Prevalence and genetic characteristics of antimicrobial-resistant <i>Escherichia coli</i> in wild birds in Japan

Antimicrobial-resistant bacteria in wild animals are a multisectoral concern worldwide. In this study, we examined fecal samples collected from wild birds in two prefectures of Japan between 2021 and 2024 using both deoxycholate-hydrogen sulfide-lactose (DHL) agar media and antimicrobial-containing DHL agar media. Of the 252 fecal samples from 11 bird species, 159 E. coli were isolated from 70 samples (27.8%) of six species, and resistance was found in 4.4% of isolates from DHL media. Using nalidixic acid (NAL)- and cefotaxime (CTX)-containing media, NAL-resistant isolates were isolated from great cormorants and spot-billed ducks, and an extended-spectrum β-lactamase (ESBL)/AmpC β-lactamase producer was isolated from great cormorants. Next-generation sequencing analysis of 19 E. coli isolates exhibiting resistance to NAL and/or CTX indicated diverse genotypes. Genetic analysis indicated that amino acid substitution of quinolone-resistance-determining-regions and qnrS were responsible for NAL resistance, and CTX-Ms (bla_CTX-M-14 in three isolates, and bla_CTX-M-15 and bla_CTX-M-55 in each) and AmpC β-lactamase (bla_MOX-4 and bla_CMY-2 in each) were responsible for CTX resistance. Despite the presence of certain resistant strains, the overall prevalence of antimicrobial-resistant E. coli remains low in wild birds, suggesting limited environmental exposure to antimicrobials and antimicrobial resistant bacteria.