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do Nascimento MCA, Smith WJM, Gebrewold M, Liu Y, Simpson SL, Bivins A, Rahal P, Ahmed W. Development and evaluation of a colorimetric LAMP based-assay targeting the Bacteroides HF183 marker for tracking sewage pollution in environmental waters. WATER RESEARCH 2024; 264:122202. [PMID: 39146849 DOI: 10.1016/j.watres.2024.122202] [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: 05/29/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024]
Abstract
Surface waters are vulnerable to contamination by human and animal feces, posing risks to human health due to potential exposure to enteric pathogens. This research developed a colorimetric loop-mediated isothermal amplification (cLAMP) assay to detect sewage associated Bacteroides dorei HF183/BacR287 (HF183) marker in wastewater and environmental water samples. The host sensitivity and host specificity of the assay were evaluated, and their performance was compared to the Bacteroides HF183 qPCR assay using control materials (gBlocks), environmental water samples seeded with untreated sewage, and ambient environmental water samples. In serial dilutions of control materials, qPCR produced quantifiable data across all dilutions, while cLAMP detected the marker down to 0.001 pg/µL of control materials, which was two orders of magnitude less sensitive than qPCR. All untreated sewage samples (n = 12) tested positive for HF183 by both the qPCR and cLAMP assays, demonstrating a host sensitivity value of 1.00 (maximum value of 1.00). The host specificity by analysing 70 non-human fecal nucleic acid samples revealed cLAMP's specificity value of 0.81 compared to qPCR's 0.64. When testing sewage-seeded environmental water samples, both methods detected HF183 for the lowest amount of sewage, indicating similar detection sensitivity. The application of cLAMP for tracking sewage pollution in environmental waters showed promising results, with moderate agreement between cLAMP and qPCR (κ = 0.510). However, cLAMP occasionally missed detections compared to qPCR, particularly in low-concentration samples. Overall, the cLAMP HF183 assay demonstrated promising potential as a rapid and sensitive method for detecting sewage pollution, offering a viable alternative to qPCR in certain environmental monitoring scenarios.
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Affiliation(s)
- Mariah C A do Nascimento
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia; Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | | | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia; State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Stuart L Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Paula Rahal
- Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:121-135. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [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: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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Hachad M, Burnet JB, Sylvestre É, Duy SV, Villemur R, Sauvé S, Prévost M, Qiu JY, Pang X, Dorner S. β-D-glucuronidase activity triggered monitoring of fecal contamination using microbial and chemical source tracking markers at drinking water intakes. WATER RESEARCH 2024; 254:121374. [PMID: 38422696 DOI: 10.1016/j.watres.2024.121374] [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: 10/23/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
Intense rainfall and snowmelt events may affect the safety of drinking water, as large quantities of fecal material can be discharged from storm or sewage overflows or washed from the catchment into drinking water sources. This study used β-d-glucuronidase activity (GLUC) with microbial source tracking (MST) markers: human, bovine, porcine mitochondrial DNA markers (mtDNA) and human-associated Bacteroidales HF183 and chemical source tracking (CST) markers including caffeine, carbamazepine, theophylline and acetaminophen, pathogens (Giardia, Cryptosporidium, adenovirus, rotavirus and enterovirus), water quality indicators (Escherichia coli, turbidity) and hydrometeorological data (flowrate, precipitation) to assess the vulnerability of 3 drinking water intakes (DWIs) and identify sources of fecal contamination. Water samples were collected under baseline, snow and rain events conditions in urban and agricultural catchments (Québec, Canada). Dynamics of E. coli, HF183 and WWMPs were similar during contamination events, and concentrations generally varied over 1 order of magnitude during each event. Elevated human-associated marker levels during events demonstrated that urban DWIs were impacted by recent contamination from an upstream municipal water resource recovery facility (WRRF). In the agricultural catchment, mixed fecal pollution was observed with the occurrences and increases of enteric viruses, human bovine and porcine mtDNA during peak contaminating events. Bovine mtDNA qPCR concentrations were indicative of runoff of cattle-derived fecal pollutants to the DWI from diffuse sources following rain events. This study demonstrated that the suitability of a given MST or CST indicator depend on river and catchment characteristics. The sampling strategy using continuous online GLUC activity coupled with MST and CST markers analysis was a more reliable source indicator than turbidity to identify peak events at drinking water intakes.
