Detecting Genes Associated with Pathogenicity and Antimicrobial Resistance in Three New Zealand Waterways

B ackground More than 100 zoonoses may be transmitted via water, among them enteric diseases are leading causes of human mortality. Traditional monitoring for zoonoses relies on culturing of indicator species, but environmental DNA (eDNA) provides an alternative, allowing direct testing for genetic loci associated with pathogenicity and/or antimicrobial resistance in zoonotic bacteria. O bjectives To evaluate whether genes associated with Shiga toxin producing Escherichia coli (STEC) and antimicrobial resistance can be monitored in waterways using culture-free sampling of eDNA combined with PCR-based testing. M ethods Water and sediment samples were collected from two sites on each of three rivers in Canterbury, New Zealand; sample sites were situated above and below reaches bordered by intensive dairy farming. Samples from each site were tested for genes typically associated with Escherichia coli , STEC serogroups O26 and O157, human pathogenic strains of STEC, and resistance to a broad range of antibiotics. R esults Both culturing and genetic testing confirmed the presence of E. coli in all samples. In contrast, presence of genes associated with STEC and antibiotic resistance varied by season and substrate. The O157 serogroup was identified at more than twice as many sites as O26, with the latter more common in autumn samples. In autumn, genes associated with pathogenic STEC were detected in one Ashley and both Rangitata River samples but were present in all spring samples, except one Ashley and one Selwyn River collection. The antibiotic resistance gene was only identified in spring, predominantly at sites downstream of intensive dairying. D iscussion While our sample is small this study indicates that genetic testing of eDNA can be a useful tool for monitoring the presence and persistence of zoonoses in waterways. How the presence of these genetic elements is related to that of pathogenic STEC and incidence of disease in humans now needs to be examined.