Microbial Source Tracking: An Emerging Technology for Microbial Water Quality Assessment: A Review
DOI:
https://doi.org/10.47430/ujmr.2381.014Keywords:
Bacteriodes, Library-dependent, Library-independent, Microbial source tracking, Water qualityAbstract
Microbial Source Tracking is a scientific approach that primarily aims to identify the sources of faecal contamination in water bodies. Microbial Source Tracking (MST) is a set of techniques employed to identify the origins of faecal contamination in water. The capacity to track faecal bacteria to their source is a crucial aspect of both public health and water quality management. The utilisation of information obtained from the method of MST would provide water quality managers with an enhanced comprehension of the origins of contamination, thus facilitating the implementation of remedial measures to impede transmission. Numerous studies have demonstrated that the gut-associated bacteria of the order Bacteroidales, specifically the Bacteroides genus, has a tendency to undergo co-evolution with the host, making it a highly viable option for MST applications. However, it is noteworthy that MST is also facilitating the scientific community with effective techniques for tracing faecal bacteria and pathogens in water sources. The methodologies utilised in MST are frequently categorised as either Library-Dependent Methods (LDMs) or Library-Independent Methods (LIMs). Microbial source tracking has been employed for diverse objectives, such as ensuring adherence to regulations, remediating pollution, and evaluating risk. The implementation of MST is expected to mitigate the prevalence of waterborne illnesses resulting from contamination. The implementation of MST has facilitated the ability to anticipate the probable origins of faecal contamination and the associated health hazards linked to compromised water systems. In addition to conventional faecal indicators, these methodologies are suggested as means to furnish supplementary insights into the origins of pollution, as well as the ecological and public health ramifications of animal-derived water contamination.
Downloads
References
Adnan, M. S., Roslen, H., and Samsuri, S. (2022). The application of total maximum daily load (TMDL) approach in water quality assessment for the Batu Pahat River. In IOP Conference Series. Earth and Environmental Science, 1022(1): 012074.https://doi.org/10.1088/1755-1315/1022/1/012074
Ahmed, W., Harwood, V.J., Nguyen, K., Young, S., Hamilton,K. and Toze, S. (2016). Utility of Helicobacter spp. associated GFD markers for detecting avian fecal pollution in natural waters of two continents. Water Research, 88: 613-622https://doi.org/10.1016/j.watres.2015.10.050
Ahmed, W., Hughes, B., and Harwood, V. J. (2016). Current status of marker genes of Bacteroides and related taxa for identifying sewage pollution in environmental waters. Water, 8(6): 231.https://doi.org/10.3390/w8060231
Ahmed, W., Zhang, Q., Lobos, A., Senkbeil, J., Sadowsky, M. J., Harwood, V. J., and Ishii, S. (2018). Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters. Environment international, 116: 308-318.https://doi.org/10.1016/j.envint.2018.04.005
Akoumianaki, I., Pagaling, E., Coull, M., Avery, L., and Potts, J. (2018). Review of monitoring techniques and sampling strategies to identify the most significant sources of faecal indicator organisms (FIO) within a catchment. In Final Project Meeting, CREW Report, 14: 1-6.
