Phenotypic and Genotypic Characterization of Antimicrobial Resistant Escherichia coli isolated from Ready-to-Eat Food in Singapore Using Disk Diffusion, Broth Microdilution and Whole Genome Sequencing Methods

Antimicrobial resistance (AMR), especially multidrug-resistance, of bacteria is posing a great threat to public health. This study aimed to determine the antimicrobial resistance profiles of Escherichia coli isolated from ready-to-eat food sold in retail food premises in Singapore. In this study, a total of 99 E. coli isolates from poultry-based dishes (n=77) and fish-based dishes (n=22), obtained between 2009 and 2014, were included for disk diffusion testing. Of the 99 isolates, 24 (24.2%) were resistant to at least one antimicrobial agent. These isolates were then subjected to broth microdilution testing against 33 antimicrobial agents to determine the minimum inhibitory concentration (MIC) of isolates. Finally whole genome sequence (WGS) was carried out on the strains in order to correlate resistant phenotypes to putative antimicrobial-related genes. Of the 24 isolates, 15 (62.5%) were found to be resistant to three or more classes of antimicrobials and thus were defined as multi-drug resistant strains. Two isolates (8.3%) were confirmed as Extended-Spectrum β-lactamase (ESBL)- producing E. coli by double disk synergy test. By analyzing the WGS contigs using BLASTn and KmerFinder, ESBL genes and transferable colistin resistance gene mcr-1 and mcr-5 were determined to be located on plasmids, which could pose a greater risk of AMR transfer among bacteria. This study showed the presence of antimicrobial resistant E. coli isolates in ready-to-eat retail food, and raises a concern on the possible transmission of antimicrobial resistant bacteria from food to humans.