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Andrianjakarivony FH, Bettarel Y, Desnues C. Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments. J Microbiol 2023:10.1007/s12275-023-00052-6. [PMID: 37261715 DOI: 10.1007/s12275-023-00052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.
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Affiliation(s)
- Felana Harilanto Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, 13005, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 13009, Marseille, France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, 34090, Montpellier, France.
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, 13005, Marseille, France
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Chaganti SR, Plouff C, Madani M, Shahraki AH, Vasquez AA, Seth R, Heath DD, Ram JL. Variation in the diversity of bacterial communities and potential sources of fecal contamination of beaches in the Huron to Erie corridor. WATER RESEARCH 2022; 222:118913. [PMID: 35940154 DOI: 10.1016/j.watres.2022.118913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/03/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week for 12 weeks in summer, were subjected to 16S rRNA analysis of amplicon sequencing and E. coli enumeration. Bacterial communities changed over time, as determined by cluster dendrogram analysis, exhibiting different communities in July and August than in June and different communities at the two beaches. After June, alpha diversity decreased and relative abundance of Enterobacter (Gammaproteobacteria) increased at Sand Point; whereas, Belle Isle maintained its alpha diversity and dominance by Betaproteobacteria and Actinobacteria. Contamination at both beaches is dominated by birds (23% to 50% of samples), while only ∼10% had evidence of human-associated bacteria. High E. coli at both beaches was often associated with precipitation. Nearshore sampling counts were higher than waist-deep sampling counts. Despite the dynamic changes in bacterial communities between the two beaches, this analysis based on 16S rRNA amplicon sequencing is able to provide information about bacterial types associated with high E. coli levels and to use bacterial sequences to more precisely determine sources and health relevance of contaminants.
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Affiliation(s)
- Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Claire Plouff
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States
| | - Mohammad Madani
- Department of Civil & Environmental Engineering, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
| | | | - Adrian A Vasquez
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States; Department of Physiology, Wayne State University, 540 E. Canfield St., Detroit, MI 48201, United States
| | - Rajesh Seth
- Department of Civil & Environmental Engineering, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada
| | - Jeffrey L Ram
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States; Department of Physiology, Wayne State University, 540 E. Canfield St., Detroit, MI 48201, United States.
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Microbial Source Tracking as a Method of Determination of Beach Sand Contamination. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137934. [PMID: 35805592 PMCID: PMC9265816 DOI: 10.3390/ijerph19137934] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023]
Abstract
Beach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring.
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An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments. WATER 2022. [DOI: 10.3390/w14111809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fecal contamination of water constitutes a serious health risk to humans and environmental ecosystems. This is mainly due to the fact that fecal material carries a variety of enteropathogens, which can enter and circulate in water bodies through fecal pollution. In this respect, the prompt identification of the polluting source(s) is pivotal to guiding appropriate target-specific remediation actions. Notably, microbial source tracking (MST) is widely applied to determine the host origin(s) contributing to fecal water pollution through the identification of zoogenic and/or anthropogenic sources of fecal environmental DNA (eDNA). A wide array of host-associated molecular markers have been developed and exploited for polluting source attribution in various aquatic ecosystems. This review is intended to provide the most up-to-date overview of genetic marker-based MST studies carried out in different water types, such as freshwaters (including surface and groundwaters) and seawaters (from coasts, beaches, lagoons, and estuaries), as well as drinking water systems. Focusing on the latest scientific progress/achievements, this work aims to gain updated knowledge on the applicability and robustness of using MST for water quality surveillance. Moreover, it also provides a future perspective on advancing MST applications for environmental research.
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Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review. Processes (Basel) 2021. [DOI: 10.3390/pr9112058] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.
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Park S, Lee C, Cho K, Ko HY, Jang SJ, Ko G. Improved real-time quantitative reverse transcription PCR detection of norovirus following removal of inhibitors. Heliyon 2021; 7:e07560. [PMID: 34345738 PMCID: PMC8319527 DOI: 10.1016/j.heliyon.2021.e07560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 07/09/2021] [Indexed: 02/04/2023] Open
Abstract
Human norovirus (HuNoV) is an important enteric virus that can cause large gastroenteritis outbreaks via the fecal-oral route from contaminated water and produce. Real-time quantitative reverse transcription PCR (RT-qPCR) is the only method to apply the routine detection of HuNoV in various samples, however, inhibitors present in the samples can affect the accuracy and sensitivity of RT-qPCR results. Here, we suggest an inhibitor-removal treatment for two types of noroviruses using two commercial kits. Two types of water sample (surface and seawater) and four types of produce (green onions, lettuces, radishes, and strawberries) were evaluated. The recovery efficiencies of noroviruses in water samples clearly increased in surface and seawater samples with the inhibitor-removal treatment compared to untreated samples. Moreover, murine norovirus-1 was well recovered from the four types of produce with the inhibitor-removal treatment. The mean recovery efficiencies of HuNoV genogroup II genotype 4 in lettuces and strawberries were also increased in the treated samples. Therefore, we suggest that the inhibitor-removal treatment could be useful for improving the accuracy and sensitivity of RT-qPCR methods for noroviruses in water and produce.
