{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:32:52Z","timestamp":1790703172704,"version":"4.1.0"},"reference-count":41,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>This study is designed to investigate Escherichia coli for the antibiotic resistance genes (ARGs) and integrons from healthy as well as diarrhoeic\/diseased animals\/birds\u2019 faecal samples. A total of eight samples were selected for the study; from each animal, two samples were taken, one from healthy animals\/birds and one from diarrhoeic\/diseased animals\/birds. Antibiotic sensitivity testing (AST) and whole genome sequencing (WGS) was performed for selected isolates. The E. coli isolates showed resistance to moxifloxacin, followed by erythromycin, ciprofloxacin, pefloxacin, tetracycline, levofloxacin, ampicillin, amoxicillin, and sulfadiazine (4\/8, 50.00% each). The E. coli isolates were 100% sensitive to amikacin, followed by chloramphenicol, cefixime, cefoperazone, and cephalothin. A total of 47 ARGs from 12 different antibiotic classes were detected among the eight isolates by WGS. The different classes of antibiotics included aminoglycoside, sulphonamide, tetracycline, trimethoprim, quinolone, fosfomycin, phenicol, macrolide, colistin, fosmidomycin, and multidrug efflux. The class 1 integrons were detected in 6\/8 (75.00%) isolates with 14 different gene cassettes.<\/jats:p>","DOI":"10.3390\/genes14061212","type":"journal-article","created":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T04:21:27Z","timestamp":1685593287000},"page":"1212","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Profiling of Antimicrobial Resistance Genes and Integron from Escherichia coli Isolates Using Whole Genome Sequencing"],"prefix":"10.3390","volume":"14","author":[{"given":"Harshrajsinh B.","family":"Joddha","sequence":"first","affiliation":[{"name":"Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafiyuddin A.","family":"Mathakiya","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuldip V.","family":"Joshi","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ravindra B.","family":"Khant","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akash V.","family":"Golaviya","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8985-4541","authenticated-orcid":false,"given":"Ankit T.","family":"Hinsu","sequence":"additional","affiliation":[{"name":"Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6402-5774","authenticated-orcid":false,"given":"Mansi R.","family":"Desai","sequence":"additional","affiliation":[{"name":"Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3246-8834","authenticated-orcid":false,"given":"Subhash J.","family":"Jakhesara","sequence":"additional","affiliation":[{"name":"Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prakash G.","family":"Koringa","sequence":"additional","affiliation":[{"name":"Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,6,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6235","DOI":"10.3390\/ijerph10126235","article-title":"Escherichia coli in Europe: An overview","volume":"10","author":"Allocati","year":"2013","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1128\/microbiolspec.ARBA-0026-2017","article-title":"Antimicrobial resistance in Escherichia coli","volume":"6","author":"Poirel","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Messele, Y.E., Alkhallawi, M., Veltman, T., Trott, D.J., McMeniman, J.P., Kidd, S.P., Low, W.Y., and Petrovski, K.R. (2022). Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia. Animals, 12.","DOI":"10.3390\/ani12172256"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nrmicro1325","article-title":"Antimicrobial-resistant bacteria in the community setting","volume":"4","author":"Furuya","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.rvsc.2010.02.016","article-title":"Phenotypic and genotypic characteristics of antimicrobial resistant Escherichia coli isolated from symbovine flies, cattle and sympatric insectivorous house martins from a farm in the Czech Republic (2006\u20132007)","volume":"89","author":"Materna","year":"2010","journal-title":"Res. Vet. