Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana
- Hamner, Steve [ Montana State University: Microbiology & Cell Biology ] [ Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA ]
- Brown, Bonnie L. [ Department of Biological Sciences, University of New Hampshire, Durham, NH ]
- Hasan, Nur A. [ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD ]
- Franklin, Michael J. [ Montana State University: Microbiology & Cell Biology ] [ Montana State University: Center for Biofilm Engineering ]
- Doyle, John [ Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT ]
- Eggers, Margaret J. [ Montana State University: Microbiology & Cell Biology ] [ Montana State University: Center for Biofilm Engineering ]
- Colwell, Rita R. [ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD ]
- Ford, Timothy E. [ Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA ]
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.