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Affiliation(s)
- Mounia Hachad
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada; Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada.
| | - Jean-Baptiste Burnet
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada; Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada
| | - Émile Sylvestre
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada; Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada
| | - Sung Vo Duy
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ, Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Richard Villemur
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Sébastien Sauvé
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ, Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Michèle Prévost
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada
| | - Judy Y Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, 116th & 85 Ave, Edmonton, AB T6G 2R3, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, 116th & 85 Ave, Edmonton, AB T6G 2R3, Canada
| | - Sarah Dorner
- Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montréal, QC, H3C 3A7, Canada
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Adhikary RK, Starrs D, Wright D, Croke B, Glass K, Lal A. Spatio-Temporal Variation in the Exceedance of Enterococci in Lake Burley Griffin: An Analysis of 16 Years' Recreational Water Quality Monitoring Data. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:579. [PMID: 38791793 PMCID: PMC11121496 DOI: 10.3390/ijerph21050579] [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: 02/20/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Recreational waterbodies with high levels of faecal indicator bacteria (FIB) pose health risks and are an ongoing challenge for urban-lake managers. Lake Burley Griffin (LBG) in the Australian Capital city of Canberra is a popular site for water-based recreation, but analyses of seasonal and long-term patterns in enterococci that exceed alert levels (>200 CFU per 100 mL, leading to site closures) are lacking. This study analysed enterococci concentrations from seven recreational sites from 2001-2021 to examine spatial and temporal patterns in exceedances during the swimming season (October-April), when exposure is highest. The enterococci concentrations varied significantly across sites and in the summer months. The frequency of the exceedances was higher in the 2009-2015 period than in the 2001-2005 and 2015-2021 periods. The odds of alert-level concentrations were greater in November, December, and February compared to October. The odds of exceedance were higher at the Weston Park East site (swimming beach) and lower at the Ferry Terminal and Weston Park West site compared to the East Basin site. This preliminary examination highlights the need for site-specific assessments of environmental and management-related factors that may impact the public health risks of using the lake, such as inflows, turbidity, and climatic conditions. The insights from this study confirm the need for targeted monitoring efforts during high-risk months and at specific sites. The study also advocates for implementing measures to minimise faecal pollution at its sources.
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Affiliation(s)
- Ripon Kumar Adhikary
- National Centre for Epidemiology and Population Health, Australian National University, Canberra 2601, Australia; (K.G.); (A.L.)
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Danswell Starrs
- Environment, Planning and Sustainable Development Directorate, ACT Government, Canberra 2601, Australia;
- Research School of Biology, Australian National University, Canberra 2601, Australia
| | - David Wright
- Lake and Dam, National Capital Authority, Canberra 2601, Australia;
| | - Barry Croke
- Institute for Water Futures, Mathematical Sciences Institute and Fenner School of Environment and Society, Australian National University, Canberra 2601, Australia;
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, Australian National University, Canberra 2601, Australia; (K.G.); (A.L.)
| | - Aparna Lal
- National Centre for Epidemiology and Population Health, Australian National University, Canberra 2601, Australia; (K.G.); (A.L.)
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Vadde KK, Phan DC, Moghadam SV, Jafarzadeh A, Matta A, Johnson D, Kapoor V. Fecal pollution source characterization in the surface waters of recharge and contributing zones of a karst aquifer using general and host-associated fecal genetic markers. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:2450-2464. [PMID: 36444711 DOI: 10.1039/d2em00418f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fecal pollution of surface waters in the karst-dominated Edwards aquifer is a serious concern as contaminated waters can rapidly transmit to groundwaters, which are used for domestic purposes. Although microbial source tracking (MST) detects sources of fecal pollution, integrating data related to environmental processes (precipitation) and land management practices (septic tanks) with MST can provide better understanding of fecal contamination fluxes to implement effective mitigation strategies. Here, we investigated fecal sources and their spatial origins at recharge and contributing zones of the Edwards aquifer and identified their relationship with nutrients in different environmental/land-use conditions. During March 2019 to March 2020, water samples (n = 295) were collected biweekly from 11 sampling sites across four creeks and analyzed for six physico-chemical parameters and ten fecal indicator bacteria (FIB) and MST-based qPCR assays targeting general (E. coli, Enterococcus, and universal Bacteroidales), human (BacHum and HF183), ruminant (Rum2Bac), cattle (BacCow), canine (BacCan), and avian (Chicken/Duck-Bac and GFD) fecal markers. Among physico-chemical parameters, nitrate-N (NO3-N) concentrations at several sites were higher than estimated national background concentrations for streams. General fecal markers were detected in the majority of water samples, and among host-associated MST markers, GFD, BacCow, and Rum2Bac were more frequently detected than BacCan, BacHum, and HF183, indicating avian and ruminant fecal contamination is a major concern. Cluster analysis results indicated that sampling sites clustered based on precipitation and septic tank density showed significant correlation (p < 0.05) between nutrients and FIB/MST markers, indicating these factors are influencing the spatial and temporal variations of fecal sources. Overall, results emphasize that integration of environmental/land-use data with MST is crucial for a better understanding of nutrient loading and fecal contamination.