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Puva\u010da, N., and de Llanos Frutos, R. (2021). Antimicrobial resistance in escherichia coli strains isolated from humans and Pet animals. Antibiotics, 10.","DOI":"10.3390\/antibiotics10010069"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Massella, E., Reid, C.J., Cummins, M.L., Anantanawat, K., Zingali, T., Serraino, A., Piva, S., Giacometti, F., and Djordjevic, S.P. (2020). Snapshot study of whole genome sequences of Escherichia coli from healthy companion animals, livestock, wildlife, humans and food in Italy. Antibiotics, 9.","DOI":"10.3390\/antibiotics9110782"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"317","DOI":"10.2217\/fmb.15.2","article-title":"Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota","volume":"10","author":"Anjum","year":"2015","journal-title":"Future Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.3389\/fmicb.2018.02066","article-title":"Antibiotics, resistome and resistance mechanisms: A bacterial perspective","volume":"9","author":"Sultan","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_10","first-page":"72","article-title":"Therapeutic limitations due to antibiotic drug resistance: Road to alternate therapies","volume":"3","author":"Bhardwaj","year":"2014","journal-title":"Front. Anti-Infect. Drug Discov."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1515\/CCLM.2000.070","article-title":"Integrons: An antibiotic resistance gene capture and expression system","volume":"38","author":"Ploy","year":"2000","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Ghaly, T.M., Gillings, M.R., Penesyan, A., Qi, Q., Rajabal, V., and Tetu, S.G. (2021). The natural history of integrons. Microorganisms, 9.","DOI":"10.3390\/microorganisms9112212"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1078\/1438-4221-00197","article-title":"The role of integrons in antibiotic resistance gene capture","volume":"292","author":"Mazel","year":"2002","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s12941-015-0100-6","article-title":"Resistance integrons: Class 1, 2 and 3 integrons","volume":"14","author":"Deng","year":"2015","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"459","DOI":"10.12688\/f1000research.14509.2","article-title":"The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies","volume":"7","author":"Petrillo","year":"2018","journal-title":"F1000Research"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"N\u00e9ron, B., Littner, E., Haudiquet, M., Perrin, A., Cury, J., and Rocha, E.P. (2022). IntegronFinder 2.0: Identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella. Microorganisms, 10.","DOI":"10.1101\/2022.02.28.482270"},{"key":"ref_18","first-page":"74","article-title":"Antimicrobial resistance pattern of Escherichia coli isolated from chickens with colibacillosis in Yazd, Iran","volume":"4","author":"Bakhshi","year":"2017","journal-title":"J. Food Qual. Hazards Control"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Touzain, F., Le Devendec, L., de Boiss\u00e9son, C., Baron, S., Jouy, E., Perrin-Guyomard, A., Blanchard, Y., and Kempf, I. (2018). Characterization of plasmids harboring bla CTX-M and bla CMY genes in E. coli from French broilers. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0188768"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"98","DOI":"10.12691\/jfnr-10-2-3","article-title":"Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Escherichia coli Isolates from Chicken Meat","volume":"10","author":"Elsharawy","year":"2022","journal-title":"J. Food Nutr. Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Awad, A.M., El-Shall, N.A., Khalil, D.S., El-Hack, M.E.A., Swelum, A.A., Mahmoud, A.H., Ebaid, H., Komany, A., Sammour, R.H., and Sedeik, M.E. (2020). Incidence, pathotyping, and antibiotic susceptibility of avian pathogenic Escherichia coli among diseased broiler chicks. Pathogens, 9.","DOI":"10.3390\/pathogens9020114"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Meshref, A.-M.E., Eldesoukey, I.E., Alouffi, A.S., Alrashedi, S.A., Osman, S.A., and Ahmed, A.M. (2021). Molecular analysis of antimicrobial resistance among Enterobacteriaceae isolated from diarrhoeic calves in Egypt. Animals, 11.","DOI":"10.3390\/ani11061712"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"8264583","DOI":"10.1155\/2017\/8264583","article-title":"Cloacael carriage and multidrug resistance Escherichia coli O157: H7 from poultry farms, eastern Ethiopia","volume":"2017","author":"Shecho","year":"2017","journal-title":"J. Vet. Med."},{"key":"ref_24","first-page":"304","article-title":"Insights into antimicrobial resistance and virulence genes of emergent multidrug resistant avian pathogenic Escherichia coli in Egypt: How closely related are they","volume":"166","author":"Ammar","year":"2015","journal-title":"Rev. Med. Vet."