Arias, D. E., Veluchamy, C., Dunfield, K. E., Habash, M. B., and Gilroyed, B. H. (2020). Hygienization and microbial metabolic adaptation during anaerobic co-digestion of swine manure and corn stover. Bioresource technology, 306: 123168https://doi.org/10.1016/j.biortech.2020.123168
Ballesté, E., Demeter, K., Masterson, B., Timoneda, N., Sala-Comorera, L., and Meijer, W. G. (2020). Implementation and integration of microbial source tracking in a river watershed monitoring plan. Science of The Total Environment, 736: 139573.https://doi.org/10.1016/j.scitotenv.2020.139573
Beer, K.D., Gargano, J.W., Roberts, V.A., Hill, V.R., Garrison, L.E., Kutty, P.K., Hilborn, E.D., Wade, T.J., Fullerton, K.E., and Yoder, J.S., (2015). Surveillance for waterborne dis-ease outbreaks associated with drinking water - United States. Morbidity and Mortality Weekly Report, 64 (31): 842-848.https://doi.org/10.15585/mmwr.mm6431a2
Bivins, A., Crank, K., Greaves, J., North, D., Wu, Z., and Bibby, K. (2020). Cross-assembly phage and pepper mild mottle virus as viral water quality monitoring tools-potential, research gaps, and way forward. Current Opinion in Environmental Science & Health, 16: 54-61.https://doi.org/10.1016/j.coesh.2020.02.001
Boehm, A. E., Graham, K. E. and Jennings, W. C. (2018). Systematic review, meta-analysis, and risk assessment of aging sewage in surface waters. Environmental Science Technology, 52: 9634-9645.https://doi.org/10.1021/acs.est.8b01948
Borer, B., Kleyer, H., and Or, D. (2022). Primary carbon sources and self-induced metabolic landscapes shape community structure in soil bacterial hotspots. Soil Biology and Biochemistry, 168: 108620.https://doi.org/10.1016/j.soilbio.2022.108620
Campos, C.J., Avant, J., Gustar, N., Lowther, J., Powell, A., Stockley, L., and Lees, D.N. (2015). Fate of human noroviruses in shellfish and water impacted by frequent sewage pollution event. Environmental Science and Technology, 49(14): 8377-8355.https://doi.org/10.1021/acs.est.5b01268
Carson, C. A., Shear, B. L., Ellersieck, M. R., and Schnell, J. D. (2023). Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Applied and Environmental Microbiology, 69(3): 1836-1839.https://doi.org/10.1128/AEM.69.3.1836-1839.2003
Chen, T., Long, W., Zhang, C., Liu, S., Zhao, L., and Hamaker, B. R. (2017). Fiber-utilizing capacity varies in Prevotella-versus Bacteroides-dominated gut microbiota. Scientific reports, 7(1): 1-7.https://doi.org/10.1038/s41598-017-02995-4
dela Peña, L. B. R. O., Labrador, K. L., Nacario, M. A. G., Bolo, N. R., and Rivera, W. L. (2021). Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR. Journal of Water and Health, 19(5): 762-774.https://doi.org/10.2166/wh.2021.119
dela Peña, L. B. R. O., Vejano, M. R. A., and Rivera, W. L. (2021). Molecular surveillance of Cryptosporidium spp. for microbial source tracking of fecal contamination in Laguna Lake, Philippines. Journal of Water and Health, 19(3): 534-544.https://doi.org/10.2166/wh.2021.059
Feng, S., and McLellan, S. L. (2019). Highly specific sewage-derived Bacteroides quantitative PCR assays target sewage-polluted waters. Applied and environmental microbiology, 85(6): e02696-18.https://doi.org/10.1128/AEM.02696-18
Fujioka, R.S., Solo-Gabriele, H.M., Byappanahalli, M.N. and Kirs, M. (2015). U.S. Recreational Water Quality Criteria: A Vision for the Future. International Journal of Environmental Research and Public Health, 12:7752-7776.https://doi.org/10.3390/ijerph120707752
Garabetian, F., Vitte, I., Sabourin, A., Moussard, H., Jouanillou, A., Mornet, L., and Lyautey, E. (2020). Uneven genotypic diversity of Escherichia coli in fecal sources limits the performance of a library-dependent method of microbial source tracking on the southwestern French Atlantic coast. Canadian Journal of Microbiology, 66(12): 698-712.https://doi.org/10.1139/cjm-2020-0244
Gitter, A., Mena, K. D., Wagner, K. L., Boellstorff, D. E., Borel, K. E., Gregory, L. F., and Karthikeyan, R. (2020). Human health risks associated with recreational waters: preliminary approach of integrating quantitative microbial risk assessment with microbial source tracking. Water, 12(2): 327.https://doi.org/10.3390/w12020327