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Affiliation(s)
- Kiran Kumar Vadde
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Duc C Phan
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Sina V Moghadam
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Arash Jafarzadeh
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Akanksha Matta
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Drew Johnson
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Vikram Kapoor
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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Li X, Ahmed W, Wu Z, Xia Y. Developing a novel Bifidobacterium phage quantitative polymerase chain reaction-based assay for tracking untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155815. [PMID: 35550888 DOI: 10.1016/j.scitotenv.2022.155815] [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: 03/24/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Microbial source tracking (MST) tools provide insights on fecal pollution levels in aquatic environments using predominantly quantitative PCR (qPCR) assays that target host-associated molecular marker genes. Existing wastewater-associated marker genes have shown limited or significant cross-reactions with non-human fecal samples. In this study, we mined the current Gut Phage Database (GPD) and designed a novel untreated wastewater-specific Bifidobacterium phage qPCR assay (i.e., Bifi assay). The sensitivity and specificity of the Bifi marker genes were assessed by collectively analyzing untreated (n = 33) and treated (n = 15) wastewater and non-human fecal samples (i.e., Rabbit, mouse, cow, horse, pig, chicken, sheep, dog, deer, kangaroos; n = 113) in Shenzhen, Guangdong Province, China and Brisbane, Australia. Bifi assay revealed 100% host-specificity against non-human fecal samples collected from Shenzhen and Brisbane. Furthermore, this marker gene was also detected in all untreated and treated wastewater samples, whose concentrations ranged from 5.54 to 6.83 log10 GC/L. In Shenzhen, the concentrations of Bifi marker gene were approximately two orders of magnitude lower than Bacteroides (HF183/BacR287 assay) and CrAssphage (CPQ_56 assay). The concentration of Bifi marker gene in untreated wastewater from Brisbane was 1.35 log10 greater than those in Shenzhen. Our results suggest that Bifi marker gene has the potential to detect and quantify the levels of human fecal pollution in Shenzhen and Brisbane. If additional detection sensitivity is required for environmental studies, Bifi marker gene should be paired with either CrAssphage or HF183/BacR287 marker genes.
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Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ziqi Wu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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7
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Williams NLR, Siboni N, Potts J, Campey M, Johnson C, Rao S, Bramucci A, Scanes P, Seymour JR. Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment. WATER RESEARCH 2022; 218:118534. [PMID: 35537251 DOI: 10.1016/j.watres.2022.118534] [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: 11/30/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.
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Affiliation(s)
- Nathan L R Williams
- Climate Change Cluster Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Jaimie Potts
- Waters, Wetlands, Coasts Science Branch, NSW Department of Primary Industries and Environment, Lidcombe, NSW, 2141, Australia
| | - Meredith Campey
- Waters, Wetlands, Coasts Science Branch, NSW Department of Primary Industries and Environment, Lidcombe, NSW, 2141, Australia
| | - Colin Johnson
- Waters, Wetlands, Coasts Science Branch, NSW Department of Primary Industries and Environment, Lidcombe, NSW, 2141, Australia
| | - Shivanesh Rao
- Waters, Wetlands, Coasts Science Branch, NSW Department of Primary Industries and Environment, Lidcombe, NSW, 2141, Australia
| | - Anna Bramucci
- Climate Change Cluster Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Peter Scanes
- Waters, Wetlands, Coasts Science Branch, NSW Department of Primary Industries and Environment, Lidcombe, NSW, 2141, Australia
| | - Justin R Seymour
- Climate Change Cluster Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.
