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Towards geospatially-resolved public-health surveillance via wastewater sequencing

Author

Listed:
  • Braden T. Tierney

    (Weill Cornell Medicine
    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
    University of Miami)

  • 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
    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
    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
    University of Miami Miller School of Medicine
    University of Miami)

  • Mario Stevenson

    (University of Miami Miller School of Medicine)

  • Ayaaz Amirali

    (University of Miami)

  • Cynthia Campos Beaver

    (University of Miami Miller School of Medicine
    University of Miami Miller School of Medicine)

  • Erin Kobetz

    (University of Miami Miller School of Medicine
    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
    Weill Cornell Medicine
    Weill Cornell Medicine)

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.

Suggested Citation

  • 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 & Alexande, 2024. "Towards geospatially-resolved public-health surveillance via wastewater sequencing," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52427-x
    DOI: 10.1038/s41467-024-52427-x
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    References listed on IDEAS

    as
    1. Mukhlid Yousif & Said Rachida & Setshaba Taukobong & Nkosenhle Ndlovu & Chinwe Iwu-Jaja & Wayne Howard & Shelina Moonsamy & Nompilo Mhlambi & Sipho Gwala & Joshua I. Levy & Kristian G. Andersen & Cath, 2023. "SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    2. Davida S. Smyth & Monica Trujillo & Devon A. Gregory & Kristen Cheung & Anna Gao & Maddie Graham & Yue Guan & Caitlyn Guldenpfennig & Irene Hoxie & Sherin Kannoly & Nanami Kubota & Terri D. Lyddon & M, 2022. "Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Zhuye Jie & Huihua Xia & Shi-Long Zhong & Qiang Feng & Shenghui Li & Suisha Liang & Huanzi Zhong & Zhipeng Liu & Yuan Gao & Hui Zhao & Dongya Zhang & Zheng Su & Zhiwei Fang & Zhou Lan & Junhua Li & Li, 2017. "The gut microbiome in atherosclerotic cardiovascular disease," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
    4. Smruthi Karthikeyan & Joshua I. Levy & Peter Hoff & Greg Humphrey & Amanda Birmingham & Kristen Jepsen & Sawyer Farmer & Helena M. Tubb & Tommy Valles & Caitlin E. Tribelhorn & Rebecca Tsai & Stefan A, 2022. "Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission," Nature, Nature, vol. 609(7925), pages 101-108, September.
    5. Wickham, Hadley, 2007. "Reshaping Data with the reshape Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 21(i12).
    6. Braden T Tierney & Yingxuan Tan & Zhen Yang & Bing Shui & Michaela J Walker & Benjamin M Kent & Aleksandar D Kostic & Chirag J Patel, 2022. "Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research," PLOS Biology, Public Library of Science, vol. 20(3), pages 1-18, March.
    7. Michael Tisza & Sara Javornik Cregeen & Vasanthi Avadhanula & Ping Zhang & Tulin Ayvaz & Karen Feliz & Kristi L. Hoffman & Justin R. Clark & Austen Terwilliger & Matthew C. Ross & Juwan Cormier & Hann, 2023. "Wastewater sequencing reveals community and variant dynamics of the collective human virome," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
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