Goh, S. G., Liang, L., and Gin, K. Y. H. (2021). Assessment of human health risks in tropical environmental waters with microbial source tracking markers. Water Research, 207: 117748.https://doi.org/10.1016/j.watres.2021.117748
Gomi, R., Haramoto, E., Wada, H., Sugie, Y., Ma, C. Y., Raya, S., and Ihara, M. (2023). Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates. Science of The Total Environment, 864: 160952.https://doi.org/10.1016/j.scitotenv.2022.160952
Gomi, R., Haramoto, E., Wada, H., Sugie, Y., Ma, C. Y., Raya, S., and Ihara, M. (2023). Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates. Science of The Total Environment, 864: 160952.https://doi.org/10.1016/j.scitotenv.2022.160952
Goodwin, K. D., Schriewer, A., Jirik, A., Curtis, K., and Crumpacker, A. (2017). Consideration of natural sources in a bacteria TMDL-lines of evidence, including beach microbial source tracking. Environmental Science & Technology, 51(14): 7775-7784.https://doi.org/10.1021/acs.est.6b05886
Green, H.C., Haugland, R.A., Varma, M., Millen, H.T., Borchardt, M.A., Field, K.G., Walters, W.A., Knight, R., Sivaganesan, M., Kelty, C.A., and Shanks, O.C., (2014). Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples. Applied Environmental Microbiology, 80(10): 3086-3094.https://doi.org/10.1128/AEM.04137-13
Hart, J. J. (2023). The Application of Microbial Source Tracking to aid in Site Prioritization for Remediation in Lower Michigan, Pp. 250-256.
Harwood, V.J., Staley, C., Badgley, B.D., Borges, K., and Korajkic, A., (2014). Microbial source tracking markers for detection of faecal contamination in environmental waters: re-lationships between pathogens and human health outcomes. Federation of European Microbiological Societies Reviews, 38(1): 1-40.https://doi.org/10.1128/9781555815769.ch2
Hendriksen, R. S., Bortolaia, V., Tate, H., Tyson, G. H., Aarestrup, F. M., and McDermott, P. F. (2019). Using genomics to track global antimicrobial resistance. Frontiers in public health, 7: 242.https://doi.org/10.3389/fpubh.2019.00242
Hinojosa, J., Green, J., Estrada, F., Herrera, J., Mata, T., Phan, D., and Kapoor, V. (2020). Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer. Water Research, 184: 116211.https://doi.org/10.1016/j.watres.2020.116211
Hjorth, M. F., Roager, H. M., Larsen, T. M., Poulsen, S. K., Licht, T. R., Bahl, M. I., and Astrup, A. (2018). Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. International Journal of Obesity, 42(3): 580-583.https://doi.org/10.1038/ijo.2017.220
Hlavsa, M.C., Roberts, V.A., Kahler, A.M., Hilborn, E.D., Mecher, T.R., Beach, M.J., Wade, T.J., and Yoder, J.S., (2015). Outbreaks of illness associated with recreational water-United States. Morbidity and Mortality Weekly Report, 64 (24): 668-672.
Hughes, B., Beale, D.J., Dennis, P.G., Cook, S., and Ahmed, W. (2017). Cross-comparison of human wastewater-associated molecular markers in relation to fecal indicator bacteria and enteric viruses in recreational beach waters. Applied Environmental Microbiology, 83(8):17-28.https://doi.org/10.1128/AEM.00028-17
Karkman, A., Pärnänen, K., and Larsson, D. J. (2019). Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nature communications, 10(1): 80.https://doi.org/10.1038/s41467-018-07992-3
Kheiri, R., and Akhtari, L. (2017). Genetic diversity and antimicrobial resistance of Escherichia coli as microbial source tracking tools of Karaj River, Iran. Water Science and Technology: Water Supply, 17(5): 1468-1478.https://doi.org/10.2166/ws.2017.051
Knapp, M. A., Geeraert, N., Kim, K. and Knee, K. L. (2020). Submarine groundwater discharge (SGD) to coastal waters of Saipan (Commonwealth of the Northern Mariana Islands, USA): implications for nitrogen sources, transport and ecological effects. Water, 12: 124-131.https://doi.org/10.3390/w12113029
Koblentz, G.D., and Tucker, J.B. (2016). Tracing an attack: the promise and pitfalls of microbial forensics. Survival, 52: 159-186.https://doi.org/10.1080/00396331003612521