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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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Conrad JW, Harwood VJ. Sewage Promotes Vibrio vulnificus Growth and Alters Gene Transcription in Vibrio vulnificus CMCP6. Microbiol Spectr 2022; 10:e0191321. [PMID: 35171011 PMCID: PMC8849060 DOI: 10.1128/spectrum.01913-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus is a naturally occurring, potentially lethal pathogen found in coastal waters, fish, and shellfish. Sewage spills in coastal waters occur when infrastructure fails due to severe storms or age, and may affect bacterial populations by altering nutrient levels. This study investigated effects of sewage on clonal and natural V. vulnificus populations in microcosms. Addition of 1% sewage to estuarine water caused the density of a pure culture of V. vulnificus CMCP6 and a natural V. vulnificus population to increase significantly, by two to three orders of magnitude, whether measured by quantitative PCR (qPCR) or culture and in batch and continuous cultures. Changes in the transcription of six virulence- and survival-associated genes in response to sewage were assessed using continuous culture. Exposure to sewage affected transcription of genes that may be associated with virulence, i.e., it modulated the oxidative stress response by altering superoxide dismutase transcription, significantly increasing sodB transcription while repressing sodA. Sewage also repressed transcription of nptA, which encodes a sodium-phosphate cotransporter. Sewage had no effect on sodC transcription or the putative virulence-associated genes hupA or wza. The effects of environmentally relevant levels of sewage on V. vulnificus populations and gene transcription suggest that sewage spills that impact warm coastal waters could lead to an increased risk of V. vulnificus infections. IMPORTANCE Vibrio vulnificus infections have profound impacts such as limb amputation and death for individuals with predisposing conditions. The warming climate is contributing to rising V. vulnificus prevalence in waters that were previously too cold to support high levels of the pathogen. Climate change is also expected to increase precipitation in many regions, which puts more pressure on wastewater infrastructure and will result in more frequent sewage spills. The finding that 1% wastewater in estuarine water leads to 100 to over 1,000-fold greater V. vulnificus concentrations suggests that human exposure to oysters and estuarine water could have greater health impacts in the future. Further, wastewater had a significant effect on gene transcription and has the potential to affect virulence during the initial environment-to-host transition.
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Affiliation(s)
- James W. Conrad
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
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10
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Goh SG, Liang L, Gin KYH. Assessment of Human Health Risks in Tropical Environmental Waters with Microbial Source Tracking Markers. WATER RESEARCH 2021; 207:117748. [PMID: 34837748 DOI: 10.1016/j.watres.2021.117748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Human specific microbial source tracking (MST) markers which are highly specific to human waste contamination offer the advantage of better association with human pathogens than traditional microbial indicators. However, the performance of these MST markers may vary across different geographical regions. The magnitude of MST markers also plays an important role in interpreting the health risks. This study aims to (i) validate the specificity and sensitivity of human markers for tropical urban catchments; (ii) identify the threshold concentrations of MST markers, i.e. human polyomaviruses (HPyVs), Bacteroides thetaiotaomicron (B. theta) and Methanobrevibacter smithii (M. smithii), that correspond to the acceptable gastrointestinal (GI) illness risks associated with swimming using the QMRA approach; and (iii) validate the threshold concentrations of MST markers using the surveillance data obtained from the tropical urban environment. Among the three MST markers, HPyVs showed the highest specificity (100%) to sewage samples, followed by M. smithii (97%) and B. theta (90%). All MST markers showed 100% sensitivity towards sewage contamination, with B. theta present in highest abundance in sewage, followed by HPyVs and M. smithii. This study demonstrates a risk-based framework to identify the threshold concentrations of MST markers associated with GI illness risks in environmental waters by considering two main influencing factors (i.e. decay and dilution factors). This study successfully validated the B. theta threshold concentration range (581 to 8073 GC/100 mL) with field data (370 to 6500 GC/100 mL) in estimating GI illness risks with an Enterococcus model. Field data showed that the MST markers at threshold concentrations were able to classify the safe level in more than 83% of the samples, according to GI illness risks from Enterococcus and adenovirus. The study also highlighted the lack of associations between MST markers and GI illness risks from norovirus. With comprehensive information on specificity, sensitivity and threshold concentrations of MST markers, increasing confidence can be placed on identifying human source contamination and evaluating the health risks posed in environmental waters in Singapore.
