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Tillett BJ, Sharley D, Almeida MIGS, Valenzuela I, Hoffmann AA, Pettigrove V. A short work-flow to effectively source faecal pollution in recreational waters - A case study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1503-1510. [PMID: 30743863 DOI: 10.1016/j.scitotenv.2018.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/01/2018] [Accepted: 07/01/2018] [Indexed: 06/09/2023]
Abstract
Microbial pollution of recreational waters poses a significant public health risk which, unless mitigated, will continue to increase with population growth. Water managers must implement strategies to accurately discriminate and source human from animal faecal contamination in complex urbanised environments. Our case-study used a new combination of chemical (i.e. ammonia) and microbial (i.e. Escherichia coli, Bacteroides spp.) faecal monitoring tools in a targeted multi-tiered approach to quickly identify pollution hot-spots and track high-risk subterranean stormwater drains in real-time. We successfully located three point sources of human faecal pollution (both episodic and constant pollution streams) within 11 catchments in a total monitoring time of four months. Alternative approaches for obtaining such fine-scale accuracy are typically labour intensive and require expensive equipment.
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Affiliation(s)
- Bree J Tillett
- Centre for Aquatic Pollution Identification and Management, School of Biosciences, The University of Melbourne, Parkville 3052, Australia; Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville 3052, Australia.
| | - David Sharley
- Centre for Aquatic Pollution Identification and Management, School of Biosciences, The University of Melbourne, Parkville 3052, Australia
| | - M Inês G S Almeida
- Centre for Aquatic Pollution Identification and Management, School of Chemistry, The University of Melbourne, Parkville 3010, Australia
| | - Isabel Valenzuela
- Centre for Aquatic Pollution Identification and Management, School of Biosciences, The University of Melbourne, Parkville 3052, Australia; Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville 3052, Australia
| | - Ary A Hoffmann
- Centre for Aquatic Pollution Identification and Management, School of Biosciences, The University of Melbourne, Parkville 3052, Australia; Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville 3052, Australia
| | - Vincent Pettigrove
- Centre for Aquatic Pollution Identification and Management, School of Biosciences, The University of Melbourne, Parkville 3052, Australia; Aquatic Pollution Prevention Partnership, College of Science, Engineering & Health, RMIT University, PO Box 71, Bundoora 3078, Australia
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Wanjugi P, Sivaganesan M, Korajkic A, Kelty CA, McMinn B, Ulrich R, Harwood VJ, Shanks OC. Differential decomposition of bacterial and viral fecal indicators in common human pollution types. WATER RESEARCH 2016; 105:591-601. [PMID: 27693971 PMCID: PMC7440646 DOI: 10.1016/j.watres.2016.09.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 05/19/2023]
Abstract
Understanding the decomposition of microorganisms associated with different human fecal pollution types is necessary for proper implementation of many water quality management practices, as well as predicting associated public health risks. Here, the decomposition of select cultivated and molecular indicators of fecal pollution originating from fresh human feces, septage, and primary effluent sewage in a subtropical marine environment was assessed over a six day period with an emphasis on the influence of ambient sunlight and indigenous microbiota. Ambient water mixed with each fecal pollution type was placed in dialysis bags and incubated in situ in a submersible aquatic mesocosm. Genetic and cultivated fecal indicators including fecal indicator bacteria (enterococci, E. coli, and Bacteroidales), coliphage (somatic and F+), Bacteroides fragilis phage (GB-124), and human-associated genetic indicators (HF183/BacR287 and HumM2) were measured in each sample. Simple linear regression assessing treatment trends in each pollution type over time showed significant decay (p ≤ 0.05) in most treatments for feces and sewage (27/28 and 32/40, respectively), compared to septage (6/26). A two-way analysis of variance of log10 reduction values for sewage and feces experiments indicated that treatments differentially impact survival of cultivated bacteria, cultivated phage, and genetic indicators. Findings suggest that sunlight is critical for phage decay, and indigenous microbiota play a lesser role. For bacterial cultivated and genetic indicators, the influence of indigenous microbiota varied by pollution type. This study offers new insights on the decomposition of common human fecal pollution types in a subtropical marine environment with important implications for water quality management applications.
