Genomic Characterization of Antimicrobial Resistance in Foodborne Diarrheagenic Escherichia coli from Chifeng, China

Objective: Recent studies have revealed the increasing severity of antimicrobial resistance (AMR) in diarrheagenic Escherichia coli (DEC), but relevant data remain limited in the Chifeng, China. This study aimed to investigate the AMR profiles and resistance gene distribution of foodborne DEC isolates in our city, providing critical insights for monitoring DEC and guiding rational antibiotic use. Methods: From 2023 to 2024,240 diarrheal stool samples were collected from sentinel hospitals. DEC isolates were identified by PCR. Antimicrobial susceptibility to 29 antibiotics was determined using broth microdilution method. Whole genome sequencing (WGS) was performed to analyze resistance genes and plasmid types with bioinformatics tools. Results: The DEC detection rate is 9.6% (23/240), predominantly enteroaggregative E. coli (EAEC, 69.5%) and enteropathogenic E. coli (EPEC, 30.5%). Resistance phenotypes show the highest rates to TET (60.9%) and nalidixic acid (56.5%), with 30.4% of isolates classified as multidrug-resistant (MDR). Genomic analysis identified nine classes of resistance genes, primarily tet(A), blaTEM-1B, and aph(3’’)-Ib. The most prevalent plasmid type was IncF (47.8%). Discussion: The findings highlight a severe AMR burden in Chifeng’s DEC strains, underscoring the urgent need for enhanced surveillance and antibiotic stewardship to curb their dissemination.