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Affiliation(s)
- S G Goh
- NUS Environmental Research Institute, National University of Singapore, T-Lab Building, #02-01, 5A Engineering Drive 1 117411, Singapore
| | - L Liang
- Department of Civil & Environmental Engineering, Faculty of Engineering, National University of Singapore, Block E1A, #07-03,1 Engineering Drive 2 117576, Singapore
| | - K Y H Gin
- NUS Environmental Research Institute, National University of Singapore, T-Lab Building, #02-01, 5A Engineering Drive 1 117411, Singapore; Department of Civil & Environmental Engineering, Faculty of Engineering, National University of Singapore, Block E1A, #07-03,1 Engineering Drive 2 117576, Singapore.
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11
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Monteiro S, Ebdon J, Santos R, Taylor H. Elucidation of fecal inputs into the River Tagus catchment (Portugal) using source-specific mitochondrial DNA, HAdV, and phage markers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147086. [PMID: 34088114 DOI: 10.1016/j.scitotenv.2021.147086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Determining the source of fecal contamination in a water body is important for the application of appropriate remediation measures. However, it has been suggested in the extant literature that this can best be achieved using a 'toolbox' of molecular- and culture-based methods. In response, this study deployed three indicators (Escherichia coli (EC), intestinal enterococci (IE) and somatic coliphages (SC)), one culture-dependent human marker (Bacteroides (GB-124) bacteriophage) and five culture-independent markers (human adenovirus (HAdV), human (HMMit), cattle (CWMit), pig (PGMit) and poultry (PLMit) mitochondrial DNA markers (mtDNA)) within the River Tagus catchment (n = 105). Water samples were collected monthly over a 13-month sampling campaign at four sites (impacted by significant specific human and non-human inputs and influenced by differing degrees of marine and freshwater mixing) to determine the dominant fecal inputs and assess geographical, temporal, and meteorological (precipitation, UV, temperature) fluctuations. Our results revealed that all sampling sites were not only highly impacted by fecal contamination but that this contamination originated from human and from a range of agricultural animal sources. HMMit was present in a higher percentage (83%) and concentration (4.20 log GC/100 mL) than HAdV (32%, 2.23 log GC/100 mL) and GB-124 bacteriophage with the latter being detected once. Animal mtDNA markers were detected, with CWMit found in 73% of samples with mean concentration of 3.74 log GC/100 mL. Correlation was found between concentrations of fecal indicators (EC, IE and SC), CWMit and season. Levels of CWMit were found to be related to physico-chemical parameters, such as temperature and UV radiation, possibly as a result of the increasing presence of livestock outside in warmer months. This study provides the first evaluation of such a source-associated 'toolbox' for monitoring surface water in Portugal, and the conclusions may inform future implementation of surveillance and remediation strategies for improving water quality.
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Affiliation(s)
- S Monteiro
- School of Environment and Technology, University of Brighton, Brighton, UK; Laboratorio Analises, Instituto Superior Tecnico, Lisbon, Portugal.
| | - J Ebdon
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - R Santos
- Laboratorio Analises, Instituto Superior Tecnico, Lisbon, Portugal
| | - H Taylor
- School of Environment and Technology, University of Brighton, Brighton, UK
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12
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Sala-Comorera L, Reynolds LJ, Martin NA, O'Sullivan JJ, Meijer WG, Fletcher NF. Decay of infectious SARS-CoV-2 and surrogates in aquatic environments. WATER RESEARCH 2021; 201:117090. [PMID: 34111729 PMCID: PMC8005746 DOI: 10.1016/j.watres.2021.117090] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 05/03/2023]
Abstract
The introduction of SARS-CoV-2 containing human stool and sewage into water bodies may raise public health concerns. However, assessment of public health risks by faecally contaminated water is limited by a lack of knowledge regarding the persistence of infectious SARS-CoV-2 in water. In the present study the decay rates of viable infectious SARS-CoV-2 and SARS-CoV-2 RNA were determined in river and seawater at 4 and 20°C. These decay rates were compared to S. typhimurium bacteriophage MS2 and pepper mild mottle virus (PMMoV). Persistence of viable SARS-CoV-2 was temperature dependent, remaining infectious for significantly longer periods of time in both freshwater and seawater at 4°C than at 20°C. T90 for infectious SARS-CoV-2 in river water was 2.3 days and 3.8 days at 20°C and 4°C, respectively. The T90 values were 1.1 days and 2.2 days in seawater at 20°C and 4°C, respectively. In contrast to the rapid inactivation of infectious SARS-CoV-2 in river and sea water, viral RNA was relatively stable. The RNA decay rates were increased in non-sterilised river and seawater, presumably due to the presence of microbiota. The decay rates of infectious MS2, MS2 RNA and PMMoV RNA differed significantly from the decay rate of SARS-CoV-2 RNA, suggesting that their use as surrogate markers for the persistence of SARS-CoV-2 in the environment is limited.
