Tweet
Nat Commun
. 2024 Sep 27;15(1):8386.
doi: 10.1038/s41467-024-52427-x. Towards geospatially-resolved public-health surveillance via wastewater sequencing
Braden T Tierney 1 2 , Jonathan Foox 3 , Krista A Ryon 3 , Daniel Butler 3 , Namita Damle 3 , Benjamin G Young 3 , Christopher Mozsary 3 , Kristina M Babler 4 5 , Xue Yin 5 , Yamina Carattini 6 , David Andrews 6 , Alexander G Lucaci 3 7 , Natasha Schaefer Solle 8 , Naresh Kumar 9 , Bhavarth Shukla 8 , Dušica Vidović 10 11 , Benjamin Currall 11 , Sion L Williams 11 , Stephan C Schürer 10 11 12 , Mario Stevenson 8 , Ayaaz Amirali 5 , Cynthia Campos Beaver 8 11 , Erin Kobetz 8 11 , Melinda M Boone 11 , Brian Reding 13 , Jennifer Laine 13 , Samuel Comerford 13 , Walter E Lamar 14 , John J Tallon Jr 15 , Jeremy Wain Hirschberg 3 , Jacqueline Proszynski 3 , Gabriel Al Ghalith 16 , Kübra Can Kurt 3 , Mark E Sharkey 6 , George M Church 17 , George S Grills 11 , Helena M Solo-Gabriele 18 , Christopher E Mason 19 20 21
Affiliations
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.
. 2024 Sep 27;15(1):8386.
doi: 10.1038/s41467-024-52427-x. Towards geospatially-resolved public-health surveillance via wastewater sequencing
Braden T Tierney 1 2 , Jonathan Foox 3 , Krista A Ryon 3 , Daniel Butler 3 , Namita Damle 3 , Benjamin G Young 3 , Christopher Mozsary 3 , Kristina M Babler 4 5 , Xue Yin 5 , Yamina Carattini 6 , David Andrews 6 , Alexander G Lucaci 3 7 , Natasha Schaefer Solle 8 , Naresh Kumar 9 , Bhavarth Shukla 8 , Dušica Vidović 10 11 , Benjamin Currall 11 , Sion L Williams 11 , Stephan C Schürer 10 11 12 , Mario Stevenson 8 , Ayaaz Amirali 5 , Cynthia Campos Beaver 8 11 , Erin Kobetz 8 11 , Melinda M Boone 11 , Brian Reding 13 , Jennifer Laine 13 , Samuel Comerford 13 , Walter E Lamar 14 , John J Tallon Jr 15 , Jeremy Wain Hirschberg 3 , Jacqueline Proszynski 3 , Gabriel Al Ghalith 16 , Kübra Can Kurt 3 , Mark E Sharkey 6 , George M Church 17 , George S Grills 11 , Helena M Solo-Gabriele 18 , Christopher E Mason 19 20 21
Affiliations
- PMID: 39333485
- PMCID: PMC11436780
- DOI: 10.1038/s41467-024-52427-x
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.