{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T16:41:17Z","timestamp":1790181677373,"version":"4.1.0"},"reference-count":84,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,6,10]],"date-time":"2022-06-10T00:00:00Z","timestamp":1654819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Science and Technolog","award":["87310"],"award-info":[{"award-number":["87310"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Extended-spectrum beta-lactamase (ESBL)-producing bacteria are a major problem for public health worldwide because of limited treatment options. Currently, only limited information is available on ESBL-producing Shiga toxin-producing Escherichia coli (STEC) in cattle farms and the surrounding aquatic environment. This study sought to track and characterise ESBL-producing STEC disseminating from a cattle farm into the water environment. Animal husbandry soil (HS), animal manure (AM), animal drinking water (ADW), and nearby river water (NRW) samples were collected from the cattle farm. Presumptive ESBL-producing STEC were isolated and identified using chromogenic media and mass spectrophotometry methods (MALDI-TOF-MS), respectively. The isolates were subjected to molecular analysis, and all confirmed ESBL-producing STEC isolates were serotyped for their O serogroups and assessed for antibiotic resistance genes (ARGs) and for the presence of selected virulence factors (VFs). A phylogenetic tree based on the multilocus sequences was constructed to determine the relatedness among isolates of ESBL-producing STEC. The highest prevalence of ESBL-producing STEC of 83.33% was observed in HS, followed by ADW with 75%, NRW with 68.75%, and the lowest was observed in AM with 64.58%. Out of 40 randomly selected isolates, 88% (n = 35) belonged to the serogroup O45 and 13% (n = 5) to the serogroup O145. The multilocus sequence typing (MLST) analysis revealed four different sequence types (STs), namely ST10, ST23, ST165, and ST117, and the predominant ST was found to be ST10. All 40 isolates carried sul1 (100%), while blaOXA, blaCTX-M, sul2, blaTEM, and qnrS genes were found in 98%, 93%, 90%, 83%, and 23% of the 40 isolates, respectively. For VFs, only stx2 was detected in ESBL-producing STEC isolates. The results of the present study indicated that a cattle environment is a potential reservoir of ESBL-producing STEC, which may disseminate into the aquatic environment through agricultural runoff, thus polluting water sources. Therefore, continual surveillance of ESBL-producing STEC non-O157 would be beneficial for controlling and preventing STEC-related illnesses originating from livestock environments.<\/jats:p>","DOI":"10.3390\/pathogens11060674","type":"journal-article","created":{"date-parts":[[2022,6,12]],"date-time":"2022-06-12T23:55:24Z","timestamp":1655078124000},"page":"674","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Prevalence and Molecular Characterisation of Extended-Spectrum Beta-Lactamase-Producing Shiga Toxin-Producing Escherichia coli, from Cattle Farm to Aquatic Environments"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2284-6619","authenticated-orcid":false,"given":"Khuliso","family":"Ramaite","sequence":"first","affiliation":[{"name":"Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Pretoria 0001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mutshiene Deogratias","family":"Ekwanzala","sequence":"additional","affiliation":[{"name":"Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Pretoria 0001, South Africa"},{"name":"Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 41346 Gothenburg, Sweden"},{"name":"Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 41346 Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3537-0354","authenticated-orcid":false,"given":"Maggy Ndombo Benteke","family":"Momba","sequence":"additional","affiliation":[{"name":"Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Pretoria 0001, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"4823","DOI":"10.1002\/2014WR016869","article-title":"Water Management: Current and Future Challenges and Research Directions","volume":"51","author":"Cosgrove","year":"2015","journal-title":"Water Resour. Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1002\/gch2.1002","article-title":"Global Challenges: Water","volume":"1","author":"Butler","year":"2017","journal-title":"Glob. Challenges"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13568-014-0051-x","article-title":"Contamination of Water Resources by Pathogenic Bacteria","volume":"4","author":"Pandey","year":"2014","journal-title":"AMB Express"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Verlicchi, P., and Grillini, V. (2020). Surface Water and Groundwater Quality in South Africa and Mozambique\u2014Analysis of the Most Critical Pollutants for Drinking Purposes and Challenges in Water Treatment Selection. Waters, 12.","DOI":"10.3390\/w12010305"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Moropeng, R.C., Budeli, P., and Momba, M.N.B. (2021). An Integrated Approach to Hygiene, Sanitation, and Storage Practices for Improving Microbial Quality of Drinking Water Treated at Point of Use: A Case Study in Makwane Village, South Africa. Int. J. Environ. Res. Public Health, 18.","DOI":"10.3390\/ijerph18126313"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1080\/10643389.2019.1692611","article-title":"Understanding Human Health Risks Caused by Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARG) in Water Environments: Current Knowledge and Questions to Be Answered","volume":"50","author":"Amarasiri","year":"2019","journal-title":"Crit. Rev. Environ. Sci. Technol."},{"key":"ref_7","unstructured":"World Health Organization (2022). Antimicrobial Resistance Surveillance in Europe 2022\u20132020 Data, World Health Organization."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"401","DOI":"10.4314\/sajas.v48i3.1","article-title":"Importance and Implications of Antibiotic Resistance Development in Livestock and Wildlife Farming in South Africa: A Review","volume":"48","author":"Gouws","year":"2018","journal-title":"S. Afr. J. Anim. Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.jgar.2019.07.031","article-title":"Antibiotic Use in Food Animals Worldwide, with a Focus on Africa: Pluses and Minuses","volume":"20","author":"Van","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.4014\/jmb.1909.09030","article-title":"Mitigating Antibiotic Resistance at the Livestock-Environment Interface: A Review","volume":"29","author":"Ma","year":"2019","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.2147\/IDR.S173867","article-title":"Antibiotic Resistance: A Rundown of a Global Crisis","volume":"11","author":"Aslam","year":"2018","journal-title":"Infect. Drug Resist."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Agga, G.E., Cook, K.L., Netthisinghe, A.M.P., Gilfillen, R.A., Woosley, P.B., and Sistani, K.R. (2019). Persistence of Antibiotic Resistance Genes in Beef Cattle Backgrounding Environment over Two Years after Cessation of Operation. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0212510"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Yoshizawa, N., Usui, M., Fukuda, A., Asai, T., Higuchi, H., Okamoto, E., Seki, K., Takada, H., and Tamura, Y. (2020). Manure Compost Is a Potential Source of Tetracycline-Resistant Escherichia Coli and Tetracycline Resistance Genes in Japanese Farms. Antibiotics, 9.","DOI":"10.3390\/antibiotics9020076"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.2147\/IDR.S170715","article-title":"Systematic Review in South Africa Reveals Antibiotic Resistance Genes Shared between Clinical and Environmental Settings","volume":"11","author":"Ekwanzala","year":"2018","journal-title":"Infect. Drug Resist."},{"key":"ref_15","unstructured":"Mateo-Sagasta, J., Zadeh, S.M., and Turral, H. (2021, February 13). Water Pollution from Agriculture: A Global Review. FAO IWMI 2017, Volume 35. Available online: http:\/\/www.fao.org\/3\/a-i7754e.pdf."},{"key":"ref_16","unstructured":"WHO (2017). Global Priority List of Antibiotic-Resistant Batceria to Guide Research, Discovery, and Development of New Antibiotics, World Health Organization."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"14372","DOI":"10.1038\/srep14372","article-title":"Pathogenic Escherichia Coli Producing Extended-Spectrum \u03b2-Lactamases Isolated from Surface Water and Wastewater","volume":"5","author":"Franz","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1111\/jam.13468","article-title":"Environmental Escherichia Coli: Ecology and Public Health Implications\u2014a Review","volume":"123","author":"Jang","year":"2017","journal-title":"J. Appl. Microbiol."},{"key":"ref_19","first-page":"24","article-title":"Epidemiology of Shiga Toxin-Producing Escherichia Coli O157:H7 in Africa in Review","volume":"33","author":"Lupindu","year":"2018","journal-title":"South. Afr. J. