Journal Article

Towards geospatially-resolved public-health surveillance via wastewater sequencing

Kumar, Naresh, Stevenson, Mario, Butler, Daniel, Currall, Benjamin, Reding, Brian, Beaver, Cynthia Campos, Grills, George S., Williams, Sion L., Laine, Jennifer, Wain Hirschberg, Jeremy, Vidović, Dušica, Yin, Xue, Young, Benjamin G., Tallon, John J., Ryon, Krista A., Al Ghalith, Gabriel, Tierney, Braden T., Damle, Namita, Schürer, Stephan C., Babler, Kristina M., Proszynski, Jacqueline, Lamar, Walter E., Lucaci, Alexander G., Mason, Christopher E., Sharkey, Mark E., Mozsary, Christopher, Boone, Melinda M., Carattini, Yamina, Shukla, Bhavarth, Solo-Gabriele, Helena M., Amirali, Ayaaz, Foox, Jonathan, Solle, Natasha Schaefer, Andrews, David, Kobetz, Erin, Comerford, Samuel, Church, George M., Can Kurt, Kübra

2024

Overview

Wastewater is a geospatially- and temporally-linked microbial fingerprint of a given population, making it a potentially valuable tool for tracking public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (N = 2238 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County, USA, from 2020-2022. We used targeted amplicon sequencing to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with positive PCR tests from University students and Miami-Dade hospital patients. Additionally, in bulk metatranscriptomic data, we demonstrate that the bacterial content of different wastewater sampling locations serving small population sizes can be used to detect putative, host-derived microorganisms that themselves have known associations with human health and diet. We also detect multiple enteric pathogens (e.g., Norovirus ) and characterize viral diversity across sites. Moreover, we observed an enrichment of antimicrobial resistance genes (ARGs) in hospital wastewater; antibiotic-specific ARGs correlated to total prescriptions of those same antibiotics (e.g Ampicillin, Gentamicin). Overall, this effort lays the groundwork for systematic characterization of wastewater that can potentially influence public health decision-making. Wastewater is a promising source of data for continuous monitoring of pathogens in communities, but analysis protocols and methods are still being established. Here, the authors develop sequencing and analysis protocols and use them to evaluate the microbial content of longitudinal wastewater samples from Miami-Dade County, USA.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38/91 / 45/23 / 631/326/1762 / 631/326/2522 / 704/158/855 / Ampicillin / Antibiotics / Antimicrobial resistance / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Bulk sampling / COVID-19 - epidemiology / COVID-19 - virology / Decision making / Florida / Gene sequencing / Gentamicin / Health surveillance / Hospital wastes / Hospitals / Humanities and Social Sciences / Humans / Medical wastes / Microorganisms / multidisciplinary / Norovirus / Pathogens / Penicillin / Public health / Public Health Surveillance / SARS-CoV-2 - genetics / SARS-CoV-2 - isolation & purification / Science / Science (multidisciplinary) / Sequence Analysis, RNA - methods / Severe acute respiratory syndrome coronavirus 2 / Wastewater / Wastewater - microbiology / Wastewater - virology / Water sampling