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Monteiro S, Machado-Moreira B, Linke R, Blanch AR, Ballesté E, Méndez J, Maunula L, Oristo S, Stange C, Tiehm A, Farnleitner AH, Santos R, García-Aljaro C. Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study. Int J Hyg Environ Health 2023; 253:114241. [PMID: 37611533 DOI: 10.1016/j.ijheh.2023.114241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/07/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.
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Affiliation(s)
- Sílvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; CERIS, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, EN. 10, 2695-066, Bobadela, Portugal.
| | - Bernardino Machado-Moreira
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal
| | - Rita Linke
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorferstr. 1a, 1060, Vienna, Austria
| | - Anicet R Blanch
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
| | - Elisenda Ballesté
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
| | - Javier Méndez
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
| | - Leena Maunula
- Dept. Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Satu Oristo
- Dept. Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Claudia Stange
- Dept. Water Microbiology, DVGW-Technologiezentrum Wasser, Germany
| | - Andreas Tiehm
- Dept. Water Microbiology, DVGW-Technologiezentrum Wasser, Germany
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorferstr. 1a, 1060, Vienna, Austria; Karl Landsteiner University of Health Sciences, Research Division Water Quality and Health, Dr.- Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; CERIS, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, EN. 10, 2695-066, Bobadela, Portugal
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2
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Rugh MB, Grant SB, Hung WC, Jay JA, Parker EA, Feraud M, Li D, Avasarala S, Holden PA, Liu H, Rippy MA, Werfhorst LCVD, Kefela T, Peng J, Shao S, Graham KE, Boehm AB, Choi S, Mohanty SK, Cao Y. Highly variable removal of pathogens, antibiotic resistance genes, conventional fecal indicators and human-associated fecal source markers in a pilot-scale stormwater biofilter operated under realistic stormflow conditions. WATER RESEARCH 2022; 219:118525. [PMID: 35533621 DOI: 10.1016/j.watres.2022.118525] [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: 02/08/2022] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Green stormwater infrastructure systems, such as biofilters, provide many water quality and other environmental benefits, but their ability to remove human pathogens and antibiotic resistance genes (ARGs) from stormwater runoff is not well documented. In this study, a field scale biofilter in Southern California (USA) was simultaneously evaluated for the breakthrough of a conservative tracer (bromide), conventional fecal indicators, bacterial and viral human-associated fecal source markers (HF183, crAssphage, and PMMoV), ARGs, and bacterial and viral pathogens. When challenged with a 50:50 mixture of untreated sewage and stormwater (to mimic highly contaminated storm flow) the biofilter significantly removed (p < 0.05) 14 of 17 microbial markers and ARGsin descending order of concentration reduction: ermB (2.5 log(base 10) reduction) > Salmonella (2.3) > adenovirus (1.9) > coliphage (1.5) > crAssphage (1.2) > E. coli (1.0) ∼ 16S rRNA genes (1.0) ∼ fecal coliform (1.0) ∼ intl1 (1.0) > Enterococcus (0.9) ∼ MRSA (0.9) ∼ sul1 (0.9) > PMMoV (0.7) > Entero1A (0.5). No significant removal was observed for GenBac3, Campylobacter, and HF183. From the bromide data, we infer that 0.5 log-units of attenuation can be attributed to the dilution of incoming stormwater with water stored in the biofilter; removal above this threshold is presumably associated with non-conservative processes, such as physicochemical filtration, die-off, and predation. Our study documents high variability (>100-fold) in the removal of different microbial contaminants and ARGs by a field-scale stormwater biofilter operated under transient flow and raises further questions about the utility of human-associated fecal source markers as surrogates for pathogen removal.
