Validation of a modified IDEXX defined-substrate assay for detection of antimicrobial resistant E. coli in environmental reservoirs

Abstract

The emergence of antimicrobial resistant (AMR) bacteria has been identified as one of the principal public health threats of the 21st century. The World Health Organization (WHO) has long recognized the threat of AMR bacteria and highlights environmental surveillance as a key step in understanding and combating the global rise of antimicrobial resistance. Here, we modified and validated an IDEXX defined-substrate assay commonly used for recreational water quality monitoring of E. coli to enumerate cefotaxime resistant E. coli in environmental reservoirs. We then applied this method to understand AMR trends in multiple environmental matrices over time. This modified IDEXX assay performed highly similarly to two widely accepted plating methods (TBX and MacConkey agar) for enumerating AMR bacteria in pure culture samples and environmental matrices, indicating it is a valid method for enumerating AMR E. coli in the environment. We detected AMR E. coli in urban surface water (63%, 15/24 samples), surface soil (35%, 8/23), and waterfowl feces (43%, 3/7). Sampling around a heavy rain event also revealed that concentrations of AMR E. coli and total E. coli co-vary over time in both surface water and surface soil. This novel method can reliably be performed outside of a laboratory setting and has very low equipment requirements, meaning it has tremendous potential to bolster global monitoring efforts, particularly in resource-restricted and highly rural settings.