{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T11:17:08Z","timestamp":1785237428503,"version":"3.55.0"},"reference-count":64,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,2,8]],"date-time":"2022-02-08T00:00:00Z","timestamp":1644278400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss Federal Food Safety and Veterinary Office and Swiss Association for Small Animal Medicine","award":["1.21.q"],"award-info":[{"award-number":["1.21.q"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Companion animal clinics contribute to the spread of antimicrobial resistant microorganisms (ARM) and outbreaks with ARM of public health concern have been described. Methods: As part of a project to assess infection prevention and control (IPC) standards in companion animal clinics in Switzerland, a total of 200 swabs from surfaces and 20 hand swabs from employees were collected during four days in a medium-sized clinic and analyzed for extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE), and methicillin-resistant staphylococci (MRS). Results: A total of 22 (11.0%) environmental specimen yielded CPE, 14 (7.0%) ESBL-E, and 7 (3.5%) MRS; MR Staphylococcus aureus were isolated from two (10.0%) hand swabs. The CPE isolates comprised Escherichia coli, Klebsiella pneumoniae, Enterobacter hormaechei, Citrobacter braakii, and Serratia marcescens. Whole genome sequencing revealed that all CPE carried closely related blaOXA-48 plasmids, suggesting a plasmidic spread within the clinic. The clinic exhibited major deficits in surface disinfection, hand hygiene infrastructure, and hand hygiene compliance. CPE were present in various areas, including those without patient contact. The study documented plasmidic dissemination of blaOXA-48 in a companion animal clinic with low IPC standards. This poses a worrisome threat to public health and highlights the need to foster IPC standards in veterinary clinics to prevent the spread of ARM into the community.<\/jats:p>","DOI":"10.3390\/antibiotics11020213","type":"journal-article","created":{"date-parts":[[2022,2,9]],"date-time":"2022-02-09T01:03:40Z","timestamp":1644368620000},"page":"213","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Massive Spread of OXA-48 Carbapenemase-Producing Enterobacteriaceae in the Environment of a Swiss Companion Animal Clinic"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5790-3636","authenticated-orcid":false,"given":"Kira","family":"Schmitt","sequence":"first","affiliation":[{"name":"Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland"},{"name":"Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Biggel","sequence":"additional","affiliation":[{"name":"Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1002-4762","authenticated-orcid":false,"given":"Roger","family":"Stephan","sequence":"additional","affiliation":[{"name":"Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8010-1180","authenticated-orcid":false,"given":"Barbara","family":"Willi","sequence":"additional","affiliation":[{"name":"Clinic for Small Animal Internal Medicine, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,8]]},"reference":[{"key":"ref_1","unstructured":"United Nations (2016, January 5). Resolution A\/RES\/71\/3: Political Declaration of the High-Level Meeting of the General Assembly on Antimicrobial Resistance. Proceedings of the Seventy-First Session of the United Nations General Assembly, New York, NY, USA."},{"key":"ref_2","unstructured":"Interagency Coordination Group on Antimicrobial Resistance (2019). No Time to Wait: Securing the Future from Drug-Resistant Infections Report to the Secretary-General of the United Nation, United Nations."},{"key":"ref_3","unstructured":"World Health Organization (2017). WHO List of Critically Important Antimicrobials for Human Medicine (WHO CIA List)."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1128\/AAC.01344-13","article-title":"Derepressed transfer properties leading to the efficient spread of the plasmid encoding carbapenemase OXA-48","volume":"58","author":"Potron","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Ledda, A., Cummins, M., Shaw, L., Jauneikaite, E., Cole, K., Lasalle, F., Barry, D., Rosmarin, C., Anaraki, S., and Wareham, D. (2020). Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399. bioRxiv.","DOI":"10.1101\/2020.06.15.148189"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Shaidullina, E., Shelenkov, A., Yanushevich, Y., Mikhaylova, Y., Shagin, D., Alexandrova, I., Ershova, O., Akimkin, V., Kozlov, R., and Edelstein, M. (2020). Antimicrobial resistance and genomic characterization of OXA-48-and CTX-M-15-co-producing hypervirulent Klebsiella pneumoniae ST23 recovered from nosocomial outbreak. Antibiotics, 9.","DOI":"10.3390\/antibiotics9120862"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"30062","DOI":"10.2807\/1560-7917.ES.2015.20.45.30062","article-title":"Carbapenemase-producing Enterobacteriaceae in Europe: Assessment by national experts from 38 countries, May 2015","volume":"20","author":"Albiger","year":"2015","journal-title":"Eurosurveillance"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1086\/591861","article-title":"National Healthcare Safety Network Team and Participating National Healthcare Antimicrobial-resistant pathogens associated with healthcare-associated infections: Annual summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006\u20132007","volume":"29","author":"Hidron","year":"2008","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1017\/ice.2016.174","article-title":"Antimicrobial-resistant pathogens associated with healthcare-associated infections: Summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2011\u20132014","volume":"37","author":"Weiner","year":"2016","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_10","first-page":"1","article-title":"Dissemination of NDM-producing Klebsiella pneumoniae and Escherichia coli high-risk clones in Catalan healthcare institutions","volume":"76","author":"Cosgaya","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1093\/jac\/dkq499","article-title":"Plasmid-mediated carbapenem-hydrolysing-lactamase KPC-2 in a Klebsiella pneumoniae isolate from Switzerland","volume":"66","author":"Poirel","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2807\/1560-7917.ES.2019.24.39.1900071","article-title":"Shedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: An outbreak in 2018","volume":"24","author":"Nigg","year":"2019","journal-title":"Eurosurveillance"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2872","DOI":"10.3389\/fmicb.2018.02872","article-title":"Hospitalized pets as a source of carbapenem-resistance","volume":"9","author":"Gentilini","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Cocca, G., Piva, S., Magno, S.D., Scarpellini, R., Giacometti, F., Serraino, A., and Giunti, M. (2021). Prevalence and Patterns of Antimicrobial Resistance among Escherichia coli and Staphylococcus spp. in a Veterinary University Hospital. Vet. Sci., 8.","DOI":"10.3390\/vetsci8120308"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.3389\/fmicb.2018.01265","article-title":"Multispecies and clonal dissemination of OXA-48 carbapenemase in Enterobacteriaceae from companion animals in Germany, 2009\u20132016","volume":"9","author":"Pulss","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1111\/jvim.15522","article-title":"Usage patterns of carbapenem antimicrobials in dogs and cats at a veterinary tertiary care hospital","volume":"33","author":"Smith","year":"2019","journal-title":"J. Vet. Intern. Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1093\/jac\/dkab028","article-title":"Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital","volume":"76","author":"Brilhante","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1093\/jac\/dkaa387","article-title":"Genomic features of plasmids coding for KPC-2, NDM-5 or OXA-48 carbapenemases in Enterobacteriaceae from Malawi","volume":"76","author":"Kumwenda","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e02146-20","DOI":"10.1128\/AAC.02146-20","article-title":"Dissemination of extended-spectrum-\u03b2-lactamase-producing enterobacter cloacae complex from a hospital to the nearby environment in guadeloupe (French West Indies): ST114 lineage coding for a successful inchi2\/st1 plasmid","volume":"65","author":"Pot","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: A genome comparison visualizer","volume":"27","author":"Sullivan","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e02093-16","DOI":"10.1128\/mBio.02093-16","article-title":"Comprehensive genome analysis of carbapenemase-producing Enterobacter spp.: New insights into phylogeny, population structure, and resistance mechanisms","volume":"7","author":"Chavda","year":"2016","journal-title":"mBio"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1093\/jac\/dkz470","article-title":"Employees of Swiss veterinary clinics colonized with epidemic clones of carbapenemase-producing Escherichia coli","volume":"75","author":"Endimiani","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s13756-020-00742-5","article-title":"Poor infection prevention and control standards are associated with environmental contamination with carbapenemase-producing Enterobacterales and other multidrug-resistant bacteria in Swiss companion animal clinics","volume":"9","author":"Schmidt","year":"2020","journal-title":"Antimicrob. Resist. Infect. Control."