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"877","DOI":"10.3168\/jds.2019-16560","article-title":"Whole-genome sequence analysis of 4 fecal blaCMY-2-producing Escherichia coli isolates from Holstein dairy calves","volume":"103","author":"Awosile","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1089\/fpd.2020.2901","article-title":"Genomic Analysis of Antibiotic-Resistant and-Susceptible Escherichia coli Isolated from Bovine Sources in Maputo, Mozambique","volume":"18","author":"Taviani","year":"2021","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"584","DOI":"10.3389\/fmicb.2020.00584","article-title":"Deadly Puppy Infection Caused by an MDR Escherichia coli O39 bla CTX\u2013M\u201315, bla CMY\u20132, bla DHA\u20131, and aac (6)-Ib-cr\u2013Positive in a Breeding Kennel in Central Italy","volume":"11","author":"Bitar","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Haley, B.J., Kim, S.W., Salaheen, S., Hovingh, E., and Van Kessel, J.A.S. (2022). Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0265445"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.foodcont.2018.12.043","article-title":"Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods","volume":"99","author":"Guo","year":"2019","journal-title":"Food Control"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Roedel, A., Vincze, S., Projahn, M., Roesler, U., Rob\u00e9, C., Hammerl, J.A., Noll, M., Al Dahouk, S., and Dieckmann, R. (2021). Genetic but no phenotypic associations between biocide tolerance and antibiotic resistance in Escherichia coli from German broiler fattening farms. Microorganisms, 9.","DOI":"10.3390\/microorganisms9030651"},{"key":"ref_31","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_32","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1089\/fpd.2017.2394","article-title":"Molecular characterization of Escherichia coli isolated from chickens with colibacillosis in Senegal","volume":"15","author":"Vounba","year":"2018","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_33","first-page":"e000250","article-title":"Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene","volume":"5","author":"Cummins","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"674","DOI":"10.3389\/fmicb.2020.00674","article-title":"Molecular characterization of fecal extended-spectrum \u03b2-lactamase-and AmpC \u03b2-lactamase-producing Escherichia coli from healthy companion animals and cohabiting humans in South Korea","volume":"11","author":"Hong","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Athanasakopoulou, Z., Reinicke, M., Diezel, C., Sofia, M., Chatzopoulos, D.C., Braun, S.D., Reissig, A., Spyrou, V., Monecke, S., and Ehricht, R. (2021). Antimicrobial resistance genes in ESBL-producing Escherichia coli isolates from animals in Greece. Antibiotics, 10.","DOI":"10.3390\/antibiotics10040389"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.4315\/0362-028X.JFP-13-510","article-title":"Characterization of antibiotic resistance in Escherichia coli isolated from shrimps and their environment","volume":"77","author":"Changkaew","year":"2014","journal-title":"J. Food Prot."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"103821","DOI":"10.1016\/j.fm.2021.103821","article-title":"Whole-genome sequencing analysis of uncommon Shiga toxin-producing Escherichia coli from cattle: Virulence gene profiles, antimicrobial resistance predictions, and identification of novel O-serogroups","volume":"99","author":"Huang","year":"2021","journal-title":"Food Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Afridi, O.K., Ali, J., and Chang, J.H. (2020). Next-generation sequencing based gut resistome profiling of broiler chickens infected with multidrug-resistant Escherichia coli. Animals, 10.","DOI":"10.3390\/ani10122350"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.femsle.2005.03.021","article-title":"Characterization of class 1 integrons-mediated antibiotic resistance among calf pathogenic Escherichia coli","volume":"245","author":"Du","year":"2005","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3036","DOI":"10.3382\/ps.2013-03312","article-title":"Characterization of integrons and their cassettes in Escherichia coli and Salmonella isolates from poultry in Korea","volume":"92","author":"Dessie","year":"2013","journal-title":"Poult. Sci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.3855\/jidc.4222","article-title":"Antibiotic resistance and resistance genes in Escherichia coli from poultry farms, southwest Nigeria","volume":"8","author":"Adelowo","year":"2014","journal-title":"J. Infect. Dev. Ctries."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/14\/6\/1212\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:46:56Z","timestamp":1760125616000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/14\/6\/1212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,1]]},"references-count":41,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,6]]}},"alternative-id":["genes14061212"],"URL":"https:\/\/doi.org\/10.3390\/genes14061212","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,1]]}}}