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Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana

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  • Steve Hamner

    (Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA 2 Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
    Department of Microbiology, Montana State University, Bozeman, MT 59717, USA)

  • Bonnie L. Brown

    (Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA)

  • Nur A. Hasan

    (CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA)

  • Michael J. Franklin

    (Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
    Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA)

  • John Doyle

    (Crow Water Quality Project, Crow Agency, Little Big Horn College, MT 59022, USA
    Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT 59022, USA)

  • Margaret J. Eggers

    (Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
    Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
    Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT 59022, USA)

  • Rita R. Colwell

    (CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA)

  • Timothy E. Ford

    (Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA 2 Department of Microbiology, Montana State University, Bozeman, MT 59717, USA)

Abstract

The Little Bighorn River is the primary source of water for water treatment plants serving the local Crow Agency population, and has special significance in the spiritual and ceremonial life of the Crow tribe. Unfortunately, the watershed suffers from impaired water quality, with high counts of fecal coliform bacteria routinely measured during run-off events. A metagenomic analysis was carried out to identify potential pathogens in the river water. The Oxford Nanopore MinION platform was used to sequence DNA in near real time to identify both uncultured and a coliform-enriched culture of microbes collected from a popular summer swimming area of the Little Bighorn River. Sequences were analyzed using CosmosID bioinformatics and, in agreement with previous studies, enterohemorrhagic and enteropathogenic Escherichia coli and other E. coli pathotypes were identified. Noteworthy was detection and identification of enteroaggregative E. coli O104:H4 and Vibrio cholerae serotype O1 El Tor, however, cholera toxin genes were not identified. Other pathogenic microbes, as well as virulence genes and antimicrobial resistance markers, were also identified and characterized by metagenomic analyses. It is concluded that metagenomics provides a useful and potentially routine tool for identifying in an in-depth manner microbial contamination of waterways and, thereby, protecting public health.

Suggested Citation

  • Steve Hamner & Bonnie L. Brown & Nur A. Hasan & Michael J. Franklin & John Doyle & Margaret J. Eggers & Rita R. Colwell & Timothy E. Ford, 2019. "Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana," IJERPH, MDPI, vol. 16(7), pages 1-18, March.
    • Handle: RePEc:gam:jijerp:v:16:y:2019:i:7:p:1097-:d:217634
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    References listed on IDEAS

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    1. John T. Doyle & Larry Kindness & James Realbird & Margaret J. Eggers & Anne K. Camper, 2018. "Challenges and Opportunities for Tribal Waters: Addressing Disparities in Safe Public Drinking Water on the Crow Reservation in Montana, USA," IJERPH, MDPI, vol. 15(4), pages 1-13, March.
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    4. C. J. Vörösmarty & P. B. McIntyre & M. O. Gessner & D. Dudgeon & A. Prusevich & P. Green & S. Glidden & S. E. Bunn & C. A. Sullivan & C. Reidy Liermann & P. M. Davies, 2010. "Erratum: Global threats to human water security and river biodiversity," Nature, Nature, vol. 468(7321), pages 334-334, November.
    5. Cynthia Agumanu McOliver & Anne K. Camper & John T. Doyle & Margaret J. Eggers & Tim E. Ford & Mary Ann Lila & James Berner & Larry Campbell & Jamie Donatuto, 2015. "Community-Based Research as a Mechanism to Reduce Environmental Health Disparities in American Indian and Alaska Native Communities," IJERPH, MDPI, vol. 12(4), pages 1-25, April.
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    Cited by:

    1. Christine Martin & Vanessa W. Simonds & Sara L. Young & John Doyle & Myra Lefthand & Margaret J. Eggers, 2021. "Our Relationship to Water and Experience of Water Insecurity among Apsáalooke (Crow Indian) People, Montana," IJERPH, MDPI, vol. 18(2), pages 1-20, January.

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