Whole-Genome Sequence Analysis of Colistin-Resistant, mcr-Harboring Escherichia coli Isolated from a Swine Slaughterhouse in Thailand

The emergence of colistin-resistant <i>Escherichia coli</i> (<i>E. coli</i>) in livestock poses a major public health concern due to its zoonotic potential and multidrug resistance (MDR). The study aimed to detect mobilized colistin resistance genes (<i>mcr-1</i> to <i>mcr-9</i>) in <i>E. coli</i> isolates, along with characterizing their antimicrobial susceptibility, resistance genes, virulence genes, and whole genome sequencing. We investigated <i>E. coli</i> contamination in a swine slaughterhouse in Nakhon Si Thammarat Province, Thailand. A total of 200 fecal samples were collected and screened for <i>E. coli</i> using selective media supplemented with colistin. A total of 200 fecal samples were collected from a swine slaughterhouse and screened for <i>E. coli</i> using selective media supplemented with colistin. Presumptive <i>E. coli</i> isolates were confirmed by PCR, followed by molecular detection of <i>mcr-1</i> to <i>mcr-9</i> genes. Antimicrobial susceptibility testing was performed using the disk diffusion method. Selected isolates were further analyzed for additional antimicrobial resistance genes and virulence associated genes by PCR. Whole genome sequencing was conducted on representative isolates exhibiting high levels of antimicrobial resistance. Our results showed that out of 200 fecal samples, 124 presumptive <i>E. coli</i> isolates were recovered from a swine slaughterhouse using selective media containing colistin. PCR confirmation identified 112 isolates (90.32%) as <i>E. coli</i>. Molecular detection of mobilized colistin resistance (<i>mcr</i>) genes (82 isolates, 73.21%) demonstrated that <i>mcr-1</i> (50.89%) was the most prevalent, followed by <i>mcr-9</i> (25.89%) and <i>mcr-3</i> (24.11%). Overall, the 82 <i>mcr E. coli</i> isolates showed the highest level of resistance to ampicillin (97.56%), followed by tetracycline (95.12%), piperacillin (73.17%), and chloramphenicol (65.85%). For non-<i>mcr E. coli</i> isolates, the highest resistance percentage was observed for ampicillin (96.67%), followed by piperacillin (80%) and tetracycline (73.33%). Among the isolates, 75% exhibited MDR phenotypes, showing 22 distinct resistance profiles. The most common MDR pattern was AMP-PIP-TE-C-S (12.5%). Additional antimicrobial resistance genes, including <i>aadA</i>, <i>ampC</i>, and <i>bla</i>_TEM, were detected in over 60% of a subset of 30 tested isolates. The virulence gene analysis revealed that <i>eae</i> (74.10%), associated with enteropathogenic <i>E. coli</i> (EPEC), was the predominant pathotype. Whole genome sequencing of five selected isolates confirmed the presence of multiple antimicrobial resistance and virulence determinants. In conclusion, this study reveals a high prevalence of MDR <i>E. coli</i> harboring colistin resistance genes (<i>mcr-1</i> to <i>mcr-9</i>) in a swine slaughterhouse in southern Thailand. The findings highlight the potential risk of zoonotic transmission of antimicrobial resistant <i>E. coli</i> through the food production chain and emphasize the importance of continuous genomic surveillance and prudent antimicrobial use in livestock production systems.