Kongprajug, A., Chyerochana, N., Somnark, P., Kampaengthong, P. L., Mongkolsuk, S., and Sirikanchana, K. (2019). Human and animal microbial source tracking in a tropical river with multiple land use activities. International Journal of Hygiene and Environmental Health, 222(4): 645-654.https://doi.org/10.1016/j.ijheh.2019.01.005
Korajkic, A., McMinn, B.R., and Harwood, V.J. (2018). Relationship between microbial in-dicators and pathogens in recreational water settings. International Journal Environmental Research and Public Health, 15(12): 28-42.https://doi.org/10.3390/ijerph15122842
Labrador, K. L., Nacario, M. A. G., Malajacan, G. T., Abello, J. J. M., Galarion, L. H., Rensing, C., and Rivera, W. L. (2020). Selecting rep-PCR markers to source track fecal contamination in Laguna Lake, Philippines. Journal of water and health, 18(1): 19-29.https://doi.org/10.2166/wh.2019.042
Marti, R., Ribun, S., Aubin, J.B., Colinon, C., Petit, S., Marjolet, L., Gourmelon, M., Schmitt, L., Breil, P., Cottet, M. and Cournoyer, B. (2017). Human-driven microbiological contamination of benthic and hyporheic sediments of an intermittent peri-urban river assessed from MST and 16S rRNA genetic structure analyses. Front Microbiology, 8: 19-23.https://doi.org/10.3389/fmicb.2017.00019
Mathai, P. P., Staley, C., and Sadowsky, M. J. (2020). Sequence-enabled community-based microbial source tracking in surface waters using machine learning classification: A review. Journal of Microbiological Methods, 177: 106050.https://doi.org/10.1016/j.mimet.2020.106050
McKee, A., Molina, M., Cyterski, M., and Couch, A. (2020). Microbial source tracking (MST) in Chattahoochee River National Recreation Area: seasonal and precipitation trends in MST marker concentrations, and associations with E. coli levels, pathogenic marker presence, and land use. Water research, 171:115435.https://doi.org/10.1016/j.watres.2019.115435
Meier, H., Spinner, K., Crump, L., Kuenzli, E., Schuepbach, G., and Zinsstag, J. (2022). State of Knowledge on the Acquisition, Diversity, Interspecies Attribution and Spread of Antimicrobial Resistance between Humans, Animals and the Environment: A Systematic Review. Antibiotics, 12(1): 73.https://doi.org/10.3390/antibiotics12010073
Nappier, S.P., Hong, T., Ichida, A., Goldstone, A., and Eftim, S.E. (2019). Occurrence of co-liphage in raw wastewater and in ambient water: a meta-analysis. Water Research, 153: 263-273.https://doi.org/10.1016/j.watres.2018.12.058
Nguyen, K.H., Senay, C., Young, S., Nayak, B., Lobos, A., Conrad, J., and Harwood, V.J., (2018). Determination of wild animal sources of fecal indicator bacteria by microbial source tracking (MST) influences regulatory decisions. Water Research, 144, 424-434.https://doi.org/10.1016/j.watres.2018.07.034
Nimer, A., Meneses, N., Watson, Z. D., Shuster, S. M. and Benford, R. (2018). Population survey and management strategies of free-roaming dogs (Canis familiaris) on Saipan, Commonwealth of the Northern Mariana Islands. Journal of Applied Animal Welfare Science, 21: 170-184.https://doi.org/10.1080/10888705.2017.1406801
Nshimyimana, J. P., Cruz, M. C., Wuertz, S., and Thompson, J. R. (2019). Variably improved microbial source tracking with digital droplet PCR. Water research, 159: 192-202.https://doi.org/10.1016/j.watres.2019.04.056
Porter, N. T., Hryckowian, A. J., Merrill, B. D., Fuentes, J. J., Gardner, J. O., Glowacki, R. W., and Martens, E. C. (2020). Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. Nature microbiology, 5(9): 1170-1181.https://doi.org/10.1038/s41564-020-0746-5
Raza, S., Kim, J., Sadowsky, M. J., and Unno, T. (2021). Microbial source tracking using metagenomics and other new technologies. Journal of Microbiology, 59: 259-269.https://doi.org/10.1007/s12275-021-0668-9
Rothenheber, D. (2017). Microbial Source Tracking in Coastal Recreational Waters of Southern Maine: Relationships Between Enterococci, Environmental Factors, Potential Pathogens, and Fecal Sources (Doctoral dissertation, University of New Hampshire), Pp. 278-289.