},{"key":"ref_24","first-page":"512","article-title":"bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands DATA SUMMARY","volume":"7","author":"Hendrickx","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Schmitt, K., Kuster, S.P., Zurfluh, K., Jud, R.S., Sykes, J.E., Stephan, R., and Willi, B. (2021). Transmission Chains of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae at the Companion Animal Veterinary Clinic\u2014Household Interface. Antibiotics, 10.","DOI":"10.3390\/antibiotics10020171"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1111\/jvim.16038","article-title":"Acquisition and carriage of multidrug-resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland","volume":"35","author":"Dazio","year":"2021","journal-title":"J. Vet. Intern. Med."},{"key":"ref_27","first-page":"1","article-title":"Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households","volume":"86","author":"Benschop","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_28","first-page":"1700497","article-title":"Sharing more than friendship\u2014Transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, finland, 2015","volume":"23","author":"Eklund","year":"2018","journal-title":"Eurosurveillance"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.vetmic.2018.02.011","article-title":"Antimicrobial resistance, multilocus sequence types and virulence profiles of ESBL producing and non-ESBL producing uropathogenic Escherichia coli isolated from cats and dogs in Switzerland","volume":"216","author":"Zogg","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.3389\/fmicb.2017.02334","article-title":"Clonal diversity, virulence potential and antimicrobial resistance of Escherichia coli causing community acquired urinary tract infection in Switzerland","volume":"8","author":"Baschera","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1093\/jac\/dkz462","article-title":"Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household","volume":"75","author":"Fluit","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.jgar.2018.10.023","article-title":"Genomic features of a highly virulent, ceftiofur-resistant, CTX-M-8-producing Escherichia coli ST224 causing fatal infection in a domestic cat","volume":"15","author":"Silva","year":"2018","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.1093\/jac\/dkab169","article-title":"Rapid spread of critical priority carbapenemase-producing pathogens in companion animals: A One Health challenge for a post-pandemic world","volume":"76","author":"Sellera","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.ijantimicag.2016.09.033","article-title":"OXA-23 and ISAba1\u2013OXA-66 class D \u03b2-lactamases in Acinetobacter baumannii isolates from companion animals","volume":"49","author":"Ewers","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.3389\/fvets.2020.608901","article-title":"Environmental Recovery of Nosocomial Bacteria in a Companion Animal Shelter Before and After Infection Control Procedures","volume":"7","author":"Horsman","year":"2021","journal-title":"Front. Vet. Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e307","DOI":"10.1002\/vetr.307","article-title":"Hand hygiene compliance in companion animal clinics and practices in Switzerland: An observational study","volume":"189","author":"Schmidt","year":"2021","journal-title":"Vet. Rec."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Schmitt, K., Zimmermann, A.B.E., Stephan, R., and Willi, B. (2021). Hand Hygiene Evaluation Using Two Different Evaluation Tools and Hand Contamination of Veterinary Healthcare Workers in a Swiss Companion Animal Clinic. Vet. Sci., 8.","DOI":"10.3390\/vetsci8110260"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Anderson, M.E., Sargeant, J.M., and Weese, J.S. (2014). Video observation of hand hygiene practices during routine companion animal appointments and the effect of a poster intervention on hand hygiene compliance. BMC Vet. Res., 10.","DOI":"10.1186\/1746-6148-10-106"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"61","DOI":"10.2460\/javma.240.1.61","article-title":"Evaluation of an educational campaign to increase hand hygiene at a small animal veterinary teaching hospital","volume":"240","author":"Shea","year":"2012","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.2460\/javma.243.7.1042","article-title":"Multimodal evaluation of the effectiveness of a hand hygiene educational campaign at a small animal veterinary teaching hospital","volume":"243","author":"Smith","year":"2013","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1086\/600379","article-title":"The World Health Organization Guidelines on Hand Hygiene in Health Care and Their Consensus Recommendations","volume":"30","author":"Pittet","year":"2009","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1016\/S0195-6701(01)90005-2","article-title":"MRSA patients: Proven methods to treat colonization and infection","volume":"48","author":"Boyce","year":"2001","journal-title":"J. Hosp. Infect."