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

## TL;DR

This study found high levels of colistin-resistant E. coli in a Thai swine slaughterhouse, highlighting risks of antibiotic resistance spreading through the food chain.

## Contribution

The study provides genomic insights into colistin-resistant E. coli isolates from livestock in Thailand, revealing high multidrug resistance and virulence gene prevalence.

## Key findings

- 73.21% of E. coli isolates harbored mcr genes, with mcr-1 being the most common.
- 75% of isolates exhibited multidrug resistance with 22 distinct resistance profiles.
- Whole genome sequencing confirmed multiple resistance and virulence genes in selected isolates.

## Abstract

The emergence of colistin-resistant Escherichia coli (E. coli) 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 (mcr-1 to mcr-9) in E. coli isolates, along with characterizing their antimicrobial susceptibility, resistance genes, virulence genes, and whole genome sequencing. We investigated E. coli contamination in a swine slaughterhouse in Nakhon Si Thammarat Province, Thailand. A total of 200 fecal samples were collected and screened for E. coli using selective media supplemented with colistin. A total of 200 fecal samples were collected from a swine slaughterhouse and screened for E. coli using selective media supplemented with colistin. Presumptive E. coli isolates were confirmed by PCR, followed by molecular detection of mcr-1 to mcr-9 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 E. coli isolates were recovered from a swine slaughterhouse using selective media containing colistin. PCR confirmation identified 112 isolates (90.32%) as E. coli. Molecular detection of mobilized colistin resistance (mcr) genes (82 isolates, 73.21%) demonstrated that mcr-1 (50.89%) was the most prevalent, followed by mcr-9 (25.89%) and mcr-3 (24.11%). Overall, the 82 mcr E. coli 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-mcr E. coli 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 aadA, ampC, and blaTEM, were detected in over 60% of a subset of 30 tested isolates. The virulence gene analysis revealed that eae (74.10%), associated with enteropathogenic E. coli (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 E. coli harboring colistin resistance genes (mcr-1 to mcr-9) in a swine slaughterhouse in southern Thailand. The findings highlight the potential risk of zoonotic transmission of antimicrobial resistant E. coli through the food production chain and emphasize the importance of continuous genomic surveillance and prudent antimicrobial use in livestock production systems.