Towards geospatially-resolved public-health surveillance via wastewater sequencing
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.
Authors
- John J. Tallon
- Xue Yin (ORCID: https://orcid.org/0000-0001-7804-2065)
- Stephan C. Schürer (ORCID: https://orcid.org/0000-0001-7180-0978)
- Cynthia Beaver (ORCID: https://orcid.org/0009-0004-0110-4503)
- Jacqueline Proszynski
- Natasha Schaefer Solle (ORCID: https://orcid.org/0000-0001-8166-2732)
- D. Vidović (ORCID: https://orcid.org/0000-0001-9798-2108)
- Braden Tierney (ORCID: https://orcid.org/0000-0002-7533-8802)
- Brian D. Reding
- Namita Damle
- Christopher Mozsary (ORCID: https://orcid.org/0000-0001-5116-4767)
- George S. Grills (ORCID: https://orcid.org/0000-0003-1037-8616)
- Alexander G. Lucaci (ORCID: https://orcid.org/0000-0002-4896-6088)
- Jennifer Laine
- Bhavarth Shukla (ORCID: https://orcid.org/0000-0003-3139-8851)
- Krista Ryon (ORCID: https://orcid.org/0000-0001-9440-2729)
- Ayaaz Amirali
- Kübra Can Kurt (ORCID: https://orcid.org/0000-0001-6862-7908)
- Kristina M. Babler (ORCID: https://orcid.org/0000-0002-7929-5803)
- Walter E. Lamar
- Mario Stevenson (ORCID: https://orcid.org/0000-0001-9651-2999)
- Jonathan Foox (ORCID: https://orcid.org/0000-0002-5705-3985)
- Erin Kobetz
- Jeremy Wain Hirschberg
- Helena M. Solo‐Gabriele (ORCID: https://orcid.org/0000-0003-3390-3823)
- Mark Sharkey
- Melinda Boone (ORCID: https://orcid.org/0000-0003-3463-4688)
- Daniel Butler (ORCID: https://orcid.org/0000-0002-3687-8419)
- Christopher E. Mason (ORCID: https://orcid.org/0000-0002-1850-1642)
- Yamina Carattini
- Benjamin Currall (ORCID: https://orcid.org/0000-0001-6023-6400)
- Naresh Kumar
- George M. Church
- David Andrews (ORCID: https://orcid.org/0000-0003-1515-3694)
- Samuel Comerford
- Gabriel Al Ghalith
- Siôn L. Williams
- B. G. Young
Institutions
- Harvard University (US)
- University of Miami (US)
- Cornell University (US)
- University of Utah (US)
- American Orchid Society (US)
- University of Miami Health System (US)
- Sylvester Comprehensive Cancer Center (US)
- Weill Cornell Medicine (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-09-27
- DOI
- https://doi.org/10.1038/s41467-024-52427-x
- Citations
- 18
- Primary Topic
- SARS-CoV-2 detection and testing
- Type
- article
- Field-Weighted Citation Impact
- 7.00
Funders
- Gastro-Intestinal Research Foundation
- Kementerian Riset Teknologi Dan Pendidikan Tinggi Republik Indonesia
- National Institutes of Health
- National Institute on Drug Abuse