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"366","DOI":"10.4161\/viru.24642","article-title":"Shiga Toxin-Producing Escherichia Coli: Factors Involved in Virulence and Cattle Colonization","volume":"4","author":"Padola","year":"2013","journal-title":"Virulence"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Kalule, J.B., Keddy, K.H., and Nicol, M.P. (2018). Characterisation of STEC and Other Diarrheic E. Coli Isolated on CHROMagarTMSTEC at a Tertiary Referral Hospital, Cape Town. BMC Microbiol., 18.","DOI":"10.1186\/s12866-018-1195-7"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Karama, M., Cenci Goga, B., Malahlela, M., Keddy, K., El-Ashram, S., and Lawan, K. (2019). Kalake Virulence Characteristics and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia Coli Isolates from Humans in South Africa: 2006\u20132013. Toxins, 11.","DOI":"10.3390\/toxins11070424"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1111\/zph.12491","article-title":"Occurrence and Characterization of Seven Major Shiga Toxin-Producing Escherichia Coli Serotypes from Healthy Cattle on Cow-Calf Operations in South Africa","volume":"65","author":"Mainga","year":"2018","journal-title":"Zoonoses Public Health"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"11930","DOI":"10.1038\/s41598-019-47948-1","article-title":"Molecular Profiling and Antimicrobial Resistance of Shiga Toxin-Producing Escherichia Coli O26, O45, O103, O121, O145 and O157 Isolates from Cattle on Cow-Calf Operations in South Africa","volume":"9","author":"Karama","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.4315\/0362-028X-73.9.1721","article-title":"Non-O157 Shiga Toxin\u2014Producing Escherichia Coli in Foods","volume":"73","author":"Mathusa","year":"2010","journal-title":"J. Food Prot."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"8662","DOI":"10.1128\/AEM.06190-11","article-title":"Serotypes and Virulence Profiles of Non-O157 Shiga Toxin-Producing Escherichia Coli Isolates from Bovine Farms","volume":"77","author":"Monaghan","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.resmic.2010.11.008","article-title":"Detection of Escherichia Coli O157:H7 Virulence Genes in Isolates from Beef, Pork, Water, Human and Animal Species in the Northwest Province, South Africa: Public Health Implications","volume":"162","author":"Ateba","year":"2011","journal-title":"Res. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1089\/fpd.2013.1704","article-title":"Global Incidence of Human Shiga Toxin-Producing Escherichia Coli Infections and Deaths: A Systematic Review and Knowledge Synthesis","volume":"11","author":"Majowicz","year":"2014","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.3201\/eid1808.111616","article-title":"Escherichia Coli O104 Associated with Human Diarrhea, South Africa, 2004\u20132011","volume":"18","author":"Tau","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1099\/acmi.0.000061","article-title":"Shiga Toxin-Producing Escherichia Coli O26:H11 Associated with a Cluster of Haemolytic Uraemic Syndrome Cases in South Africa, 2017","volume":"1","author":"Smith","year":"2019","journal-title":"Access Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1128\/CMR.00022-13","article-title":"Recent Advances in Understanding Enteric Pathogenic Escherichia Coli","volume":"26","author":"Croxen","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.scitotenv.2019.07.119","article-title":"Molecular Characteristics and Genotypic Diversity of Enterohaemorrhagic Escherichia Coli O157:H7 Isolates in Gauteng Region, South Africa","volume":"692","author":"Bolukaoto","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1016\/j.diagmicrobio.2010.11.011","article-title":"Characteristics of Infections Caused by Extended-Spectrum \u03b2-Lactamase-Producing Escherichia Coli FromC Community Hospitals in South Africa","volume":"69","author":"Peirano","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.diagmicrobio.2014.10.006","article-title":"Characterization of ESBL-Producing Escherichia Coli ST131 Isolates from Port Elizabeth","volume":"81","author":"Gqunta","year":"2015","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e03206","DOI":"10.1016\/j.heliyon.2020.e03206","article-title":"Extended-Spectrum Beta-Lactamase (ESBL)-Producing Enterobacteriaceae in Cattle Production \u2013 a Threat around the World","volume":"6","author":"Ferreira","year":"2020","journal-title":"Heliyon"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"4846159","DOI":"10.1155\/2018\/4846159","article-title":"Isolation of Extended-Spectrum \u03b2-Lactamase- (ESBL-) Producing Escherichia Coli and Klebsiella Pneumoniae from Patients with Community-Onset Urinary Tract