Faecal source tracking to understand the role of introduced predators and avian species on water quality assessments in the Makiriri Reserve, Dannevirke

Escherichia coli are used as indicators of faecal contamination in water quality assessments, but ‘naturalised’ non-faecal E. coli and non-pathogenic E. coli-like bacteria can confound routine measurements. Contrary to livestock and human activities, wildlife has not thoroughly been studied as a source of faecal contamination in waterways but could contribute too. We examined the profile of E. coli populations in gut contents and faeces from bird and introduced predator species in the
M?kirikiri Reserve, Dannevirke, and compared to water, soil, sediment and biofilm samples taken within the reserve to determine whether avian and/or invasive mammal species contribute faecal bacteria in the environment.

E. coli (n=420) were recovered from animal and environmental samples (n=106). Initial characterisation of E. coli was using real time PCR targeting the uidA gene, and a subset were further typed by sequencing a region of the hypervariable gnd gene to generate a specific gnd sequence type (gST). These data informed which isolates underwent further phylogenetic analysis
using whole genome sequencing. E. coli populations from sample enrichments were analysed using metabarcoding and gnd amplicon sequencing.

Analyses showed a significant difference in diversity of E. coli gSTs between samples of animal and environmental source, with a lower diversity in animal samples, but also that some gSTs were present in both sample types. Two gSTs (535 and 258) were present in 85 and 71% of samples, respectively. Cryptic Escherichia species, phenotypically similar to E. coli, were isolated and detected by metabarcoding, but only in low abundance.

These data support the hypothesis that introduced predators and avian species contribute to faecal contamination of the environment. The data gathered should allow future comparison of isolates with strains isolated from wildlife.