{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T10:16:38Z","timestamp":1790417798487,"version":"4.1.0"},"reference-count":73,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T00:00:00Z","timestamp":1614297600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Canadian Federal Genomics Research and Development Initiative","award":["GRDI"],"award-info":[{"award-number":["GRDI"]}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2015-04871"],"award-info":[{"award-number":["RGPIN-2015-04871"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Antibiotic resistance (AR) phenotypes and acquired resistance determinants (ARDs) detected by in silico analysis of genome sequences were examined in 55 Shiga toxin-producing Escherichia coli (STEC) isolates representing diverse serotypes recovered from surfaces waters and sediments in a mixed use urban\/agricultural landscape in British Columbia, Canada. The isolates displayed decreased susceptibility to florfenicol (65.5%), chloramphenicol (7.3%), tetracycline (52.7%), ampicillin (49.1%), streptomycin (34.5%), kanamycin (20.0%), gentamycin (10.9%), amikacin (1.8%), amoxicillin\/clavulanic acid (21.8%), ceftiofur (18.2%), ceftriaxone (3.6%), trimethoprim-sulfamethoxazole (12.7%), and cefoxitin (3.6%). All surface water and sediment isolates were susceptible to ciprofloxacin, nalidixic acid, ertapenem, imipenem and meropenem. Eight isolates (14.6%) were multidrug resistant. ARDs conferring resistance to phenicols (floR), trimethoprim (dfrA), sulfonamides (sul1\/2), tetracyclines (tetA\/B), and aminoglycosides (aadA and aph) were detected. Additionally, narrow-spectrum \u03b2-lactamase blaTEM-1b and extended-spectrum AmpC \u03b2-lactamase (cephalosporinase) blaCMY-2 were detected in the genomes, as were replicons from plasmid incompatibility groups IncFII, IncB\/O\/K\/Z, IncQ1, IncX1, IncY and Col156. A comparison with surveillance data revealed that AR phenotypes and ARDs were comparable to those reported in generic E. coli from food animals. Aquatic environments in the region are potential reservoirs for the maintenance and transmission of antibiotic resistant STEC, associated ARDs and their plasmids.<\/jats:p>","DOI":"10.3390\/antibiotics10030237","type":"journal-article","created":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T21:02:34Z","timestamp":1614373354000},"page":"237","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8075-6104","authenticated-orcid":false,"given":"Yvonne","family":"Ma","sequence":"first","affiliation":[{"name":"Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Chen","sequence":"additional","affiliation":[{"name":"Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Fong","sequence":"additional","affiliation":[{"name":"Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Nadya","sequence":"additional","affiliation":[{"name":"Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Allen","sequence":"additional","affiliation":[{"name":"Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chad","family":"Laing","sequence":"additional","affiliation":[{"name":"National Centre for Animal Diseases, Canadian Food Inspection Agency, Lethbridge, AB T1J 3Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim","family":"Ziebell","sequence":"additional","affiliation":[{"name":"Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ed","family":"Topp","sequence":"additional","affiliation":[{"name":"London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura M.","family":"Carroll","sequence":"additional","affiliation":[{"name":"Department of Food Science, Cornell University, Ithaca, NY 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4168-5662","authenticated-orcid":false,"given":"Martin","family":"Wiedmann","sequence":"additional","affiliation":[{"name":"Department of Food Science, Cornell University, Ithaca, NY 14853, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascal","family":"Delaquis","sequence":"additional","affiliation":[{"name":"Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2468-2483","authenticated-orcid":false,"given":"Siyun","family":"Wang","sequence":"additional","affiliation":[{"name":"Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,2,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1056\/NEJM198303243081203","article-title":"hemorrhagic colitis associated with a rare Escherichia coli serotype","volume":"308","author":"Riley","year":"1983","journal-title":"N. Engl. J. Med."