Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed

The Tijuana River watershed is binational, flowing from Tijuana, Mexico into San Diego and Imperial Beach, USA. Older sewage and stormwater infrastructure in Tijuana has not paced with population growth, causing overflows into this watershed during major rainfall or equipment failures. The public health consequences of this impaired watershed on the surrounding communities remains unknown. Here, we performed untargeted metagenomic sequencing to better characterize the sewage contamination in the Tijuana River, identifying potential pathogens and molecular indicators of antibiotic resistance in surface waters. In 2019-2020, water samples were collected within 48 hours of major rainfall events at 5 transborder flow sites and at the mouth of the river in the estuary. After filtration, DNA was extracted and sequenced, and sequences were run through the Kaiju taxonomic classification program. A pathogen profile of the most abundant disease-causing microbes and viruses present in each of the samples was constructed, and specific markers of fecal contamination were identified and linked to each site. Results from diversity analysis between the sites showed clear distinction as well as instances of grouping, and antibiotic resistant species were found at each site. This serves as a baseline characterization of microbial exposures to these local communities.