Towards geospatially-resolved public-health surveillance via wastewater sequencing

Braden T. Tierney (), Jonathan Foox, Krista A. Ryon, Daniel Butler, Namita Damle, Benjamin G. Young, Christopher Mozsary, Kristina M. Babler, Xue Yin, Yamina Carattini, David Andrews, Alexander G. Lucaci, Natasha Schaefer Solle, Naresh Kumar, Bhavarth Shukla, Dušica Vidović, Benjamin Currall, Sion L. Williams, Stephan C. Schürer, Mario Stevenson, Ayaaz Amirali, Cynthia Campos Beaver, Erin Kobetz, Melinda M. Boone, Brian Reding, Jennifer Laine, Samuel Comerford, Walter E. Lamar, John J. Tallon, Jeremy Wain Hirschberg, Jacqueline Proszynski, Gabriel Al Ghalith, Kübra Can Kurt, Mark E. Sharkey, George M. Church, George S. Grills, Helena M. Solo-Gabriele () and Christopher E. Mason ()
Additional contact information
Braden T. Tierney: Weill Cornell Medicine
Jonathan Foox: Weill Cornell Medicine
Krista A. Ryon: Weill Cornell Medicine
Daniel Butler: Weill Cornell Medicine
Namita Damle: Weill Cornell Medicine
Benjamin G. Young: Weill Cornell Medicine
Christopher Mozsary: Weill Cornell Medicine
Kristina M. Babler: University of Utah
Xue Yin: University of Miami
Yamina Carattini: University of Miami Miller School of Medicine
David Andrews: University of Miami Miller School of Medicine
Alexander G. Lucaci: Weill Cornell Medicine
Natasha Schaefer Solle: University of Miami Miller School of Medicine
Naresh Kumar: University of Miami Miller School of Medicine
Bhavarth Shukla: University of Miami Miller School of Medicine
Dušica Vidović: University of Miami Miller School of Medicine
Benjamin Currall: University of Miami Miller School of Medicine
Sion L. Williams: University of Miami Miller School of Medicine
Stephan C. Schürer: University of Miami Miller School of Medicine
Mario Stevenson: University of Miami Miller School of Medicine
Ayaaz Amirali: University of Miami
Cynthia Campos Beaver: University of Miami Miller School of Medicine
Erin Kobetz: University of Miami Miller School of Medicine
Melinda M. Boone: University of Miami Miller School of Medicine
Brian Reding: University of Miami
Jennifer Laine: University of Miami
Samuel Comerford: University of Miami
Walter E. Lamar: University of Miami Health System
John J. Tallon: University of Miami
Jeremy Wain Hirschberg: Weill Cornell Medicine
Jacqueline Proszynski: Weill Cornell Medicine
Gabriel Al Ghalith: Seed Health
Kübra Can Kurt: Weill Cornell Medicine
Mark E. Sharkey: University of Miami Miller School of Medicine
George M. Church: Harvard Medical School and the Wyss Institute
George S. Grills: University of Miami Miller School of Medicine
Helena M. Solo-Gabriele: University of Miami
Christopher E. Mason: Weill Cornell Medicine

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-52427-x

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