},{"key":"ref_2","first-page":"1073","article-title":"Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome","volume":"365","author":"Tarr","year":"2005","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.2215\/CJN.08921209","article-title":"Acute neurological involvement in diarrhea-associated hemolytic uremic syndrome","volume":"5","author":"Nathanson","year":"2010","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Melton-Celsa, A., Mohawk, K., Teel, L., and O\u2019Brien, A. (2011). Pathogenesis of Shiga-Toxin Producing Escherichia coli, Springer.","DOI":"10.1007\/82_2011_176"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e236","DOI":"10.1017\/S095026881900116X","article-title":"Global and regional source attribution of Shiga toxin-producing Escherichia coli infections using analysis of outbreak surveillance data","volume":"147","author":"Pires","year":"2019","journal-title":"Epidemiol. Infect."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Goldwater, P.N., and Bettelheim, K.A. (2012). Treatment of enterohemorrhagic Escherichia coli (EHEC) infection and hemolytic uremic syndrome (HUS). BMC Med., 10.","DOI":"10.1186\/1741-7015-10-12"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1086\/315239","article-title":"Quinolone antibiotics induce shiga toxin\u2013encoding bacteriophages, toxin production, and death in mice","volume":"181","author":"Zhang","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2440","DOI":"10.1093\/jac\/dkv162","article-title":"Antibiotic treatment of verocytotoxin-producing Escherichia coli (VTEC) infection: A systematic review and a proposal","volume":"70","author":"Agger","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e4565","DOI":"10.1136\/bmj.e4565","article-title":"Validation of treatment strategies for enterohaemorrhagic Escherichia coli O104:H4 induced haemolytic uraemic syndrome: Case-control study","volume":"345","author":"Menne","year":"2012","journal-title":"BMJ"},{"key":"ref_10","first-page":"75","article-title":"STEC as a veterinary problem. Diagnostics and prophylaxis in animals","volume":"73","author":"Wieler","year":"2003","journal-title":"Methods Mol. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.3389\/fmicb.2015.01536","article-title":"Race against antimicrobial resistance requires coordinated action\u2014An overview","volume":"6","author":"Premanandh","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1016\/S1473-3099(13)70318-9","article-title":"Antibiotic resistance\u2014The need for global solutions","volume":"13","author":"Laxminarayan","year":"2013","journal-title":"Lancet Infect. Dis."},{"key":"ref_13","unstructured":"World Health Organization (WHO) (2021, January 18). Antimicrobial Resistance Global Report on Surveillance 2014. Available online: http:\/\/www.who.int\/drugresistance\/documents\/surveillancereport\/en."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1093\/infdis\/170.6.1606","article-title":"Characteristics of antibiotic-resistant Escherichia coli O157:H7 in Washington State, 1984\u20131991","volume":"170","author":"Kim","year":"1994","journal-title":"J. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1128\/AEM.67.4.1558-1564.2001","article-title":"Identification and characterization of integron-mediated antibiotic resistance among Shiga toxin-producing Escherichia coli isolates","volume":"67","author":"Zhao","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1093\/jac\/dki161","article-title":"Identification of antimicrobial resistance and class 1 integrons in Shiga toxin-producing Escherichia coli recovered from humans and food animals","volume":"56","author":"Singh","year":"2005","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1089\/fpd.2005.2.348","article-title":"Antimicrobial resistance and class 1 integrons in pathogenic Escherichia coli from dairy farms","volume":"2","author":"Murinda","year":"2005","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1093\/jac\/dkl127","article-title":"Phenotypic and genotypic characterization of antimicrobial resistance in Escherichia coli O111 isolates","volume":"57","author":"Guerra","year":"2006","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.vetmic.2009.04.011","article-title":"Verocytotoxin-producing Escherichia coli (VTEC)","volume":"140","author":"Karmali","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/nrmicro3380","article-title":"Molecular mechanisms of antibiotic resistance","volume":"13","author":"Blair","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1111\/j.1365-2958.1989.tb00153.x","article-title":"A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: Integrons","volume":"3","author":"Stokes","year":"1989","journal-title":"Mol. