Integrated genomic and phenotypic characterization of antimicrobial resistance in Shiga toxin-producing Escherichia coli from asymptomatic carriers in Japan

Shiga toxin-producing Escherichia coli (STEC) carried by asymptomatic individuals constitute an important reservoir for community transmission, but large-scale analyses of antimicrobial resistance (AMR) in carrier-derived STEC remain limited. In this study, to obtain fundamental information relevant to the eradication of STEC carriage, we analyzed 495 STEC strains isolated from stool-screened asymptomatic carriers in Japan. All the isolates had been previously subjected to whole-genome sequencing and were classified into more than 100 serotypes, predominantly O156:H25 (13.5%), O174:H21 (7.7%), and O105:H7 (6.1%). Genome-based analysis revealed at least one antimicrobial resistance gene (ARG) in 83 isolates (16.8%), with aph(3″)-Ib, aph(6)-Id, sul2, tet(A), and blaTEM-1 being the most prevalent. Most carrier-derived STEC belonged to phylogroup B1, whereas ARGs were identified in isolates from diverse phylogenetic lineages. Comparative analysis revealed that the AMR profiles of carrier-derived STEC were similar to those of human commensal E. coli, whereas cattle commensal isolates exhibited a higher ARG prevalence. Phenotypic susceptibility testing revealed that resistance to ampicillin (n = 33) and tetracycline (n = 50) was the most common, whereas resistance to fluoroquinolones (n = 1) was infrequent and no resistance was observed to fosfomycin (n = 0) or amikacin (n = 0). Together, these findings provide a comprehensive overview of AMR in STEC from asymptomatic carriers in Japan and support the continued effectiveness of several antimicrobial agents while underscoring the importance of ongoing genomic surveillance.