{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T21:41:12Z","timestamp":1786657272806,"version":"build-2736575974"},"reference-count":48,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Science and Technology Program Projects of the Inner Mongolia Autonomous Region","award":["2025YFDZ0091"],"award-info":[{"award-number":["2025YFDZ0091"]}]},{"name":"Central Government Guidance Fund for Local Science and Technology Development Projects","award":["2025ZY0147"],"award-info":[{"award-number":["2025ZY0147"]}]},{"name":"\u201cGovernment-Industry-Academia-Research-Funding\u201d Innovation Consortium Project","award":["2022RC-Consortium-1"],"award-info":[{"award-number":["2022RC-Consortium-1"]}]},{"name":"Inner Mongolia Autonomous Region Major Science and Technology Project","award":["2020ZD0006"],"award-info":[{"award-number":["2020ZD0006"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Enterotoxigenic Escherichia coli (ETEC)-induced neonatal calf diarrhea (NCD) causes significant economic losses to the cattle industry; therefore, understanding its antibiotic resistance is crucial for developing targeted prevention and treatment strategies. However, reports on antibiotic resistance in bovine ETEC are currently limited. This study conducted whole-genome sequencing (WGS) and antimicrobial susceptibility testing on ETEC F5- and F5-F41-positive strains isolated from neonatal calf diarrhea samples in Inner Mongolia, China. The results showed that both ETEC F5- and ETEC F5-F41-positive strains are multidrug-resistant, containing ceftriaxone (CRO), ceftazidime (CAZ)) and ciprofloxacin (CIP), which are listed as the highest priority critically important antimicrobial (HP-CIAs) by the World Health Organization (WHO). Combined analysis using the Comprehensive Antibiotic Resistance Database (CARD) and ResFinder 4.1 predictive analysis revealed that the chromosomes and plasmids of the 2 ETEC-positive strains contained 11 classes of antibiotic resistance genes, with the top 3 categories in terms of the number of resistance genes being aminoglycosides, \u03b2-lactamases, and chloramphenicols. In addition, various bacterial efflux pumps, including RND, MFS, SMR, and the ABC efflux pump family, were detected. A total of 74 antimicrobial resistance genes were identified in the 2 strains, belonging to 5 categories of drug resistance mechanisms; the antimicrobial resistance phenotype was consistent with the genotype. This study provides a reference for the prevention and treatment of diarrhea caused by ETEC.<\/jats:p>","DOI":"10.3390\/ani16010151","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T10:53:50Z","timestamp":1767610430000},"page":"151","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole-Genome Sequencing and Antimicrobial Resistance Analysis of Enterotoxigenic Escherichia coli F5 and F5-F41 Strains Isolated from Neonatal Calves in Inner Mongolia, China"],"prefix":"10.3390","volume":"16","author":[{"given":"Mengyuan","family":"Xie","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hewei","family":"Shang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangliang","family":"Lv","sequence":"additional","affiliation":[{"name":"Hinggan League Animal Disease Prevention and Control Center, Hinggan League 137400, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pingping","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenhao","family":"Li","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Yuan","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianqu","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiumin","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Center Biology Co., Ltd., Beijing 102600, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojing","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"100238","DOI":"10.1016\/j.vas.2022.100238","article-title":"Vaccination for the prevention of neonatal calf diarrhea in cow-calf operations: A scoping review","volume":"15","author":"Maier","year":"2022","journal-title":"Vet. Anim. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"105818","DOI":"10.1016\/j.prevetmed.2022.105818","article-title":"A scoping review of neonatal calf diarrhea case definitions","volume":"211","author":"Wilson","year":"2023","journal-title":"Prev. Vet. Med."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Jessop, E., Li, L., Renaud, D.L., Verbrugghe, A., Macnicol, J., and Gamsj\u00e4ger, L. (2024). Neonatal calf diarrhea and gastrointestinal microbiota: Etiologic agents and microbiota manipulation for treatment and prevention of diarrhea. Vet. Sci., 11.","DOI":"10.3390\/vetsci11030108"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"229","DOI":"10.3168\/jds.S0022-0302(85)80814-6","article-title":"Enterotoxigenic Escherichia coli infections in newborn calves: A review","volume":"68","author":"Acres","year":"1985","journal-title":"J. Dairy. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/s41545-020-0051-0","article-title":"Antibiotic resistance genes from livestock waste: Occurrence, dissemination, and treatment","volume":"3","author":"He","year":"2020","journal-title":"NPJ Clean. Water"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.fct.2019.01.033","article-title":"Importance of antibiotic residues in animal food","volume":"125","year":"2019","journal-title":"Food Chem. Toxicol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2742","DOI":"10.1038\/s41598-024-52536-z","article-title":"Escherichia coli resistance mechanism AcrAB-TolC efflux pump interactions with commonly used antibiotics: A molecular dynamics study","volume":"14","author":"Smith","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1038\/nrmicro1464","article-title":"Multidrug-resistance efflux pumps? not just for resistance","volume":"4","author":"Piddock","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_9","first-page":"69","article-title":"Survey on the prevalence of E. coli K99 in large-scale cattle farms in the surrounding areas of Hohhot","volume":"44","author":"Liu","year":"2023","journal-title":"J. Anim. Ecol."},{"key":"ref_10","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_11","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies fromshort and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-119"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"W451","DOI":"10.1093\/nar\/gki487","article-title":"GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses","volume":"33","author":"Besemer","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1016\/j.cmi.2022.05.024","article-title":"External validation of WGS-based anti-microbial susceptibility prediction tools, KOVER-AMR and ResFinder 4.1, for Escherichia coli clinical isolates","volume":"28","author":"Verschuuren","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_15","first-page":"D517","article-title":"CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance data-base","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Huygens, J., Daeseleire, E., Mahillon, J., Van Elst, D., Decrop, J., and Meirlaen, J. (2021). Presence of antibiotic residues and antibiotic resistant bacteria in cattle manure intended for fertilization of agricultural fields: A one health perspective. Antibiotics, 10.","DOI":"10.3390\/antibiotics10040410"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1089\/fpd.2015.1959","article-title":"Entero-toxigenic Escherichia coli subclinical infection in pigs: Bacteriological and genotypic characterization and antimicrobial resistance profiles","volume":"12","author":"Moredo","year":"2015","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_18","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\u2014A threat around the world","volume":"6","author":"Palmeira","year":"2020","journal-title":"Heliyon"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Husna, A., Rahman, M.M., Badruzzaman, A.T.M., Sikder, M.H., Islam, M.R., and Rahman, M.T. (2023). Extended-spectrum \u03b2-lactamases (ESBL): Challenges and opportunities. Biomedicines, 11.","DOI":"10.3390\/biomedicines11112937"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1128\/AAC.01285-07","article-title":"Diversity of ex-tended-spectrum \u03b2-lactamases and class C \u03b2-lactamases among cloacal Escherichia coli isolates in Belgian broiler farms","volume":"52","author":"Smet","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1","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_22","doi-asserted-by":"crossref","first-page":"4163","DOI":"10.1038\/s41598-024-54169-8","article-title":"Genome-wide identification of fitness-genes in aminoglycoside-resistant Escherichia coli during antibiotic stress","volume":"14","author":"Wellner","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nm1347","article-title":"Fluoroquinolone-modifying enzyme: A new adaptation of a common aminoglycoside acetyltransferase","volume":"12","author":"Robicsek","year":"2005","journal-title":"Nat. Med."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3205","DOI":"10.1128\/AAC.00625-07","article-title":"Occurrence of tetracycline resistance genes among Escherichia coli isolates from the phase 3 clinical trials for tigecycline","volume":"51","author":"Tuckman","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.ijfoodmicro.2011.01.003","article-title":"Distribution and transferability of tetracycline resistance determinants in Escherichia coli isolated from meat and meat products","volume":"145","author":"Koo","year":"2011","journal-title":"Int. J. Food Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3109\/1040841X.2015.1136261","article-title":"Macrolide resistance mechanisms in Enterobacteriaceae: Focus on azithromycin","volume":"43","author":"Gomes","year":"2016","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e00742-20","DOI":"10.1128\/AEM.00742-20","article-title":"Prevalence of cefotaxime-resistant Escherichia coli isolates from healthy cattle and sheep in northern Spain: Phenotypic and genome-based characterization of antimicrobial susceptibility","volume":"86","author":"Tello","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Kerek, \u00c1., Rom\u00e1n, I., Szab\u00f3, \u00c1., Kov\u00e1cs, D., Kardos, G., and Kov\u00e1cs, L. (2025). Antibiotic resistance genes in Escherichia coli\u2014Literature review. Crit. Rev. Microbiol., 1\u201335.","DOI":"10.1080\/1040841X.2025.2492156"},{"key":"ref_29","first-page":"337","article-title":"Expression of the mphB gene for macro-lide 2\u2032-phosphotransferase II from Escherichia coli in Staphylococcus aureus","volume":"159","author":"Noguchi","year":"1998","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Haley, B.J., Kim, S.W., Salaheen, S., and