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1128\/MMBR.00056-13","article-title":"Integrons: Past, Present, and Future","volume":"78","author":"Gillings","year":"2014","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1128\/AAC.01707-08","article-title":"Resistance plasmid families in Enterobacteriaceae","volume":"53","author":"Carattoli","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"242","DOI":"10.3389\/fmicb.2015.00242","article-title":"Genomics of microbial plasmids: Classification and identification based on replication and transfer systems and host taxonomy","volume":"6","author":"Shintani","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.plasmid.2015.12.001","article-title":"Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids","volume":"83","author":"Losada","year":"2016","journal-title":"Plasmid"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tig.2014.07.003","article-title":"Whole-genome sequencing to control antimicrobial resistance","volume":"30","author":"Ellington","year":"2014","journal-title":"Trends Genet."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1093\/jac\/dkv186","article-title":"WGS accurately predicts antimicrobial resistance in Escherichia coli","volume":"70","author":"Tyson","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"36","DOI":"10.3389\/fcimb.2016.00036","article-title":"Phenotypic and genotypic characteristics of Shiga toxin-producing Escherichia coli isolated from surface waters and sediments in a Canadian urban-agricultural landscape","volume":"6","author":"Nadya","year":"2016","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"E63","DOI":"10.2527\/jas.2006-421","article-title":"Prevalence and pathogenicity of Shiga toxin-producing Escherichia coli in beef cattle and their products","volume":"85","author":"Hussein","year":"2007","journal-title":"J. Anim. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"143","DOI":"10.3389\/fcimb.2016.00143","article-title":"Molecular and phylogenetic characterization of non-O157 Shiga toxin-producing Escherichia coli strains in China","volume":"6","author":"Bai","year":"2016","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1089\/fpd.2008.0096","article-title":"DNA Sequencing and identification of serogroup-specific genes in the Escherichia coli O118 O antigen gene cluster and demonstration of antigenic diversity but only minor variation in DNA sequence of the O antigen clusters of E. coli O118 and O151","volume":"5","author":"Liu","year":"2008","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Wu, G., Day, M.J., Mafura, M.T., Nunez-Garcia, J., Fenner, J.J., Sharma, M., Van Essen-Zandbergen, A., Rodr\u00edguez, I., Dierikx, C., and Kadlec, K. (2013). Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0075392"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1128\/MMBR.00015-09","article-title":"Pathogenomics of the Virulence Plasmids of Escherichia coli","volume":"73","author":"Johnson","year":"2009","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1093\/jac\/dks369","article-title":"Complete nucleotide sequence of pHN7A8, an F33:A-:B- type epidemic plasmid carrying blaCTX-M-65, fosA3 and rmtB from China","volume":"68","author":"He","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.plasmid.2012.03.001","article-title":"Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae","volume":"68","author":"Johnson","year":"2012","journal-title":"Plasmid"},{"key":"ref_37","first-page":"1","article-title":"Characteristics of clinical Shiga toxin-producing Escherichia coli Isolated from British Columbia","volume":"2013","author":"Allen","year":"2013","journal-title":"BioMed Res. Int."},{"key":"ref_38","unstructured":"Health Canada (2021, January 18). Categorization of Antimicrobial Drugs Based on Importance in Human Medicine, Available online: https:\/\/www.canada.ca\/en\/health-canada\/services\/drugs-health-products\/veterinary-drugs\/antimicrobial-resistance\/categorization-antimicrobial-drugs-based-importance-human-medicine.html."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.scitotenv.2012.10.106","article-title":"Phenotypic antibiotic resistance of Escherichia coli and E. coli O157 isolated from water, sediment and biofilms in an agricultural watershed in British Columbia","volume":"443","author":"Bartlett","year":"2013","journal-title":"Sci. Total. Environ."