Infections in Jimma University Specialized Hospital, Southwest Ethiopia","volume":"2018","author":"Abayneh","year":"2018","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1093\/cid\/cis942","article-title":"Community-Associated Extended-Spectrum \u03b2-Lactamase-Producing Escherichia Coli Infection in the United States","volume":"56","author":"Doi","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"4318306","DOI":"10.1155\/2019\/4318306","article-title":"Antimicrobial Resistance Factors of Extended-Spectrum Beta-Lactamases Producing Escherichia Coli and Klebsiella Pneumoniae Isolated from Cattle Farms and Raw Beef in North-West Province, South Africa","volume":"2019","author":"Montso","year":"2019","journal-title":"Biomed Res. Int."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.cimid.2015.12.004","article-title":"Occurrence of Non-O157 Shiga Toxin-Producing Escherichia Coli in Two Commercial Swine Farms in the Eastern Cape Province, South Africa","volume":"44","author":"Iwu","year":"2016","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"333","DOI":"10.3389\/fcimb.2019.00333","article-title":"The First Isolation and Molecular Characterization of Shiga Toxin-Producing Virulent Multi-Drug Resistant Atypical Enteropathogenic Escherichia Coli O177 Serogroup From South African Cattle","volume":"9","author":"Montso","year":"2019","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1017\/S0950268819000566","article-title":"Zoonotic Approach to Shiga Toxin-Producing Escherichia Coli: Integrated Analysis of Virulence and Antimicrobial Resistance in Ruminants and Humans","volume":"147","author":"Oporto","year":"2019","journal-title":"Epidemiol. Infect."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1111\/nyas.14036","article-title":"Complexities in Understanding Antimicrobial Resistance across Domesticated Animal, Human, and Environmental Systems","volume":"1441","author":"Graham","year":"2019","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1089\/fpd.2014.1770","article-title":"Prevalence of Escherichia Coli O157:H7 in Surface Water near Cattle Feedlots","volume":"11","author":"Tanaro","year":"2014","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1016\/j.scitotenv.2014.05.069","article-title":"Persistence of Escherichia Coli O157 and Non-O157 Strains in Agricultural Soils","volume":"490","author":"Ma","year":"2014","journal-title":"Sci. Total Environ."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature10388","article-title":"Antibiotic Resistance Is Ancient","volume":"477","author":"King","year":"2011","journal-title":"Nature"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2510","DOI":"10.3389\/fmicb.2017.02510","article-title":"Occurrence and Genomic Characterization of ESBL-Producing, MCR-1-Harboring Escherichia Coli in Farming Soil","volume":"8","author":"Zheng","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Manyi-Loh, C.E., Mamphweli, S.N., Meyer, E.L., Makaka, G., Simon, M., and Okoh, A.I. (2016). An Overview of the Control of Bacterial Pathogens in Cattle Manure. Int. J. Environ. Res. Public Health, 13.","DOI":"10.3390\/ijerph13090843"},{"key":"ref_48","first-page":"1","article-title":"Shiga Toxin-Producing Escherichia Coli (STEC) Ecology in Cattle and Management Based Options for Reducing Fecal Shedding","volume":"3","author":"Callaway","year":"2013","journal-title":"Agric. food Anal. Bacteriol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"15202","DOI":"10.1073\/pnas.1409836111","article-title":"Bloom of Resident Antibiotic-Resistant Bacteria in Soil Following Manure Fertilization","volume":"111","author":"Wichmann","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e02227-15","DOI":"10.1128\/mBio.02227-15","article-title":"Antimicrobial Resistance in Agriculture","volume":"7","author":"Thanner","year":"2016","journal-title":"MBio"},{"key":"ref_51","first-page":"1086","article-title":"Fate and Transport of Antibiotic Residues and Antibiotic Resistance Genes","volume":"1108","author":"Mackie","year":"2009","journal-title":"J. Environ. Qual."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Farrokh, C., Jordan, K., Auvray, F., Glass, K., Oppegaard, H., Raynaud, S., Thevenot, D., Condron, R., De Reu, K., and Govaris, A. (2012). International Journal of Food Microbiology Review of Shiga-Toxin-Producing Escherichia Coli (STEC ) and Their Signi Fi Cance in Dairy Production. Int. J. Food Microbiol.","DOI":"10.1016\/j.ijfoodmicro.2012.08.008"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"37","DOI":"10.2527\/af.2016-0021","article-title":"Shiga Toxin-Producing Escherichia Coli and Current Trends in Diagnostics","volume":"6","author":"Conrad","year":"2016","journal-title":"Anim. Front."