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/2047-2994-3-34","article-title":"The effect of improved hand hygiene on nosocomial MRSA control","volume":"3","author":"Marimuthu","year":"2014","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1016\/j.ajic.2009.07.003","article-title":"The World Health Organization hand hygiene observation method","volume":"37","author":"Sax","year":"2009","journal-title":"Am. J. Infect. Control."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1093\/jac\/dkab382","article-title":"Transmission and molecular characteristics of blaNDM-producing Escherichia coli between companion animals and their healthcare providers in Guangzhou, China","volume":"77","author":"Wang","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"297","DOI":"10.5326\/JAAHA-MS-6903","article-title":"2018 AAHA Infection Control, Prevention, and Biosecurity Guidelines","volume":"54","author":"Stull","year":"2018","journal-title":"J. Am. Anim. Hosp. Assoc."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1214\/ss\/1009213286","article-title":"Interval Estimation for a Binomial Proportion","volume":"16","author":"Brown","year":"2001","journal-title":"Stat. Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"62","DOI":"10.3389\/fvets.2018.00062","article-title":"High prevalence of extended-spectrum \u03b2-lactamase producing Enterobacteriaceae among clinical isolates from cats and dogs admitted to a veterinary hospital in Switzerland","volume":"5","author":"Zogg","year":"2018","journal-title":"Front. Vet. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1128\/AAC.05539-11","article-title":"Molecular identification of extended-spectrum-\u03b2-lactamase genes from Enterobacteriaceae isolated from healthy human carriers in Switzerland","volume":"56","author":"Geser","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1093\/jac\/dki412","article-title":"Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum \u03b2-lactamases","volume":"57","author":"Woodford","year":"2006","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"3115","DOI":"10.1128\/AEM.00258-15","article-title":"Extended-spectrum-\u03b2-lactamase-producing Enterobacteriaceae isolated from vegetables imported from the Dominican Republic, India, Thailand, and Vietnam","volume":"81","author":"Zurfluh","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.diagmicrobio.2010.12.002","article-title":"Multiplex PCR for detection of acquired carbapenemase genes","volume":"70","author":"Poirel","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1093\/jac\/dkl481","article-title":"Multiplex PCR for rapid detection of genes encoding acquired metallo-\u03b2-lactamases","volume":"59","author":"Ellington","year":"2007","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1128\/jcm.33.1.24-27.1995","article-title":"Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci by PCR","volume":"33","author":"Evers","year":"1995","journal-title":"J. Clin. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1128\/JCM.38.3.1032-1035.2000","article-title":"Multiplex PCR for detection of genes for Staphylococcus aureus enterotoxins, exfoliative toxins, toxic shock syndrome toxin 1, and methicillin resistance","volume":"38","author":"Mehrotra","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1111\/j.1469-0691.2011.03715.x","article-title":"Rapid detection, differentiation and typing of methicillin-resistant Staphylococcus aureus harbouring either mecA or the new mecA homologue mecALGA251","volume":"18","author":"Stegger","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_57","unstructured":"CLSI (2018). Performance Standards for Antimicrobial Susceptibility Testing, CLSI. [28th ed.]."},{"key":"ref_58","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_59","unstructured":"Seemann, T. (2021, October 01). Shovill. Available online: https:\/\/github.com\/tseemann\/shovill."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","article-title":"Ribosomal multilocus sequence typing: Universal characterization of bacteria from domain to strain","volume":"158","author":"Jolley","year":"2012","journal-title":"Microbiology"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e20","DOI":"10.7717\/peerj-cs.20","article-title":"CFSAN SNP pipeline: An automated method for constructing snp matrices fromnext-generation sequence data","volume":"1","author":"Davis","year":"2015","journal-title":"PeerJ Comput. Sci."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/2\/213\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:15:56Z","timestamp":1760134556000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/2\/213"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,8]]},"references-count":64,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["antibiotics11020213"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics11020213","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,8]]}}}