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Affiliation(s)
- Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Nicola F Fletcher
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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13
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Ahmed W, Gyawali P, Hamilton KA, Joshi S, Aster D, Donner E, Simpson SL, Symonds EM. Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow. Front Microbiol 2021; 12:632850. [PMID: 34177821 PMCID: PMC8226142 DOI: 10.3389/fmicb.2021.632850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/29/2021] [Indexed: 12/26/2022] Open
Abstract
Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except blaVIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd. (ESR), Porirua, New Zealand
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, United States.,Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Sayalee Joshi
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, United States.,Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - David Aster
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA, Australia
| | | | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, St. Petersburg, FL, United States
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14
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Bonanno Ferraro G, Suffredini E, Mancini P, Veneri C, Iaconelli M, Bonadonna L, Montagna MT, De Giglio O, La Rosa G. Pepper Mild Mottle Virus as Indicator of Pollution: Assessment of Prevalence and Concentration in Different Water Environments in Italy. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:117-125. [PMID: 33432501 DOI: 10.1007/s12560-020-09458-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Pepper mild mottle virus (PMMoV), a plant pathogenic virus belonging to the family Virgoviridae, has been proposed as a potential viral indicator for human faecal pollution in aquatic environments. The present study investigated the occurrence, amount and diversity of PMMoV in water environments in Italy. A total of 254 water samples, collected between 2017 and 2019 from different types of water, were analysed. In detail, 92 raw sewage, 32 treated sewage, 16 river samples, 9 estuarine waters, 20 bathing waters, 67 groundwater samples and 18 drinking waters were tested. PMMoV was detected in 79% and 75% of untreated and treated sewage samples, respectively, 75% of river samples, 67% and 25% of estuarine and bathing waters and 13% of groundwater samples. No positive was detected in drinking water. The geometric mean of viral concentrations (genome copies/L) was ranked as follows: raw sewage (2.2 × 106) > treated sewage (2.9 × 105) > river waters (6.1 × 102) > estuarine waters (4.8 × 102) > bathing waters (8.5 × 101) > groundwater (5.9 × 101). A statistically significant variation of viral loads could be observed between raw and treated sewage and between these and all the other water matrices. PMMoV occurrence and viral loads did not display seasonal variation in raw sewage nor correlation with faecal indicator bacteria in marine waters and groundwater. This study represents the first report on the occurrence and quantification PMMoV in different water environments in Italy. Further studies are required to evaluate the suitability of PMMoV as a viral indicator for human faecal pollution and for viral pathogens in waters.
