Faecal source tracking and the identification of naturalised Escherichia coli to assist with establishing water quality and faecal contamination levels

E. coli are routinely measured as faecal indicator bacteria (FIB) to provide indications of microbial water quality in parallel with other physico-chemical parameters. Recent evidence indicates that some ‘naturalised’ Escherichia species indistinguishable from E. coli, are widespread in the environment but are rarely associated with humans or ruminants. The omnipresence of these cryptic Escherichia species within the environment has led water managers to consider whether they confound microbial water quality assessments as they are phenotypically identical to E. coli in current standard detection methods. Likewise, elevated numbers of E. coli phylogroups B1 and B2 dominating a sample are potentially indicative of non-recent faecal sources as they may also persist in the environment.

This work used water samples collected from sites (observed land uses of dairy, urban and sheep & beef) with historically elevated numbers of E. coli as part of the Ministry for the Environment Quantitative Microbial Risk Assessment (QMRA) Pilot Study (Leonard et al., 2020). The study aims were to determine the prevalence of E. coli phylogroups B1 and B2, and naturalised Escherichia species (Escherichia marmotae and Escherichia ruysiae), and determine any correlation with pathogen detection.

Pathogens were present in 93.1% (27 of 29) and 88.2% of water samples where B1 and/or B2 were present at 10 or greater, or greater than 15 isolates per sample respectively.

By targeting gnd, a hypervariable allele found in many Enterobacteriaceae, E. coli metabarcoding and population analysis of DNA recovered from water sample enrichments indicated that there were no significant variations of gnd diversity between urban, dairy and sheep and beef samples at the gnd sequence type (gST) level. Principle component analysis broadly grouped E. coli populations from each sample according to observed land use and faecal source marker (human, ruminant, and wildfowl). Cryptic Escherichia clades were rare at a relative abundance of <1% of reads per sample.E. coli phylogroups B1 and B2 were identified frequently in the water samples from sites with historically high E. coli levels. B1 and B2 phylogroups of E. coli are derived from faecal material and are known to persist in waterways, and therefore, when identified as the dominant E. coli group(s) in a water sample, they are potentially naturalised E. coli and indicative of aged faecal sources.An important finding from this study was that where these naturalised E. coli phylogroup B1 and B2 were found to be the dominant E. coli in a water sample, it was in association with one or more pathogens. This indicates that naturalised faecal E. coli present in a waterway are still likely to represent a significant health risk.