Spread and Molecular Characteristics of Enterobacteriaceae Carrying fosA-Like Genes from Farms in China

In this study, we aimed to investigate the occurrence and molecular characteristics of fosfomycin-resistant Enterobacteriaceae isolates from pig, chicken and pigeon farms in Guangxi Province of China. A total of 200 fosfomycin-resistant strains were obtained from food animals and their surrounding environments, with the fosA, fosA3, and fosA7.5 genes being detected in 26% (52/200), 10% (20/200), and 5% (10/200), respectively. Surprisingly, three fosA7.5-producing E. coli isolates were found to be concomitant with fosA3. Most of the fosA-like-gene-positive isolates were multidrug-resistant strains and consistently possessed bla(CTX-M-1/CTX-M-9), floR, and bla(TEM) genes. Only fosA3 was successfully transferred to the recipient strains, and the 29 fosA3-carrying transconjugants exhibited high-level resistance to fosfomycin (MIC ≥ 512 μg/mL). Multilocus sequence typing (MLST) combined with enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) analyses indicated that fosA3 or fosA7.5 genes were spread by horizontal transfer as well as via clonal transmission between E. coli. We used the PCR mapping method to explore the genetic contexts of fosA-like genes, and two representative strains (fEc.1 and fEcg99-1) were fully sequenced. Six different genetic structures surrounding fosA3 were detected and one infrequent context was discovered among the conjugable fosA3-positive E. coli isolates. The five genetic environments of fosA were identified and found to be highly similar to the partial sequence of transposon Tn2921. Furthermore, whole-genome sequencing (WGS) results showed that fosA7.5 was colocalized with mcr-3, bla(CMY-63), sul3, tet(A), dfrA, and a number of virulence-related factors on the same chromosomes of strains, and various insertion sequences (IS3/ISL3) were detected upstream or downstream of fosA7.5. The phylogenetic analysis revealed that both fosA7.5- and fosA3-carrying E. coli ST602 and fosA7.5-carrying E. coli ST2599 were closely related to E. coli isolates from humans, which may indicate that they pose a threat to human health. IMPORTANCE Here, we report the widespread and complex genetic environments of fosA-like genes in animal-derived strains in China. The fosA7.5 gene was identified in this study and was found to confer resistance to fosfomycin. The high prevalence of fosA-like genes in farms indicates that food animals serve as a potential reservoir for the resistance genes. This study also discovered that fosfomycin resistance genes were always associated with mobile elements, which would accelerate the transmission of fosA-like genes in strains. Importantly, E. coli ST602 and ST2599 carrying fosA3 or fosA7.5 from food animals had high similarity to E. coli isolates from humans, suggesting that fosA-like genes can be transmitted to humans through the food chain, thus posing a serious threat to public health. Therefore, the prevalence of fosA-like genes isolated from animals should be further monitored.