Whole-Genome Sequencing and Antimicrobial Resistance Analysis of Enterotoxigenic Escherichia coli F5 and F5-F41 Strains Isolated from Neonatal Calves in Inner Mongolia, China

(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, β-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.