Prevalence of Fosfomycin-Resistant Escherichia coli from Livestock, Companion Animals, and the Environment in Japan, and Genomic Characterization of Transferable fos Genes.

Fosfomycin is a highest priority critically important antimicrobial in medical settings and is approved for use in cattle, fish, and humans in Japan. Breakpoints for fosfomycin differ between the antimicrobial susceptibility test guidelines of the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Although important for public health, information on the prevalence of fosfomycin-resistant bacteria and mobile fosfomycin resistance genes (fos) in bacteria of nonhuman origin remains insufficient. In this study, we investigated Escherichia coli strains isolated from animals (cattle, pigs, chickens, and dogs) and the association of these with environments in Japan to determine the prevalence of fosfomycin-resistant E. coli based on CLSI and EUCAST, as well as fos gene prevalence. Susceptibility testing for fosfomycin was retrospectively conducted in 2,057 E. coli, and fos genes were detected in fosfomycin-resistant E. coli. Whole-genome sequencing of fos-positive E. coli was performed. The resistance rates to fosfomycin according to CLSI and EUCAST guidelines were 0.6% and 11.7%, respectively. The fosA3 gene was detected in three E. coli isolates (from one cow and two dogs) in Japan. Two fosA3-positive strains harbored the blaCTX-M-14 or blaCTX-M-65 gene located on the same plasmids. The genetic structures of fosA3-carrying plasmids were almost identical to those reported in Japan and China. Herein, we report the prevalence of fosfomycin resistance in Japan, including fosfomycin-nonapproved fields, showing that these may serve as reservoirs of fosfomycin-resistant bacteria and fos genes carried on globally disseminated mobile genetic elements.