Rusiñol, M., Hundesa, A., Cárdenas-Youngs, Y., Fernández-Bravo, A., Pérez-Cataluña, A., Moreno-Mesonero, L., and Girones, R. (2020). Microbiological contamination of conventional and reclaimed irrigation water: Evaluation and management measures. Science of The Total Environment, 710: 136298.https://doi.org/10.1016/j.scitotenv.2019.136298
Schramm, M., Gitter, A., and Gregory, L. (2022). Total Maximum Daily Loads and Escherichia coli Trends in Texas Freshwater Streams. Journal of Contemporary Water Research & Education, 176(1): 36-49.https://doi.org/10.1111/j.1936-704X.2022.3374.x
Serwecińska, L., Kiedrzyńska, E., and Kiedrzyński, M. (2021). A catchment-scale assessment of the sanitary condition of treated wastewater and river water based on fecal indicators and carbapenem-resistant Acinetobacter spp. Science of the Total Environment, 750: 142266.https://doi.org/10.1016/j.scitotenv.2020.142266
Shanks, O. C., and Korajkic, A. (2020). Microbial source tracking: characterization of human fecal pollution in environmental waters with HF183 quantitative real-time PCR. In Microbial Forensics. Academic Press. pp. 71-87.https://doi.org/10.1016/B978-0-12-815379-6.00006-4
Shanks, O.C., Green, H., Korajkic, A. and Field, K.G., 2016. Overview of microbial source tracking methods targeting human fecal pollution sources. Manual of Environmental Microbiology, pp.3-4.https://doi.org/10.1128/9781555818821.ch3.4.3
Shanks, O.C., Kelty, C.A., Oshiro, R., Haugland, R.A., Madi, T., Brooks, L., Field, K.G., and Sivaganesan, M. (2016). Data acceptance criteria for standardized human-associated fecal source identification quantitative real-time PCR methods. Applied Environmental Microbiology, 82: 2773-2782.https://doi.org/10.1128/AEM.03661-15
Shenhav, L., Thompson, M., Joseph, T. A., Briscoe, L., Furman, O., Bogumil, D., and Halperin, E. (2019). FEAST: fast expectation-maximization for microbial source tracking. Nature methods, 16(7): 627-632.https://doi.org/10.1038/s41592-019-0431-x
Soller, J., Bartrand, T., Ravenscroft, J., Molina, M., Whelan, G., Schoen, M., and Ashbolt, N., (2018). Estimated human health risks from recreational exposures to stormwater runoff containing animal fecal material. Environmental Modelling Software, 72: 21-32.https://doi.org/10.1016/j.envsoft.2015.05.018
Staley, C., Gordon, K.V., Schoen, M.E., and Harwood, V.J. (2012). Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters. Applied Environmental Microbiology, 78:7317-7326.https://doi.org/10.1128/AEM.01430-12
Stange, C., and Tiehm, A. (2020). Occurrence of antibiotic resistance genes and microbial source tracking markers in the water of a karst spring in Germany. Science of The Total Environment, 742: 140529.https://doi.org/10.1016/j.scitotenv.2020.140529
Steele, J.A., Blackwood, A.D., Griffith, J.F., Noble, R.T., and Schiff, K.C. (2018). Quantification of pathogens and markers of fecal contamination during storm events along popular surfing beaches in San Diego, California. Water Research, 136: 137-149.https://doi.org/10.1016/j.watres.2018.01.056
Sun, D., Jeannot, K., Xiao, Y., and Knapp, C. W. (2019). Horizontal gene transfer mediated bacterial antibiotic resistance. Frontiers in microbiology, 10: 1933.https://doi.org/10.3389/fmicb.2019.01933
