A Metagenomic Approach to Evaluating Surface Water Quality in Haiti
Abstract
:1. Introduction
2. Materials and Methods
2.1. Water Sampling and Shipping
2.2. Metagenomic Sequencing and Bioinformatics Analysis
3. Results
3.1. Environmental Sampling
3.2. Sequencing Analysis
4. Discussion
4.1. Limitations
4.2. Seasonal Differences
4.3. Bacterial Diversity
4.4. Phage and Virulence Factor Diversity
4.5. Fungal and Protozoan Diversity
4.6. Cholera and EHEC Concerns
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Site (Approximate Position on Map) | Coordinates | Description |
---|---|---|
January 2018 | ||
1. Rio Frio, Maïssade | 19.1703 N 72.1353 W | Small tadpoles and fishes were visible in this water. Water depth was 2–3 feet and the water was very turbid. |
2. Rivière Guayamouc, Hinche | 19.1494 N 72.0092 W | Trash piles and foraging pigs were present on the river banks. The water was extremely turbid. |
3. Rivière de Thomonde, Thomonde | 19.0082 N 71.9520 W | Many people washed clothes and bathed at this site. The water was turbid and sediment a unique silver gray color. |
4. Rivière La Thème, Mirebalais | 18.8356 N 72.1071 W | The water was turbid and served as irrigation for the sweet potato field nearby. Algae growth was present on the river banks. Trash bags and other plastics were floating on the sides of the river. |
5a. Rivière Lascahobas, Lascahobas | 18.8308 N 71.9451 W | The water was clear with a visible rocky bed. The sample was easily filtered. However, the river bank contained numerous plastic waste products. |
July 2017 (samples collected during this time were not replicated) | ||
1. Rio Frio, Maïssade | 19.1703 N 72.1353 W | People crossed their vehicles here, bathed, and washed clothes. |
3. Rivière de Thomonde, Thomonde | 19.0082 N 71.9520 W | The water was clear and this site was upriver of considerable activity, but was also used for bathing and washing clothes. |
4. Rivière La Thème, Mirebalais | 18.8356 N 72.1071 W | This site contained the most contaminated water comparatively. There was open defecation on the side of the river, trash piles, and many people washing clothes. |
5b. Tributary of Rivière la Peigne, Lascahobas | 18.8204 N 71.9464 W | Water from this site came from a groundwater spring through a water pipe out of the side of a mountain. Many people were bathing near the pipe, with clothes washing below the sampling point. |
6. Rivière Artibonite, below the Lac de Péligre | 18.9026 N 72.0604 W | Water was collected about a mile below the dam where it was released at the bottom of the reservoir. |
7. Rivière Cabestor, Cabestor | 18.8689 N 72.0011 W | Water from the Rivière Cabestor mixed with water from a small creek near the MFH birthing center. At this sampling point, vehicles crossed the river, and people bathed and washed clothes. |
Site Location | Elevation (Meters) | Average Temperature (°C) | Average Precipitation (mm) | ||
---|---|---|---|---|---|
January 2018 | July 2017 | January 2018 | July 2017 | ||
Maïssade | 270 | 22.4 | 25.8 | 30.8 | 151 |
Hinche | 238 | 21.6 | 25 | 28.1 | 155.2 |
Thomonde | 284 | Monthly data not available for this site, ~10 miles from Hinche | |||
Mirebalais | 120 | 22.2 | 25.7 | 23.5 | 150.3 |
Lascahobas | 219 | 20.3 | 23.7 | 29.5 | 136.3 |
Cabestor | 300 | Monthly data not available on this site, <10 miles from Lascahobas | |||
Lac de Péligre | 175 | Monthly data not available for these sites (both for above and below the Lac de Péligre) |
Site | Replicate | January 2018 | |||
---|---|---|---|---|---|
E. coli | V. cholerae | V. cholerae Intl1 | Stx2-converting phage | ||
Maïssade | 1 | 0.12 | ND | 1.61 | ND |
2 | 0.01 | <0.01 | 4.91 | 8.45 | |
3 | <0.01 | ND | ND | 0.70 | |
Hinche | 1 | 0.04 | ND | 2.69 | 0.22 |
2 | <0.01 | <0.01 | 4.8 | ND | |
3 | <0.01 | ND | 0.11 | ND | |
Thomonde | 1 | 0.03 | <0.01 | 6.93 | ND |
2 | 0.01 | <0.01 | 6.05 | 0.52 | |
3 | 0.03 | 0.02 | 3.52 | 7.11 | |
Mirebalais | 1 | <0.01 | ND | 7.59 | 4.31 |
2 | <0.01 | ND | 18.45 | 9.82 | |
3 | 0.01 | <0.01 | 7.55 | 7.62 | |
Lascahobas | 1 | 0.19 | <0.01 | 2.13 | 1.78 |
2 | 0.06 * | ND | 6.40 | 0.11 | |
3 | 0.02 | ND | ND | 0.36 | |
July 2017 | |||||
Maïssade | 1 | 1.11 | <0.01 ** | 17.65 | ND |
Mirebalais | 1 | 0.16 | <0.01 *** | 7.18 | ND |
Lascahobas | 1 | 3.57 | <0.01 *** | 3.09 | 0.77 |
Below Péligre | 1 | 0.14 | ND | ND | ND |
Cabestor | 1 | 0.34 | ND | ND | ND |
Above Péligre | 1 | 0.08 | <0.01 *** | 3.31 | ND |
Viruses and Bacteriophages | Virulence Associated Genes | Classes of AMR Genes Detected |
---|---|---|
Enterobacteria phage HK630 | Klebsiella pneumoniae: orf6, GI 42543951, tnpA | Aminoglycosides: aadA, aadA5, aadA7, aadA16, aadA10, aac1, aac3 Ia, aph6 Id, aph, ant2’’ Ia |
Siphoviridae_u_s | Enterobacter aerogenes: traM, tniB, ssb, korC | Sulphonamide sul2 |
Escherichia virus P1 | V. cholerae: intI1, GI 42567126 *, VCA0118 *, CARB-6 * | Trimethoprim: dfrC |
Viruses_u_s | Serratia marcescens: orfA, intI3 | Beta-lactam: blaOXA, blaAIM |
Stx2-converting phage 1717 | E. coli: qacEdelta1, aphA7 | Macrolide: mphE, ermA |
Human mastadenovirus C | Pseudomonas aeruginosa: intI1, accC1, aadA6 | Phenicol: dha1 |
Enterobacteria phage BP-4795 | Salmonella Infantis: tnpR | |
G7cvirus_u_s | Pseudomonas putida: qacEdelta1 | |
Myoviridae_u_s | Proteus mirabilis: sul1 | |
Vibrio phage CTX | Morganella morganii: oxa-2 |
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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
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 StyleRoy, 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