Data for: Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes

Municipal wastewater provides a representative sample of human fecal waste
across a catchment area and contains a wide diversity of microbes.
Sequencing wastewater samples provides information about human-associated
and medically-important microbial populations, and may be useful to assay
disease prevalence and antimicrobial resistance (AMR). Here, we present a
study in which we used untargeted metatranscriptomic sequencing on RNA
extracted from 275 sewage influent samples obtained from eight wastewater
treatment plants (WTPs) representing approximately 16 million people in
Southern California between August 2020 – August 2021. We characterized
bacterial and viral transcripts, assessed metabolic pathway activity, and
identified over 2,000 AMR genes/variants across all samples. Because we
did not deplete ribosomal RNA, we have a unique window into AMR carried as
ribosomal mutants. We show that AMR diversity varied between WTPs and that
the relative abundance of many individual AMR genes/variants increased
over time and may be connected to antibiotic use during the
COVID-19 pandemic. Similarly, we detected transcripts mapping to human
pathogenic bacteria and viruses suggesting RNA sequencing is a powerful
tool for wastewater-based epidemiology and that there are geographical
signatures to microbial transcription. We captured the transcription of
gene pathways common to bacterial cell processes, including central carbon
metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We
also posit that due to the ubiquity of many viruses and bacteria in
wastewater, new biological targets for microbial water quality assessment
can be developed. To the best of our knowledge, our study provides the
most complete longitudinal metatranscriptomic analysis of a large
population’s wastewater to date and demonstrates our ability to monitor
the presence and activity of microbes in complex samples . By sequencing
RNA, we can track the relative abundance of expressed AMR genes/variants
and metabolic pathways, increasing our understanding of AMR activity
across large human populations and sewer sheds.