-title":"Antimicrob. Agents Chemother."},{"key":"50268_CR90","doi-asserted-by":"publisher","first-page":"30586","DOI":"10.2807\/1560-7917.ES.2017.22.31.30586","volume":"22","author":"M Hern\u00e1ndez","year":"2017","unstructured":"Hern\u00e1ndez, M. et al. Co-occurrence of colistin-resistance genes mcr-1 and mcr-3 among multidrug-resistant Escherichia coli isolated from cattle, Spain, September 2015. Eurosurveillance 22, 30586 (2017).","journal-title":"Eurosurveillance"},{"key":"50268_CR91","doi-asserted-by":"publisher","first-page":"1217","DOI":"10.3389\/fmicb.2018.01217","volume":"9","author":"P Alba","year":"2018","unstructured":"Alba, P. et al. Molecular epidemiology of mcr-encoded colistin resistance in Enterobacteriaceae from food-producing animals in Italy revealed through the EU harmonized antimicrobial resistance monitoring. Front. Microbiol. 9, 1217 (2018).","journal-title":"Front. Microbiol."},{"key":"50268_CR92","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.vetmic.2019.01.011","volume":"230","author":"Z Wang","year":"2019","unstructured":"Wang, Z. et al. Genetic environment of colistin resistance genes mcr-1 and mcr-3 in Escherichia coli from one pig farm in China. Vet. Microbiol. 230, 56\u201361 (2019).","journal-title":"Vet. Microbiol."},{"key":"50268_CR93","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-22084-4","volume":"8","author":"J Zhang","year":"2018","unstructured":"Zhang, J. et al. Molecular detection of colistin resistance genes (mcr-1, mcr-2 and mcr-3) in nasal\/oropharyngeal and anal\/cloacal swabs from pigs and poultry. Sci. Rep. 8, 3705 (2018).","journal-title":"Sci. Rep."},{"key":"50268_CR94","doi-asserted-by":"publisher","first-page":"01757","DOI":"10.1128\/AAC.01757-17","volume":"61","author":"L Liu","year":"2017","unstructured":"Liu, L., Feng, Y., Zhang, X., McNally, A. & Zong, Z. New variant of mcr-3 in an extensively drug-resistant Escherichia coli clinical isolate carrying mcr-1 and blaNDM-5. Antimicrob. Agents Chemother. 61, 01757\u201317 (2017).","journal-title":"Antimicrob. Agents Chemother."},{"key":"50268_CR95","doi-asserted-by":"publisher","first-page":"dlab092","DOI":"10.1093\/jacamr\/dlab092","volume":"3","author":"M Castanheira","year":"2021","unstructured":"Castanheira, M., Simner, P. J. & Bradford, P. A. Extended-spectrum \u03b2-lactamases: An update on their characteristics, epidemiology and detection. JAC-antimicrobial resistance 3, dlab092 (2021).","journal-title":"JAC-antimicrobial resistance"},{"key":"50268_CR96","doi-asserted-by":"publisher","first-page":"e1135","DOI":"10.1002\/mbo3.1135","volume":"9","author":"K Zurfluh","year":"2020","unstructured":"Zurfluh, K., Treier, A., Schmitt, K. & Stephan, R. Mobile fosfomycin resistance genes in Enterobacteriaceae\u2014an increasing threat. Microbiologyopen 9, e1135 (2020).","journal-title":"Microbiologyopen"},{"key":"50268_CR97","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1111\/zph.12825","volume":"68","author":"Z Zhang","year":"2021","unstructured":"Zhang, Z. et al. Dissemination of IncFII plasmids carrying fosA3 and blaCTX\u2010M\u201055 in clinical isolates of Salmonella enteritidis. Zoonoses Public Health 68, 760\u2013768 (2021).","journal-title":"Zoonoses Public Health"},{"key":"50268_CR98","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1016\/j.jgar.2018.10.025","volume":"15","author":"JD Palmeira","year":"2018","unstructured":"Palmeira, J. D., Ferreira, H., Madec, J.-Y. & Haenni, M. Pandemic Escherichia coli ST648 isolate harbouring fosA3 and blaCTX-M-8 on an IncI1\/ST113 plasmid: A new successful combination for the spread of fosfomycin resistance? J. Glob. Antimicrob. Resist. 15, 254\u2013255 (2018).","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"50268_CR99","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/jac\/dkx489","volume":"73","author":"A Lupo","year":"2018","unstructured":"Lupo, A., Saras, E., Madec, J.-Y. & Haenni, M. Emergence of blaCTX-M-55 associated with fosA, rmtB and mcr gene variants in Escherichia coli from various animal species in France. J. Antimicrob. Chemother. 73, 867\u2013872 (2018).","journal-title":"J. Antimicrob. Chemother."},{"key":"50268_CR100","doi-asserted-by":"crossref","unstructured":"Liu, H. et al. Build a bioinformatic analysis platform and apply it to routine analysis of microbial genomics and comparative genomics. Res. Square, PPR485749 (2022).","DOI":"10.21203\/rs.2.21224\/v6"},{"key":"50268_CR101","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"50268_CR102","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455\u2013477 (2012).","journal-title":"J. Comput. Biol."},{"key":"50268_CR103","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068\u20132069 (2014).","journal-title":"Bioinformatics"},{"key":"50268_CR104","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13073-014-0090-6","volume":"6","author":"M Inouye","year":"2014","unstructured":"Inouye, M. et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6, 1\u201316 (2014).","journal-title":"Genome Med"},{"key":"50268_CR105","doi-asserted-by":"publisher","first-page":"000728","DOI":"10.1099\/mgen.0.000728","volume":"7","author":"K Bessonov","year":"2021","unstructured":"Bessonov, K. et al. ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data. Microb. Genomics 7, 000728 (2021).","journal-title":"Microb. Genomics"},{"key":"50268_CR106","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","volume":"67","author":"E Zankari","year":"2012","unstructured":"Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640\u20132644 (2012).","journal-title":"J. Antimicrob. Chemother."},{"key":"50268_CR107","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia, V. et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75, 3491\u20133500 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"50268_CR108","doi-asserted-by":"publisher","first-page":"2764","DOI":"10.1093\/jac\/dkx217","volume":"72","author":"E Zankari","year":"2017","unstructured":"Zankari, E. et al. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J. Antimicrob. Chemother. 72, 2764\u20132768 (2017).","journal-title":"J. Antimicrob. Chemother."},{"key":"50268_CR109","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","volume":"31","author":"AJ Page","year":"2015","unstructured":"Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691\u20133693 (2015).","journal-title":"Bioinformatics"},{"key":"50268_CR110","doi-asserted-by":"publisher","first-page":"e000056","DOI":"10.1099\/mgen.0.000056","volume":"2","author":"AJ Page","year":"2016","unstructured":"Page, A. J. et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb. Genomics 2, e000056 (2016).","journal-title":"Microb. Genomics"},{"key":"50268_CR111","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312\u20131313 (2014).","journal-title":"Bioinformatics"},{"key":"50268_CR112","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","volume":"34","author":"W De Coster","year":"2018","unstructured":"De Coster, W., D\u2019hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666\u20132669 (2018).","journal-title":"Bioinformatics"},{"key":"50268_CR113","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540\u2013546 (2019).","journal-title":"Nat. Biotechnol."},{"key":"50268_CR114","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963 (2014).","journal-title":"PLoS One"},{"key":"50268_CR115","doi-asserted-by":"publisher","first-page":"e000206","DOI":"10.1099\/mgen.0.000206","volume":"4","author":"J Robertson","year":"2018","unstructured":"Robertson, J. & Nash, J. H. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb. Genomics 4, e000206 (2018).","journal-title":"Microb. Genomics"},{"key":"50268_CR116","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","volume":"34","author":"P Siguier","year":"2006","unstructured":"Siguier, P., P\u00e9rochon, J., Lestrade, L., Mahillon, J. & Chandler, M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34, D32\u2013D36 (2006).","journal-title":"Nucleic Acids Res"},{"key":"50268_CR117","doi-asserted-by":"publisher","first-page":"700","DOI":"10.3390\/microorganisms10040700","volume":"10","author":"B N\u00e9ron","year":"2022","unstructured":"N\u00e9ron, B. et al. IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella. Microorganisms 10, 700 (2022).","journal-title":"Microorganisms"},{"key":"50268_CR118","doi-asserted-by":"publisher","first-page":"27","DOI":"10.21105\/joss.00027","volume":"1","author":"CT Brown","year":"2016","unstructured":"Brown, C. T. & Irber, L. sourmash: a library for MinHash sketching of DNA. J. open source Softw. 1, 27 (2016).","journal-title":"J. open source Softw."},{"key":"50268_CR119","unstructured":"Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997, (2013)."},{"key":"50268_CR120","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"50268_CR121","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","volume":"33","author":"JR Conway","year":"2017","unstructured":"Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938\u20132940 (2017).","journal-title":"Bioinformatics"},{"key":"50268_CR122","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res"},{"key":"50268_CR123","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498\u20132504 (2003).","journal-title":"Genome Res"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-50268-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-50268-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-50268-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T16:21:27Z","timestamp":1720628487000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-50268-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,10]]},"references-count":123,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["50268"],"URL":"https:\/\/doi.org\/10.1038\/s41467-024-50268-2","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,10]]},"assertion":[{"value":"27 February 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 July 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"5811"}}