COS 100-1 - Longitudinal metatranscriptomic sequencing of Southern California wastewater

Background/Question/Methods

Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples can provide information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). As most studies sequence DNA from wastewater samples, we are likely missing critical information about the transcriptional activity and potential metabolism of microbes, along with the presence of RNA viruses, which can impact human health.

Results/Conclusions

Here, we present a study in which we sequenced RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing 16 million people in Southern California between August 2020 – August 2021. As part of this project, we characterized bacterial, archaeal, and viral transcripts, assessed metabolic pathway activity, and identified AMR genes. We found that microbial transcript diversity differed between WTPs and changed over time. Notably, reads derived from several taxa of interest, such as Neisseria, Klebsiella, Astrovirus, and Norovirus, increased in relative abundance over the year. Through our analyses, we captured active transcription of genes and full pathways common to bacterial cell processes including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We identified over 2,000 unique AMR genes and variants through CARD annotations being actively transcribed across our samples, indicating a wide diversity of AMR mechanisms, and show that AMR diversity varies by WTP and time. Importantly, we did not remove rRNA reads, which allowed us to capture rRNA genes that carried AMR resistance. We observed that the relative abundance of individual AMR genes/variants generally increased over time, supporting the hypothesis that overall AMR is increasing.