Co-Occurrence of crAssphage with Antibiotic Resistance Genes in an Impacted Urban Watershed

Environments that receive fecal pollution are reservoirs of antibiotic resistance. Recent metagenomic observations suggest that the fecal pollution indicator crAssphage correlates with the occurrence of antibiotic resistance genes (ARGs) in the environment. Expanding the utility of crAssphage to represent the environmental occurrence of ARGs would potentially facilitate ARG management in environments contaminated with fecal pollution. In this study, we analyzed a suite of molecular indicators for ARGs and crAssphage over a 30 day sampling period in an urban stream that receives combined sewer overflows. The sampled stream showed high levels of ARGs and crAssphage with statistically significantly elevated levels during wet weather events. The observed correlation between crAssphage and ARG molecular detection was high when all were measured using digital droplet polymerase chain reaction (PCR). Quantitative PCR and digital droplet PCR quantifications of crAssphage showed only moderate agreement, emphasizing the importance of detection technology when making quantitative comparisons. Overall, this study demonstrates the potential of a crAssphage fecal indicator to correlate with ARG occurrence when employing a "toolbox" approach to fecal pollution management.