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Affiliation(s)
- G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M T Montagna
- Department of Biomedical Sciences and Human Oncology, Section of Hygiene, University of Bari Aldo Moro, Bari, Italy
| | - O De Giglio
- Department of Biomedical Sciences and Human Oncology, Section of Hygiene, University of Bari Aldo Moro, Bari, Italy
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
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15
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Ahmed W, Payyappat S, Cassidy M, Harrison N, Besley C. Interlaboratory accuracy and precision among results of three sewage-associated marker genes in urban environmental estuarine waters and freshwater streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140071. [PMID: 32887015 DOI: 10.1016/j.scitotenv.2020.140071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/06/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
The application of quantitative polymerase chain reaction (qPCR) based microbial source tracking (MST) marker genes are increasingly being used to identify contaminating sources and inform management decisions. In this study, we assessed interlaboratory agreement on duplicate environmental water samples collected from estuarine and freshwater locations, by comparing results of qPCR based testing for Bacteroides HF183, crAssphage CPQ_056, and pepper mild mottle virus (PMMoV). The overall agreements (co-detection and non-co-detection) between CSIRO Land and Water (CLW) laboratory and Sydney Water (SW) laboratory for the HF183, crAssphage CPQ_056 and PMMoV marker genes for duplicate water samples were 74, 75 and 74%, respectively. Cohene's kappa (k) revealed fair to moderate agreements and acceptable relative percent difference (RPD) values of <15% for duplicate samples. The pooled mean abundances of HF183, CPQ_056, and PMMoV in measurable samples at the CLW laboratory were 5.19 ± 0.93, 5.12 ± 0.82, and 4.42 ± 0.65 log10 copies/L, respectively. However, the pooled mean abundances were significantly lower at the SW laboratory, HF183 (4.58 ± 0.84 log10 copies/L), crAssphage CPQ_056 (4.20 ± 0.63 log10 copies/L), and PMMoV (3.89 ± 0.41 log10 copies/L). At individual sample level, most of the paired samples had <1 log10 difference. Significant positive Spearman rank correlations were obtained between two laboratories for the HF183 (Rs = 0.65; p < 0.05), CPQ_056 (Rs = 0.79; p < 0.05), and PMMoV (Rs = 0.54; p < 0.05) marker genes. Several factors such as standards, qPCR platforms, PCR inhibitors, nucleic acid extraction efficiency and low levels of targets in some samples may have contributed to the observed discrepancies. Results presented in this study highlight the importance of standardized protocol, laboratory equipment (such as digital PCR), sample processing strategies and appropriate quality controls that may need implementation to further improve accuracy and precision of results between laboratories.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Nathan Harrison
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
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16
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Bunce JT, Robson A, Graham DW. Seasonal influences on the use of genetic markers as performance indicators for small wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:139928. [PMID: 32540662 DOI: 10.1016/j.scitotenv.2020.139928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
The development of microbial source tracking methods has resulted in an array of genetic faecal markers for assessing human health risks posed from surface water pollution. However, their use as performance metrics at wastewater treatment plants (WWTPs) has not been explored extensively. Here we compared three Bacteroides (HF183, HumM2, AllBac) and two E. coli (H8, RodA) genetic markers for summer and winter performance monitoring at twelve small rural (<250 PE) and three larger WWTPs in NE England. Small WWTPs are of interest because they are poorly understood and their impact on surface water quality may be underestimated. Overall, genetic marker data showed significant differences in treatment performance at smaller versus larger WWTPs. For example, effluent abundances of HF183 and HumM2 were significantly higher in smaller systems (p = 0.003 for HumM2; p = 0.02 for HF183). Genetic markers also showed significant differences in performance between seasons (p < 0.01, n = 120), with human-specific markers (i.e., HF183, HumM2, H8) being generally better for summer WWTP monitoring. In contrast, Bacteroides markers were much more suitable for winter monitoring, possibly because the E. coli markers are less sensitive to differences in temperature and sunlight conditions. Overall, Bacteroides markers best described WWTP treatment performance across all samples, although seasonal differences suggest caution is needed when markers are used for performance monitoring. Genetic markers definitely provide rapid and new information about WWTP performance, but more spatially diverse studies are needed to refine their use for routine WWTP monitoring.
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Affiliation(s)
- Joshua T Bunce
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Aidan Robson
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK.
