Monitoring and characterization of colistin resistant Escherichia coli in pig farm and environment following the cessation in use of colistin

Abstract

The growing cases of colistin resistance due to plasmid mediated mcr genes family in Enterobacteriaceae is catastrophic to public health. In this study, our team performed the nation-wide surveillance of mcr-positive Escherichia coli (MCRPE) in healthy pigs across Thailand. Then we monitored longitudinally over the representative pig farm after colistin was withdrawn and genomic characterization was carried out. Among the 696 samples collected from 49 provinces of Thailand, the low carriage rate of mcr-1 or combination of mcr-1 and mcr-3 (4.45% and 0.43%) were detected. MCRPE isolates were multidrug-resistant (MDR) against 3–14 types of antimicrobial and enterotoxin genes were largely found. For the longitudinal monitoring, 170 samples were collected from farrowing sows and suckling piglets, wastewater, and farm workers from 2017-2020. The results showed that mcr-1 were recovered from pig carriages for 3.5 years after withdrawal, but in a declining trend. From DNA fingerprinting methods, diverse E. coli clones were distributed on the farm and showed MDR traits. From whole genome sequencing data of 6 selected MCRPE, mcr-1.1 was located on the high stability IncI2 and IncX4 plasmid. Whereas, mcr-3 variants (mcr-3.2 and mcr-3.5) were found on IncFII and IncHI2 plasmids which either contained MDR region, bacteriocin or efflux pump. Identical plasmids were discovered between pigs and environment from different investigation years. MCRPE isolates showed both phenotypic and genotypic MDR characteristics as well as antiseptic and biocides resistant genes. Our study concluded that in the absence of colistin selective pressure, the persistence or elimination of the mcr-bearing E. coli varies depending on the plasmid background and co-selection by other antibiotics usage such as aminoglycosides and cephalosporins as well as farm management.