Objective To characterize the epidemiology and antimicrobial resistance of diarrheagenic Escherichia coli (DEC) in Baoshan District of Shanghai from 2023 to 2024, to explore the relationship between resistance genes and phenotypes, and to provide evidence for resistance-gene surveillance and rational clinical use of antimicrobial agents.

Methods Stool specimens of diarrheal patients were collected from one tertiary general hospital and one community hospital in Baoshan District. DEC was identified through isolation and culture, biochemical testing, mass spectrometry, and polymerase chain reaction (PCR). Antimicrobial susceptibility was determined through the broth microdilution method. Resistance genes were profiled through comparing the whole-genome sequencing results with Comprehensive Antibiotic Resistance Database (CARD).

Results A total of 60 DEC isolates were obtained, including Enterotoxigenic E. coli (ETEC, 37 isolates), Enteroaggregative E. coli (EAEC, 16 isolates), and Enteropathogenic E. coli (EPEC, 7 isolates), accounting for 61.66%, 26.67%, and 11.67%, respectively. Cases clustered mainly from May to October and were distributed across all age groups. Nine isolates were susceptible to all 23 tested antimicrobial agents; the remaining isolates showed high resistance to ampicillin (56.67%), tetracycline (TET) (40.00%), trimethoprim/sulfamethoxazole (SXT) (45.00%), and to certain cephalosporins. Thirty-one isolates (51.67%) were multidrug-resistant (MDR), with the most common pattern being AMP-CFZ-SXT-TET (ampicillin-cefazolin-trimethoprim/sulfamethoxazole-tetracycline). Five isolates were resistant to extended-spectrum β-lactamases (ESBLs). In total, 71 distinct resistance determinants were detected, with a mean of 48 per isolate; high-frequency determinants were mainly efflux pump and regulatory genes (e.g., emrK, acrS, acrE). No statistically significant differences in resistance genotypes or phenotypes were observed among EAEC, EPEC, and ETEC. Genotype-phenotype concordance was not uniformly high; the highest concordance (>95%) was observed for tetracyclines and folate-pathway inhibitors. Concordance rates for β-lactams, phenicols, quinolones and fluoroquinolones, aminoglycosides, and macrolides were 73.08%, 50.00%, 25.00%, 13.33%, and 0, respectively.

Conclusion Antimicrobial resistance among E. coli in Baoshan District is relatively severe, with widespread multidrug-resistant profiles and a certain correlation between resistance genes and phenotypic resistance. Joint surveillance of both genotypes and phenotypes should be enhanced and integrated assessment should be conducted based on both genotypic data and phenotypic data, so as to provide a reference for clinical treatment and public health prevention and control.