Genetic environment of colistin resistance genes mcr-1 and mcr-3 in Escherichia coli from one pig farm in China

Abstract

The aim of this study was to assess the presence of mobile colistin resistance in bacteria isolated from the swine production environment and to analyze the genomic environment of the new colistin resistance gene mcr-3. Anal swabs and environmental samples were collected from a commercial pig farm. Direct sample testing (DST) for mcr genes and isolation of colistin-resistant isolates was performed. The mcr-3-positive isolates were subjected to whole genome sequencing (WGS). Transferability and genomic location analyses of mcr-3 gene were performed using conjugation and S1 nuclease-PFGE with Southern blotting assays, respectively. The antimicrobial susceptibility profiles of the mcr-carrying isolates were determined using the agar dilution method. A total of 65 samples were collected. The DST rates of mcr-1 (64.6%, 42/65) and mcr-3 (40.0%, 26/65) were considerably higher than the rates of mcr-1-positive E. coli (49.2%, 32/65) and mcr-3-positive E. coli (7.7%, 5/65) isolated from these samples, respectively. The five mcr-3-positive isolates were derived from different sources (pig, fly and soil) and four of the five isolates were also positive for mcr-1. The mcr-3 genes were located on IncP-1 plasmids in three isolates or IncHI2 plasmids in two isolates. Several mobile elements, including IS4321, ΔTnAs2 or ISKpn40, were identified in the flanking regions of mcr-3 in the E. coli isolates. In conclusion, the mobile colistin resistance genes mcr-1 and mcr-3 are prevalent in the monitored pig farm and its surrounding environment. Due to their location on broad-host range IncP-1 plasmids and their proximity to different IS sequences, mcr-3 gene might have excellent opportunities for transmission.