Hovingh, E. (2023). Genome-wide analysis of Escherichia coli isolated from dairy animals identifies virulence factors and genes enriched in multi-drug-resistant strains. Antibiotics, 12.","DOI":"10.3390\/antibiotics12101559"},{"key":"ref_31","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_32","doi-asserted-by":"crossref","first-page":"1648","DOI":"10.3201\/eid1510.090696","article-title":"Escherichia coli as reservoir for macrolide resistance genes","volume":"15","author":"Nguyen","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Urban-Chmiel, R., Marek, A., St\u0119pie\u0144-Py\u015bniak, D., Wieczorek, K., Dec, M., and Nowaczek, A. (2022). Antibiotic resistance in bacteria\u2014A review. Antibiotics, 11.","DOI":"10.3390\/antibiotics11081079"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.ijantimicag.2005.02.006","article-title":"Mechanisms of quinolone resistance in Escherichia coli and Salmonella: Recent developments","volume":"25","author":"Hopkins","year":"2005","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"4593","DOI":"10.1128\/JCM.38.12.4593-4598.2000","article-title":"Characterization of chloramphenicol and florfenicol resistance in Escherichia coli associated with bovine diarrhea","volume":"38","author":"White","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Li, Q., Li, Z., Wang, Y., Chen, Y., Sun, J., and Yang, Y. (2022). Antimicrobial resistance and transconjugants characteristics of sul3 Positive Escherichia coli isolated from animals in Nanning, Guangxi province. Animals, 12.","DOI":"10.3390\/ani12080976"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Miranda, A., \u00c1vila, B., D\u00edaz, P., Rivas, L., Bravo, K., and Astudillo, J. (2016). Emergence of plasmid-borne dfrA14 trimethoprim resistance gene in Shigella sonnei. Front. Cell Infect. Microbiol., 6.","DOI":"10.3389\/fcimb.2016.00077"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Ayoub Moubareck, C. (2020). Polymyxins and bacterial membranes: A review of antibacterial activity and mechanisms of resistance. Membranes, 10.","DOI":"10.3390\/membranes10080181"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Hu, J., Li, J., Huang, X., Xia, J., Cui, M., and Huang, Y. (2023). Genomic traits of multidrug resistant enterotoxigenic Escherichia coli isolates from diarrheic pigs. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1244026"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1093\/jac\/dkg050","article-title":"The importance of efflux pumps in bacterial antibiotic resistance","volume":"51","author":"Webber","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"129","DOI":"10.4103\/ijmr.IJMR_2079_17","article-title":"Efflux pump inhibitors for bacterial pathogens: From bench to bed-side","volume":"149","author":"Sharma","year":"2019","journal-title":"Indian. J. Med. Res."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Algammal, A.M., El-Kholy, A.W., Riad, E.M., Mohamed, H.E., Elhaig, M.M., and Yousef, S.A.A. (2020). Genes encoding the virulence and the antimicrobial resistance in enterotoxigenic and shi-ga-toxigenic E. coli isolated from diarrheic calves. Toxins, 12.","DOI":"10.3390\/toxins12060383"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/0717-6287-47-28","article-title":"Characterization of Escherichia coli virulence genes, pathotypes and antibiotic resistance properties in diarrheic calves in Iran","volume":"47","author":"Shahrani","year":"2014","journal-title":"Biol. Res."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e00749-24","DOI":"10.1128\/aem.00749-24","article-title":"Host species shapes genotype, antimicrobial resistance, and virulence profiles of enterotoxigenic Escherichia coli (ETEC) from livestock in the United States","volume":"90","author":"Fu","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Xie, M., Chen, Y., Shang, H., He, X., and Xu, X. (2025). Prevalence and antimicrobial resistance of Salmonella enterica isolated from cattle farms in Inner Mongolia. BMC Vet. Res., 21.","DOI":"10.1186\/s12917-025-04901-x"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Muteeb, G., Rehman, M.T., Shahwan, M., and Aatif, M. (2023). Origin of antibiotics and antibiotic resistance, and their impacts on drug development: A narrative review. Pharmaceuticals, 16.","DOI":"10.20944\/preprints202306.1921.v1"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Vidovic, N., and Vidovic, S. (2020). Antimicrobial resistance and food animals: Influence of livestock environment on the emergence and dissemination of antimicrobial resistance. Antibiotics, 9.","DOI":"10.3390\/antibiotics9020052"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"211","DOI":"10.33321\/cdi.2004.28.19","article-title":"Foodborne disease outbreaks in Australia, 1995 to 2000","volume":"28","author":"Gould","year":"2004","journal-title":"Commun. Dis. Intell. Q. Rep."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/1\/151\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T11:07:42Z","timestamp":1767611262000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/1\/151"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":48,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["ani16010151"],"URL":"https:\/\/doi.org\/10.3390\/ani16010151","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,5]]}}}