Longitudinal Monitoring Reveals Persistence of Colistin-Resistant Escherichia coli on a Pig Farm Following Cessation of Colistin Use

Abstract

Colistin-resistant bacteria harboring plasmid-mediated mcr genes are of concern as they may be a cause of serious nosocomial infections. It is hypothesized that cessation of colistin use as a feed additive for pigs will reduce the occurrence and distribution of mcr genes in farms. The aim of this study was to investigate this hypothesis by longitudinal monitoring and characterizing of mcr positive Escherichia coli (MCRPE) isolates after colistin was withdrawn on a central Thailand pig farm that previously had a high frequency of MCRPE. Colistin use ceased at the beginning of 2017, and subsequently 170 samples were collected from farrowing sows and suckling piglets (n = 70), wastewater (n = 50) and farm workers (n = 50) over a 3.5-year period. Bacteria were identified by MALDI-TOF mass spectrometry and minimal inhibitory concentrations were determined by broth microdilution. The antibiogram of mcr positive E. coli isolates was determined using the Vitek2 automated susceptibility machine, and multiplex and simplex PCRs were performed for mcr-1–8 genes. MCRPE containing either mcr-1 or mcr-3 were isolated from pigs throughout the investigation period, but with a declining trend, whereas MCRPE isolates were recovered from humans only in 2017. MCRPE were still being recovered from wastewater in 2020. Most MCRPE isolates possessed the virulence genes Stap, Stb, or Stx2e, reflecting pathogenic potential in pigs, and showed high rates of resistance to ampicillin, gentamicin and tetracycline. Pulsed-field gel electrophoresis and multi-locus sequence typing showed that diverse MCRPE clones were distributed on the farm. The study identified a decline of pathogenic MCRPE following withdrawal of colistin, with pigs being the primary source, followed by wastewater. However, short-term therapeutic usage of other antibiotics could enhance the re-occurrence of mcr-carrying bacteria. Factors including the environment, management, and gene adaptations that allow maintenance of colistin resistance require further investigation, and longer-term studies are needed.

High Fecal Prevalence of mcr-Positive Escherichia coli in Veal Calves at Slaughter in France

“…Our results confirmed that mcr -positive isolates were resistant to other antibiotics [ 10 , 25 , 26 ]. Except for one isolate, all mcr -positive strains were MDR and 56.1% of them were resistant to ciprofloxacin.…”

“…The occurrence and distribution of mcr genes was monitored after the withdrawal of colistin at pig and chicken farms. Studies showed different results, and the association between colistin withdrawal and control of the spread of mcr genes was not evidenced [ 25 , 31 , 32 , 33 ]. It should be stressed, however, that in the absence of colistin use, treatment with other antibiotics might co-select mcr genes and favor their spread.…”

Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy

“…Probably, the wide diffusion of tet genes observed in this study is consequent to previous recurrent treatments that have established long-term selective resistant bacteria harboring these genetic elements in the farm environments [ 21 ]. Moreover, other environmental sources of resistance pollution by genetic determinants (water, food, or wild birds) cannot be ruled out [ 22 , 23 ].…”

Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm

“…The six MCRPE strains submitted for whole genome sequencing had colistin MIC values of 4–8 mg/L and had different PFGE profiles and ST types 8 . These MCRPE strains transferred mcr -1 and mcr -3 genes to recipient E. coli J53 at conjugative transfer frequency rate of 1.7–2 × 10 −4 .…”

“…Despite numerous cases of colistin resistant Enterobacteriaceae being reported from livestock and humans in Thailand, detailed genomic characterization of mcr -positive E. coli , particularly amongst livestock isolates, is still limited. In this study, six mcr- positive E. coli strains with multi-drug resistance traits 8 were subjected to whole genome sequencing (WGS) and characterization of the plasmids for better understanding of mcr genes dissemination between pigs and the farm environment.…”