A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

Roy, Monika A.; Arnaud, Jean M.; Jasmin, Paul M.; Hamner, Steve; Hasan, Nur A.; Colwell, Rita R.; Ford, Timothy E.

doi:10.3390/ijerph15102211

Open AccessArticle

A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

by

Monika A. Roy

^1,2,

Jean M. Arnaud

¹,

Paul M. Jasmin

³,

Steve Hamner

¹,

Nur A. Hasan

^4,5,

Rita R. Colwell

^4,5 and

Timothy E. Ford

^1,*

¹

Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA

²

Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA

³

Equipes mobiles d’intervention rapide (EMIRA) du Ministère de la Santé Publique et de la Population (MSPP), Hinche HT 5111, Haiti

⁴

CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA

⁵

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

^*

Author to whom correspondence should be addressed.

Int. J. Environ. Res. Public Health 2018, 15(10), 2211; https://doi.org/10.3390/ijerph15102211

Submission received: 8 August 2018 / Revised: 10 September 2018 / Accepted: 4 October 2018 / Published: 10 October 2018

(This article belongs to the Special Issue Water, Sanitation and Hygiene Related Disease)

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Abstract

The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.

Keywords: cholera; metagenomic analysis; bioinformatics; whole genome sequencing; principle components analysis; water quality; environmental sampling; Haiti

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MDPI and ACS Style

Roy, M.A.; Arnaud, J.M.; Jasmin, P.M.; Hamner, S.; Hasan, N.A.; Colwell, R.R.; Ford, T.E. A Metagenomic Approach to Evaluating Surface Water Quality in Haiti. Int. J. Environ. Res. Public Health 2018, 15, 2211. https://doi.org/10.3390/ijerph15102211

AMA Style

Roy MA, Arnaud JM, Jasmin PM, Hamner S, Hasan NA, Colwell RR, Ford TE. A Metagenomic Approach to Evaluating Surface Water Quality in Haiti. International Journal of Environmental Research and Public Health. 2018; 15(10):2211. https://doi.org/10.3390/ijerph15102211

Chicago/Turabian Style

Roy, Monika A., Jean M. Arnaud, Paul M. Jasmin, Steve Hamner, Nur A. Hasan, Rita R. Colwell, and Timothy E. Ford. 2018. "A Metagenomic Approach to Evaluating Surface Water Quality in Haiti" International Journal of Environmental Research and Public Health 15, no. 10: 2211. https://doi.org/10.3390/ijerph15102211

APA Style

Roy, M. A., Arnaud, J. M., Jasmin, P. M., Hamner, S., Hasan, N. A., Colwell, R. R., & Ford, T. E. (2018). A Metagenomic Approach to Evaluating Surface Water Quality in Haiti. International Journal of Environmental Research and Public Health, 15(10), 2211. https://doi.org/10.3390/ijerph15102211

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

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