Symonds, E.M., Young, S., Verbyla, M.E., McQuaig-Ulrich, S.M., Ross, E., Jiménez, J.A., Harwood, V.J. and Breitbart, M. (2017). Microbial source tracking in shellfish harvesting waters in the Gulf of Nicoya, Costa Rica. Water Research, 111: 177-184.https://doi.org/10.1016/j.watres.2017.01.004
Tan, H., Zhai, Q., and Chen, W. (2019). Investigations of Bacteroides spp. towards next- Teaf generation probiotics. Food Research International, 116: 637-644.https://doi.org/10.1016/j.foodres.2018.08.088
Tang, S., Orsi, R. H., Luo, H., Ge, C., Zhang, G., Baker, R. C., and Wiedmann, M. (2019). Assessment and comparison of molecular subtyping and characterization methods for Salmonella. Frontiers in microbiology, 1591.https://doi.org/10.3389/fmicb.2019.01591
Tarek, M. H., Hubbart, J., and Garner, E. (2023). Microbial source tracking to elucidate the impact of land-use and physiochemical water quality on fecal contamination in a mixed land-use watershed. Science of The Total Environment, 872: 162181.https://doi.org/10.1016/j.scitotenv.2023.162181
Teaf, C. M., Flores, D., Garber, M., and Harwood, V. J. (2018). Toward forensic uses of microbial source tracking. Microbiology Spectrum, 6(1): 6-1.https://doi.org/10.1128/microbiolspec.EMF-0014-2017
Tiwari, A., Oliver, D. M., Bivins, A., Sherchan, S. P., and Pitkänen, T. (2021). Bathing water quality monitoring practices in Europe and the United States. International Journal of Environmental Research and Public Health, 18(11), 5513.https://doi.org/10.3390/ijerph18115513
Vale, F.F. (2016). Microarrays/DNA chips for the detection of waterborne pathogens. Methods in Molecular Biology, 1452: 143-153.https://doi.org/10.1007/978-1-4939-3774-5_9
Wexler, A. G., and Goodman, A. L. (2017). An insider's perspective: Bacteroides as a window into the microbiome. Nature microbiology, 2(5): 1-11.https://doi.org/10.1038/nmicrobiol.2017.26
Whitley, L., Hutchings, P., Cooper, S., Parker, A., Kebede, A., Joseph, S., and Mulejaa, A. (2019). A framework for targeting water, sanitation and hygiene interventions in pastoralist populations in the Afar region of Ethiopia. International Journal of Hygiene and Environmental Health, 222(8): 1133-1144.https://doi.org/10.1016/j.ijheh.2019.08.001
Yoshida, N., Emoto, T., Yamashita, T., Watanabe, H., Hayashi, T., Tabata, T., and Hirata, K. I. (2018). Bacteroides vulgatus and Bacteroides dorei reduce gut microbial lipopolysaccharide production and inhibit atherosclerosis. Circulation, 138(22): 2486-2498.https://doi.org/10.1161/CIRCULATIONAHA.118.033714
Yuknavage, K., Arriola, J., Benavente, D., Camacho, R., Chambers, D., and Derrington, E. (2018). Commonwealth of the Northern Mariana Islands. Water Quality Assessment, 5(6): 178-185.
Zhang, Q., Gallard, J., Wu, B., Harwood, V. J., Sadowsky, M. J., Hamilton, K. A., and Ahmed, W. (2019). Synergy between quantitative microbial source tracking (qMST) and quantitative microbial risk assessment (QMRA): A review and prospectus. Environment international, 130, 104703.https://doi.org/10.1016/j.envint.2019.03.051
Zhang, Y., Wu, R., Lin, K., Wang, Y., and Lu, J. (2020). Performance of host-associated genetic markers for microbial source tracking in China. Water research, 175, 115670.https://doi.org/10.1016/j.watres.2020.115670
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 UMYU Journal of Microbiology Research
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