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1128\/CMR.11.3.450","article-title":"Pathogenesis and Diagnosis of Shiga Toxin-Producing Escherichia Coli Infections","volume":"11","author":"Paton","year":"1998","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"e0159866","DOI":"10.1371\/journal.pone.0159866","article-title":"Influence of Season and Feedlot Location on Prevalence and Virulence Factors of Seven Serogroups of Escherichia Coli in Feces of Western-Canadian Slaughter Cattle","volume":"11","author":"Stanford","year":"2016","journal-title":"PLoS ONE"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1016\/j.vetmic.2012.10.015","article-title":"Characterization of Extended-Spectrum Beta-Lactamase (ESBL)-Carrying Plasmids and Clones of Enterobacteriaceae Causing Cattle Mastitis in France","volume":"162","author":"Dahmen","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2468","DOI":"10.1093\/jac\/dkt219","article-title":"Within-Farm Dynamics of ESBL\/AmpC-Producing Escherichia Coli in Veal Calves: A Longitudinal Approach","volume":"68","author":"Hordijk","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"16457","DOI":"10.1038\/s41598-019-52859-2","article-title":"The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia Coli Clinical Isolates from Pretoria, South Africa","volume":"9","author":"Mbelle","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-Spectrum Beta-Lactamases in the 21st Century: Characterization, Epidemiology, and Detection of This Important Resistance Threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_60","first-page":"28564","article-title":"Environmental Dissemination of Antibiotic Resistance Genes and Correlation to Anthropogenic Contamination with Antibiotics","volume":"5","author":"Berglund","year":"2015","journal-title":"Infect. Ecol. Epidemiol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"9519718","DOI":"10.1155\/2018\/9519718","article-title":"The Growing Genetic and Functional Diversity of Extended Spectrum Beta-Lactamases","volume":"2018","author":"Rahman","year":"2018","journal-title":"BioMed Res. Int."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/1040841X.2020.1715339","article-title":"Prevalence of Extended-Spectrum \u03b2-Lactamases in the Local Farm Environment and Livestock: Challenges to Mitigate Antimicrobial Resistance","volume":"46","author":"Lee","year":"2020","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/s13756-019-0552-0","article-title":"Distribution of Quinolone Resistance Gene (Qnr) in ESBL-Producing Escherichia Coli and Klebsiella Spp. in Lom\u00e9, Togo","volume":"8","author":"Salah","year":"2019","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Manyi-Loh, C., Mamphweli, S., Meyer, E., and Okoh, A. (2018). Antibiotic Use in Agriculture and Its Consequential Resistance in Environmental Sources: Potential Public Health Implications. Molecules, 23.","DOI":"10.3390\/molecules23040795"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/ijerph17020552","article-title":"Distribution of Antibiotic Resistance Genes in Three Different Natural Water Bodies-a Lake, River and Sea","volume":"17","author":"Su","year":"2020","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Iweriebor, B.C., Iwu, C.J., Obi, L.C., Nwodo, U.U., and Okoh, A.I. (2015). Multiple Antibiotic Resistances among Shiga Toxin Producing Escherichia Coli O157 in Feces of Dairy Cattle Farms in Eastern Cape of South Africa. BMC Microbiol., 15.","DOI":"10.1186\/s12866-015-0553-y"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1111\/j.1574-695X.2009.00564.x","article-title":"Detection of BlaSHV, BlaTEM and BlaCTX-M Antibiotic Resistance Genes in Randomly Selected Bacterial Pathogens from the Steve Biko Academic Hospital","volume":"56","author":"Ehlers","year":"2009","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e00148-20","DOI":"10.1128\/mSystems.00148-20","article-title":"Emergence of mcr-9.1 in Extended-Spectrum-\u03b2-Lactamase-Producing Clinical Enterobacteriaceae in Pretoria, South Africa: Global Evolutionary Phylogenomics, Resistome, and Mobilome","volume":"5","author":"Maningi","year":"2020","journal-title":"mSystems"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Ndlovu, T., Le Roux, M., Khan, W., and Khan, S. (2015). Co-Detection of Virulent Escherichia Coli Genes in Surface Water Sources. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0116808"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"4022","DOI":"10.1128\/JCM.01598-13","article-title":"Virulence Gene Profiles and Population Genetic Analysis for Exploration of Pathogenic Serogroups of Shiga Toxin-Producing Genus-Species Escherichia Coli","volume":"51","author":"Kobayashi","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13099-017-0169-x","article-title":"Prevalence, Virulence Potential, and Pulsed - Field Gel Electrophoresis Profiling of Shiga Toxin - Producing Escherichia Coli Strains from Cattle","volume":"9","author":"Dong","year":"2017","journal-title":"Gut Pathog."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/cid\/ciw708","article-title":"Emerging Public Health Challenges of Shiga Toxin-Producing Escherichia Coli Related to Changes in the Pathogen, the Population, and the Environment","volume":"64","author":"Griffin","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1128\/JCM.37.11.3491-3496.1999","article-title":"Escherichia Coli O157:H7 and O157:H(-) Strains That Do Not Produce Shiga Toxin: Phenotypic and Genetic Characterization of Isolates Associated with Diarrhea and Hemolytic-Uremic Syndrome","volume":"37","author":"Schmidt","year":"1999","journal-title":"J. Clin. Microbiol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/antibiotics10091038","article-title":"Human-Associated Methicillin-Resistant Staphylococcus Aureus Clonal Complex 80 Isolated from Cattle and Aquatic Environments","volume":"10","author":"Ramaite","year":"2021","journal-title":"Antibiotics"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.1007\/s11368-015-1081-y","article-title":"Development of a Rapid Approach for the Enumeration of Escherichia Coli in Riverbed Sediment: Case Study, the Apies River, South Africa","volume":"15","author":"Abia","year":"2015","journal-title":"J. Soils Sediments"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1089\/fpd.2010.0769","article-title":"Detection of Shiga Toxin\u2013Producing Escherichia Coli O26, O45, O103, O111, O113, O121, O145, and O157 Serogroups by Multiplex Polymerase Chain Reaction of the Wzx Gene of the O-Antigen Gene Cluster","volume":"8","author":"DebRoy","year":"2011","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","article-title":"Sex and Virulence in Escherichia Coli: An Evolutionary Perspective","volume":"60","author":"Wirth","year":"2006","journal-title":"Mol. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"6932","DOI":"10.1007\/s11356-014-3905-5","article-title":"Occurrence of Sulfonamide-, Tetracycline-, Plasmid-Mediated Quinolone- and Macrolide-Resistance Genes in Livestock Feedlots in Northern China","volume":"22","author":"Mu","year":"2015","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1089\/mdr.2016.0082","article-title":"Characterizing the Multidrug Resistance of Non-O157 Shiga Toxin-Producing Escherichia Coli Isolates from Cattle Farms and Abattoirs","volume":"23","author":"Kennedy","year":"2017","journal-title":"Microb. Drug Resist."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"278","DOI":"10.3934\/microbiol.2016.3.278","article-title":"Incidence of Top 6 Shiga Toxigenic Escherichia Coli within Two Ontario Beef Processing Facilities: Challenges in Screening and Confirmation Testing","volume":"2","author":"Bannon","year":"2016","journal-title":"AIMS Microbiol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Edgar, R.C. (2004). MUSCLE: A Multiple Sequence Alignment Method with Reduced Time and Space Complexity. BMC Bioinformatics, 5.","DOI":"10.1186\/1471-2105-5-113"},{"key":"ref_83","first-page":"512","article-title":"Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees","volume":"10","author":"Tamura","year":"1993","journal-title":"Mol. Biol. Evol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive Tree of Life (ITOL) v3: An Online Tool for the Display and Annotation of Phylogenetic and Other Trees","volume":"44","author":"Letunic","year":"2016","journal-title":"Nucleic Acids Res."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/11\/6\/674\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:27:54Z","timestamp":1760138874000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/11\/6\/674"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,10]]},"references-count":84,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6]]}},"alternative-id":["pathogens11060674"],"URL":"https:\/\/doi.org\/10.3390\/pathogens11060674","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,10]]}}}