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.4315\/0362-028X-61.11.1511","article-title":"Antibiotic resistance of Escherichia coli O157:H7 and O157:NM isolated from animals, food, and humans","volume":"61","author":"Meng","year":"1998","journal-title":"J. Food Prot."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"4170","DOI":"10.1128\/AEM.00537-13","article-title":"Assessment of virulence factors characteristic of human Escherichia coli pathotypes and antimicrobial resistance in O157:H7 and non-O157:H7 isolates from livestock in Spain","volume":"79","author":"Cabal","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_42","first-page":"74","article-title":"Genetic characterization of Shiga toxin-producing Escherichia coli O26:H11 strains isolated from animal, food, and clinical samples","volume":"5","author":"Lucchesi","year":"2015","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_43","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_44","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1093\/jac\/dkw371","article-title":"Antimicrobial resistance in Shiga toxin-producing Escherichia coli serogroups O157 and O26 isolated from human cases of diarrhoeal disease in England, 2015","volume":"72","author":"Day","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1016\/j.resmic.2005.03.006","article-title":"Antimicrobial resistance of Shiga toxin (verotoxin)-producing Escherichia coli O157:H7 and non-O157 strains isolated from humans, cattle, sheep and food in Spain","volume":"156","author":"Mora","year":"2005","journal-title":"Res. Microbiol."},{"key":"ref_46","unstructured":"Centers for Disease Control and Prevention (CDC) (2021, January 18). National Antimicrobial Resistance Monitoring System for Enteric Bacteria, Available online: https:\/\/www.cdc.gov\/narms\/index.html."},{"key":"ref_47","unstructured":"British Columbia Center of Disease Control (BCCDC) (2021, January 18). Antimicrobial Resistance Trends in the Province of British Columbia, Available online: http:\/\/www.bccdc.ca\/resource-gallery\/Documents\/AMR%202014%20Report-3NOV2015_FINAL.pdf."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1016\/j.tim.2014.04.007","article-title":"Fluoroquinolone resistance: Mechanisms, impact on bacteria, and role in evolutionary success","volume":"22","author":"Redgrave","year":"2014","journal-title":"Trends Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Fasugba, O., Gardner, A., Mitchell, B.G., and Mnatzaganian, G. (2015). Ciprofloxacin resistance in community- and hospital-acquired Escherichia coli urinary tract infections: A systematic review and meta-analysis of observational studies. BMC Infect. Dis., 15.","DOI":"10.1186\/s12879-015-1282-4"},{"key":"ref_50","unstructured":"Public Health Agency of Canada (PHAC) (2021, February 01). Human Antimicrobial Use Report, Available online: https:\/\/www.canada.ca\/en\/public-health\/services\/publications\/drugs-health-products\/human-antimicrobial-use-report-2014.html."},{"key":"ref_51","unstructured":"Public Health Agency of Canada (PHAC) (2021, February 01). Antimicrobial Resistance Surveillance System (CARSS) Report, Available online: https:\/\/www.canada.ca\/en\/public-health\/services\/publications\/drugs-health-products\/canadian-antimicrobial-resistance-surveillance-system-report-2016.html."},{"key":"ref_52","first-page":"1160","article-title":"Trends in antimicrobial use in Marine Harvest Canada farmed salmon production in British Columbia (2003\u20132011)","volume":"54","author":"Morrison","year":"2013","journal-title":"Can. Vet. J."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e02703-16","DOI":"10.1128\/AEM.02703-16","article-title":"Whole-genome analysis of antimicrobial-resistant and extraintestinal pathogenic Escherichia coli in river water","volume":"83","author":"Gomi","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1128\/AEM.01445-06","article-title":"Occurrence of virulence and antimicrobial resistance genes in Escherichia coli isolates from different aquatic ecosystems within the St. Clair River and Detroit River Areas","volume":"73","author":"Hamelin","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.ijheh.2016.07.015","article-title":"Antibiotic resistance and virulence genes in coliform water isolates","volume":"219","author":"Stange","year":"2016","journal-title":"Int. J. Hyg. Environ. Health"},{"key":"ref_56","first-page":"173","article-title":"Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer","volume":"7","author":"Penders","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_57","first-page":"1","article-title":"Acquired antibiotic resistance genes: An overview","volume":"2","author":"Mevius","year":"2011","journal-title":"Front. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Dougherty, T.J., and Pucci, M.J. (2012). Efflux-mediated antimicrobial resistance. Antibiotic Discovery and Development, Springer.","DOI":"10.1007\/978-1-4614-1400-1"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1128\/CMR.00036-08","article-title":"AmpC \u03b2-lactamases","volume":"22","author":"Jacoby","year":"2009","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1093\/jac\/dkh007","article-title":"Molecular analysis of florfenicol-resistant Escherichia coli isolates from pigs","volume":"53","author":"Blickwede","year":"2004","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1099\/jmm.0.016162-0","article-title":"Plasmid-borne florfenicol and ceftiofur resistance encoded by the floR and blaCMY-2 genes in Escherichia coli isolates from diseased cattle in France","volume":"59","author":"Meunier","year":"2010","journal-title":"J. Med. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1492","DOI":"10.1093\/jac\/dku011","article-title":"High diversity of plasmids harbouring blaCMY-2 among clinical Escherichia coli isolates from humans and companion animals in the upper Midwestern USA","volume":"69","author":"Bortolaia","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Falardeau, J., Johnson, R.P., Pagotto, F., and Wang, S. (2017). Occurrence, characterization, and potential predictors of verotoxigenic Escherichia coli, Listeria monocytogenes, and Salmonella in surface water used for produce irrigation in the Lower Mainland of British Columbia, Canada. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0185437"},{"key":"ref_64","first-page":"49","article-title":"Antibiotic susceptibility testing by a standardized single disk method","volume":"36","author":"Bauer","year":"1966","journal-title":"Tech. Bull. Regist. Med. Technol."},{"key":"ref_65","unstructured":"Clinical and Laboratory Standards Institute (CLSI) (2011). Performance Standards for Antimicrobial Susceptibility Testing: Twenty-First Informational Supplement, Clinical and Laboratory Standards Institute. CLSI Document M100-S21."},{"key":"ref_66","unstructured":"Clinical and Laboratory Standards Institute (CLSI) (2018). Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals, Clinical and Laboratory Standards Institute. [5th ed.]."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1476-0711-9-12","article-title":"Antimicrobial resistance in equine faecal Escherichia coli isolates from North West England","volume":"9","author":"Ahmed","year":"2010","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Fong, K., Lu, Y.T.L., Brenner, T., Falardeau, J., and Wang, S. (2021). CRISPR and prophage diversity across Salmonella & verotoxin-producing Escherichia coli. BMC Genom.","DOI":"10.3389\/fmicb.2022.853703"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"D57","DOI":"10.1093\/nar\/gkr1163","article-title":"BioProject and BioSample databases at NCBI: Facilitating capture and organization of metadata","volume":"40","author":"Barrett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/bioinformatics\/btq284","article-title":"A computational genomics pipeline for prokaryotic sequencing projects","volume":"26","author":"Kislyuk","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree of Life (iTOL) v4: Recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Walter, J., Noll, I., Feig, M., Weiss, B., Claus, H., Werner, G., Eckmanns, T., Hermes, J., and Abu Sin, M. (2017). Decline in the proportion of methicillin resistance among Staphylococcus aureus isolates from non-invasive samples and in outpatient settings, and changes in the co-resistance profiles: An analysis of data collected within the Antimicrobial Resistance Surveillance Network, Germany 2010 to 2015. BMC Infect. Dis., 17.","DOI":"10.1186\/s12879-017-2271-6"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/3\/237\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:29:37Z","timestamp":1760160577000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/3\/237"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,26]]},"references-count":73,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2021,3]]}},"alternative-id":["antibiotics10030237"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics10030237","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,26]]}}}