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Affiliation(s)
- SungJun Park
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.,N-Bio, Seoul National University, Seoul, Republic of Korea
| | - Cheonghoon Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Kyuseon Cho
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Hye Young Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Sung Jae Jang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.,N-Bio, Seoul National University, Seoul, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
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Lee J, Park S, Lee C, Cho K, Jeong YS, Kim YM, Park KS, Choi JD, Sin Y, Ko G. Male-Specific and Somatic Coliphage Profiles from Major Aquaculture Areas in Republic of Korea. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:240-249. [PMID: 32666472 DOI: 10.1007/s12560-020-09438-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Human and animal feces are important sources of various types of microbial contamination in water. Especially, enteric viruses, the major agents of waterborne infection, can attain long-term survival in water environments due to their strong resistance to various environmental factors including pH, salinity, and temperature. Coliphages are promising viral indicators for fecal contamination in water environments. Here, we investigated the seasonal and spatial distribution of male-specific and somatic coliphages in surface water and seawater at three major aquaculture areas, including Goseong Bay, Aphae Island, and Gomso Bay, in Republic of Korea over a period of 1 year. We selected 6 surface water and 14 seawater sampling sites for each study area and collected a total of 480 water samples from March 2014 to February 2015. Overall, surface water samples contained higher occurrences of coliphages than seawater samples. The high coliphage concentrations were detected in spring (March to May 2014). The differences in geographical features and patterns in land usage of the three aquaculture areas may have affected the coliphage concentration and occurrence. Moreover, environmental factors such as cumulative precipitation were strongly correlated with coliphage concentrations. Therefore, we suggest that further longitudinal studies on coliphage concentrations and distributions should be performed to support the application of coliphages in tracking fecal contamination in water.
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Affiliation(s)
- JaeYoon Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - SungJun Park
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- N-Bio, Seoul National University, Seoul, Republic of Korea
| | - Cheonghoon Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
| | - Kyuseon Cho
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Yong Seok Jeong
- Department of Biology, College of Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Young-Mog Kim
- Marine-Integrated Bionics Research Center, Pukyong National University, Busan, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | - Kwon-Sam Park
- Department of Food Science and Biotechnology, Kunsan National University, Gunsan, Republic of Korea
| | - Jong Duck Choi
- Department of Seafood Science and Technology, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Yongsik Sin
- Department of Environmental Engineering & Biotechnology, Mokpo National Maritime University, Mokpo, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.
- N-Bio, Seoul National University, Seoul, Republic of Korea.
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
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Ishii S. Ecology of Pathogens and Antibiotic-resistant Bacteria in Environments: Challenges and Opportunities. Microbes Environ 2019; 34:1-4. [PMID: 30930405 PMCID: PMC6440737 DOI: 10.1264/jsme2.me3401rh] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Satoshi Ishii
- Department of Soil, Water, and Climate, University of Minnesota.,BioTechnology Institute, University of Minnesota
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Cho K, Lee C, Park S, Kim JH, Choi YS, Kim MS, Koo ES, Yoon HJ, Kang JH, Jeong YS, Choi JD, Ko G. Use of coliphages to investigate norovirus contamination in a shellfish growing area in Republic of Korea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:30044-30055. [PMID: 30076551 DOI: 10.1007/s11356-018-2857-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
A number of severe norovirus outbreaks due to the consumption of contaminated shellfish have been reported recently. In this study, we evaluated the distribution of coliphage densities to determine their efficacy as fecal indicators of enteric viruses, including noroviruses, in water samples collected from a shellfish growing area in Republic of Korea over a period of approximately 1 year. Male-specific and somatic coliphages in water samples were analyzed using the single agar layer method, and norovirus genogroups I and II, which infect mainly humans, were analyzed using duplex reverse transcription quantitative PCR. Male-specific and somatic coliphages were detected widely throughout the study area. Several environmental parameters, including salinity, precipitation, temperature, and wind speed were significantly correlated with coliphage concentrations (P < 0.05). Moreover, the concentrations of male-specific coliphages were positively correlated with the presence of human noroviruses (r = 0.443; P < 0.01). The geospatial analysis with coliphage concentrations using a geographic information system revealed that densely populated residential areas were the major source of fecal contamination. Our results indicate that coliphage monitoring in water could be a useful approach to prevent norovirus contamination in shellfish.
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Affiliation(s)
- Kyuseon Cho
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
| | - Cheonghoon Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
- Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
| | - SungJun Park
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
- N-Bio, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
| | - Jin Hwi Kim
- Department of Civil and Environmental Engineering, Dongguk University, 1 Pildong-ro, Jung-gu, Seoul, Republic of Korea
| | - Yong Seon Choi
- Department of Biology, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Man Su Kim
- Department of Biology, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Eung Seo Koo
- Department of Biology, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Hyun Jin Yoon
- Department of Seafood Science and Technology, Gyeongsang National University, 38 Cheondaegukchi-gil, Tongyeong-si, Gyeongsangnam-do, Republic of Korea
| | - Joo-Hyon Kang
- Department of Civil and Environmental Engineering, Dongguk University, 1 Pildong-ro, Jung-gu, Seoul, Republic of Korea
| | - Yong Seok Jeong
- Department of Biology, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Jong Duck Choi
- Department of Seafood Science and Technology, Gyeongsang National University, 38 Cheondaegukchi-gil, Tongyeong-si, Gyeongsangnam-do, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea.
- N-Bio, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea.
- Center for Human and Environmental Microbiome, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea.
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