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Affiliation(s)
- Pauline Wanjugi
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Asja Korajkic
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Catherine A Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Brian McMinn
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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Griffith JF, Weisberg SB, Arnold BF, Cao Y, Schiff KC, Colford JM. Epidemiologic evaluation of multiple alternate microbial water quality monitoring indicators at three California beaches. WATER RESEARCH 2016; 94:371-381. [PMID: 27040577 DOI: 10.1016/j.watres.2016.02.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Advances in molecular methods provide new opportunities for directly measuring pathogens or host-associated markers of fecal pollution instead of relying on fecal indicator bacteria (FIB) alone for beach water quality monitoring. Adoption of new indicators depends on identifying relationships between either the presence or concentration of the indicators and illness among swimmers. Here we present results from three epidemiologic studies in which a broad range of bacterial and viral indicators of fecal contamination were measured simultaneously by either culture or molecular methods along with Enterococcus to assess whether they provide better health risk prediction than current microbial indicators of recreational water quality. METHODS We conducted prospective cohort studies at three California beaches -- Avalon Bay (Avalon), Doheny State Beach (Doheny), Surfrider State Beach (Malibu) -- during the summers of 2007, 2008 and 2009. The studies enrolled 10,785 swimmers across the beaches and recorded each swimmer's water exposure. Water and sand samples were collected several times per day at multiple locations at each beach and analyzed for up to 41 target indicators using 67 different methodologies. Interviewers contacted participants by phone 10-14 days later and recorded symptoms of gastrointestinal illness occurring after their beach visit. Regression models were used to evaluate the association between water quality indicators and gastrointestinal illness among swimmers at each beach. RESULTS F+ coliphage (measured using EPA Method 1602) exhibited a stronger association with GI illness than did EPA Method 1600 at the two beaches where it was measured, while a molecular method, F+ RNA Coliphage Genotype II, was the only indicator significantly associated with GI illness at Malibu. MRSA, a known pathogen, had the strongest association with GI illness of any microbe measured at Avalon. There were two methods targeting human-associated fecal anaerobic bacteria that were more strongly associated with GI illness than EPA Method 1600, but only at Avalon. No indicator combinations consistently had a higher odds ratio than EPA Method 1600, but one composite indicator, based on the number of pathogens detected at a beach, was significantly associated with gastrointestinal illness at both Avalon and Doheny when freshwater flow was high. DISCUSSION While EPA Method1600 performed adequately at two beaches based on its consistency of association with gastrointestinal illness and the precision of its estimated associations, F+ coliphage measured by EPA Method 1602 had a stronger association with GI illness under high risk conditions at the two beaches where it was measured. One indicator, F+ Coliphage Genotype II was the only indicator significantly associated with GI illness at Malibu. Several indicators, particularly those targeting human associated bacteria, exhibited relationships with GI illness that were equal to or greater than that of EPA Method 1600 at Avalon, which has a focused human fecal source. Our results suggest that site-specific conditions at each beach determine which indicator or indicators best predict GI illness.
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Affiliation(s)
- John F Griffith
- Department of Microbiology, Southern California Coastal Water Research Project, 3535 Harbor Blvd. Suite 110, Costa Mesa, CA 92626, USA.
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA
| | - Benjamin F Arnold
- Division of Epidemiology, School of Public Health, University of California, Berkeley, USA
| | - Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA
| | - Kenneth C Schiff
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA, USA
| | - John M Colford
- Division of Epidemiology, School of Public Health, University of California, Berkeley, USA
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Walsh CJ, Guinane CM, Hill C, Ross RP, O'Toole PW, Cotter PD. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database. BMC Microbiol 2015; 15:183. [PMID: 26377179 PMCID: PMC4573289 DOI: 10.1186/s12866-015-0515-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/08/2015] [Indexed: 01/12/2023] Open
Abstract
Background The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated. Results We identified 74 clusters of note from 59 unique members of the Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Synergistetes. The most commonly identified class of bacteriocin was the >10 kDa class, formerly known as bacteriolysins, followed by lantibiotics and sactipeptides. Conclusions Multiple bacteriocin gene clusters were identified in a dataset representative of the human gut microbiota. Interestingly, many of these were associated with species and genera which are not typically associated with bacteriocin production. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0515-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Calum J Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Paul W O'Toole
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland. .,APC Microbiome Institute, University College Cork, Cork, Ireland.
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