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17
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Ahmed W, Payyappat S, Cassidy M, Harrison N, Marinoni O, Besley C. Prevalence and abundance of traditional and host-associated fecal indicators in urban estuarine sediments: Potential implications for estuarine water quality monitoring. WATER RESEARCH 2020; 184:116109. [PMID: 32818744 DOI: 10.1016/j.watres.2020.116109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/25/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to determine the prevalence and abundance of sewage and animal fecal contamination of sediment at seven estuarine locations in Sydney, NSW, Australia. Sediment samples were tested for the occurrence of microbial targets including molecular marker genes of enterococci (ENT), Bacteroides HF183 (HF183), Methanobrevibacter smithii (nifH), human adenovirus (HAdV) and emerging sewage-associated marker genes crAssphage (CPQ_056) and Lachnospiraceae (Lachno3) and animal feces-associated marker genes, including avian feces-associated Helicobacter spp. (GFD), canine-feces associated Bacteroides (DogBact), cattle-feces associated (cowM2) and horse feces-associated Bacteroides (HoF597). Results from this study showed that urban estuarine sediment can act as a reservoir of fecal indicator bacteria (FIB) and several microbial source tracking (MST) marker genes, including previously unreported Lachno3. The sewage-associated marker gene CPQ_056 was most prevalent, in 63.8% of sediment samples, while the avian associated marker gene GFD had the highest mean abundance. The GFD marker gene was highly abundant and widely detected in sediment samples from all seven locations compared to the other animal feces-associated marker genes. In all, 31 (44.9%) sediment samples were positive for at least two sewage-associated marker genes. However, the non-quantifiable detection of the HAdV marker gene did not always align with the detection of two or more sewage-associated marker genes. In addition, the most frequent wet weather overflow exposure occurred at locations that did not have a consistent pattern of detection of the sewage-associated marker genes, suggesting sediments may not be a suitable measure of recent sewage contamination. To assist water quality and public health managers better understand past microbial contamination of estuarine sediment, further studies seem justified to explore the role of decay of MST marker genes in sediment. Further work is also needed on the role of resuspension of MST marker genes from sediment during storm events to the water column as a source of contamination for both the GFD and sewage-associated marker genes.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
| | - Nathan Harrison
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
| | - Oswald Marinoni
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
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18
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Holcomb DA, Stewart JR. Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality. Curr Environ Health Rep 2020; 7:311-324. [PMID: 32542574 PMCID: PMC7458903 DOI: 10.1007/s40572-020-00278-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination. RECENT FINDINGS This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.
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Affiliation(s)
- David A Holcomb
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Dr., Chapel Hill, NC, 27599-7435, USA
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Dr., Chapel Hill, NC, 27599-7431, USA.
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19
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Kongprajug A, Chyerochana N, Mongkolsuk S, Sirikanchana K. Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8232-8244. [PMID: 32484662 DOI: 10.1021/acs.est.0c01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log10 copies/g and 0.41 log10 copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log10 copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.
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Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
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20
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Ahmed W, Payyappat S, Cassidy M, Harrison N, Besley C. Sewage-associated marker genes illustrate the impact of wet weather overflows and dry weather leakage in urban estuarine waters of Sydney, Australia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135390. [PMID: 31838427 DOI: 10.1016/j.scitotenv.2019.135390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 05/18/2023]
Abstract
This study investigates the impact of wet weather overflows (WWOs) at three estuarine locations in Sydney, NSW, Australia. WWOs can occur when infiltration of stormwater leads to an excess volume of flow within the sewerage system, resulting in the release of diluted sewage into the environment. Sewage contamination poses a risk to human health due to the presence of pathogens. The magnitude of sewage contamination was monitored using established and novel sewage-associated marker genes, Bacteroides HF183, pepper mild mottle virus (PMMoV), crAssphage CPQ_056, Lachnospiraceae (Lachno3) marker genes along with culturable fecal indicator bacteria (FIB) Escherichia coli (E. coli) and enterococci. Water samples were collected at two water depths (0.5 m below the water surface and 1 m above the bottom surface) during one dry weather and two storm events. Analysis of sewage-associated marker genes showed greater (i.e., 3-5 orders of magnitude) concentrations in water samples collected during the storm events compared to dry weather event. Water samples were also analysed for four animal feces-associated marker genes targeting avian (GFD), dog (BacCan-UCD), cow (cowM2) and horse (HoF597) species to determine the extent of animal fecal contamination. Among the four marker genes, cowM2 and HoF597 could not be detected, while GFD marker gene was consistently present and BacCan-UCD was occasionally detected. Overall results suggested that after rainfall, untreated sewage from WWOs was present at sampling locations. In addition, microbial source tracking (MST) monitoring was able to distinguish the presence of a leaking sewer impacting on the recreational area during dry weather condition. This study demonstrated the capability of the MST monitoring approach to understand sources (sewage or animal) of fecal contamination. This capability will greatly enhance management decisions assisting in the prioritisation of remediation efforts of the sewerage system to improve estuarine bathing water quality and diminish human health risk.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Nathan Harrison
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
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