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Affiliation(s)
- Megyn B Rugh
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA 90095, USA
| | - Stanley B Grant
- Department of Civil and Environmental Engineering, Occoquan Watershed Monitoring Laboratory, Virginia Tech, 9408 Prince William Street, Manassas VA 20110, USA; Center for Coastal Studies, Virginia Tech, 1068A Derring Hall (0420), Blacksburg, VA 24061, USA
| | - Wei-Cheng Hung
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA 90095, USA
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA 90095, USA
| | - Emily A Parker
- Department of Civil and Environmental Engineering, Occoquan Watershed Monitoring Laboratory, Virginia Tech, 9408 Prince William Street, Manassas VA 20110, USA
| | - Marina Feraud
- Bren School of Environmental Science and Management, 2400 Bren Hall, UC Santa Barbara, Santa Barbara CA 93106, USA
| | - Dong Li
- Bren School of Environmental Science and Management, 2400 Bren Hall, UC Santa Barbara, Santa Barbara CA 93106, USA
| | - Sumant Avasarala
- Department of Chemical and Environmental Engineering, Bourns Hall A239, UC Riverside, Riverside, CA 92521, USA
| | - Patricia A Holden
- Bren School of Environmental Science and Management, 2400 Bren Hall, UC Santa Barbara, Santa Barbara CA 93106, USA
| | - Haizhou Liu
- Department of Chemical and Environmental Engineering, Bourns Hall A239, UC Riverside, Riverside, CA 92521, USA
| | - Megan A Rippy
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA 90095, USA; Center for Coastal Studies, Virginia Tech, 1068A Derring Hall (0420), Blacksburg, VA 24061, USA
| | - Laurie C Van De Werfhorst
- Bren School of Environmental Science and Management, 2400 Bren Hall, UC Santa Barbara, Santa Barbara CA 93106, USA
| | - Timnit Kefela
- Bren School of Environmental Science and Management, 2400 Bren Hall, UC Santa Barbara, Santa Barbara CA 93106, USA
| | - Jian Peng
- Orange County Environmental Resources, 2301 North Glassell Street, Orange, CA 92865, USA
| | - Stella Shao
- GSI Environmental Inc., 19200 Von Karman Ave, St 800, Irvine, CA 92612, USA
| | - Katherine E Graham
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Samuel Choi
- Orange County Sanitation District, 10844 Ellis Avenue, Fountain Valley, CA 92708, USA
| | - Sanjay K Mohanty
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA 90095, USA
| | - Yiping Cao
- Orange County Sanitation District, 10844 Ellis Avenue, Fountain Valley, CA 92708, USA; Source Molecular Corporation, 15280 NW 79th 10 Court, St 107, Miami Lakes, FL 33016, USA.
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3
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Alafeef M, Dighe K, Moitra P, Pan D. Monitoring the Viral Transmission of SARS-CoV-2 in Still Waterbodies Using a Lanthanide-Doped Carbon Nanoparticle-Based Sensor Array. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:245-258. [PMID: 35036178 PMCID: PMC8751013 DOI: 10.1021/acssuschemeng.1c06066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/13/2021] [Indexed: 05/02/2023]
Abstract
The latest epidemic of extremely infectious coronavirus disease 2019 (COVID-19) has created a significant public health concern. Despite substantial efforts to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific location, shortcomings in the surveillance of predominantly asymptomatic infections constrain attempts to identify the epidemiological spread of the virus. Continuous surveillance of wastewater streams, including sewage, offers opportunities to track the spread of SARS-CoV-2, which is believed to be found in fecal waste. To demonstrate the feasibility of SARS-CoV-2 detection in wastewater systems, we herein present a novel facilely constructed fluorescence sensing array based on a panel of three different lanthanide-doped carbon nanoparticles (LnCNPs). The differential fluorescence response pattern due to the counterion-ligand interactions allowed us to employ powerful pattern recognition to effectively detect SARS-CoV-2 and differentiate it from other viruses or bacteria. The sensor results were benchmarked to the gold standard RT-qPCR, and the sensor showed excellent sensitivity (1.5 copies/μL) and a short sample-to-results time of 15 min. This differential response of the sensor array was also explained from the differential mode of binding of the LnCNPs with the surface proteins of the studied bacteria and viruses. Therefore, the developed sensor array provides a cost-effective, community diagnostic tool that could be potentially used as a novel epidemiologic surveillance approach to mitigate the spread of COVID-19.
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Affiliation(s)
- Maha Alafeef
- Bioengineering
Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Biomedical
Engineering Department, Jordan University
of Science and Technology, Irbid 22110, Jordan
- Departments
of Diagnostic Radiology and Nuclear Medicine and Pediatrics, University of Maryland Baltimore, Health Sciences
Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201, United
States
- Department
of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Ketan Dighe
- Bioengineering
Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Parikshit Moitra
- Departments
of Diagnostic Radiology and Nuclear Medicine and Pediatrics, University of Maryland Baltimore, Health Sciences
Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201, United
States
| | - Dipanjan Pan
- Bioengineering
Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Departments
of Diagnostic Radiology and Nuclear Medicine and Pediatrics, University of Maryland Baltimore, Health Sciences
Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201, United
States
- Department
of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
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4
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Linke RB, Zeki S, Mayer R, Keiblinger K, Savio D, Kirschner AKT, Reischer GH, Mach RL, Sommer R, Farnleitner AH. Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking. Front Microbiol 2021; 12:660566. [PMID: 34745021 PMCID: PMC8565874 DOI: 10.3389/fmicb.2021.660566] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular diagnostic methods are increasingly applied for food and environmental analysis. Since several steps are involved in sample processing which can affect the outcome (e.g., adhesion of DNA to the sample matrix, inefficient precipitation of DNA, pipetting errors and (partial) loss of the DNA pellet during DNA isolation), quality control is essential at all processing levels. In soil microbiology, particular attention has been paid to the inorganic component of the sample matrix affecting DNA extractability. In water quality testing, however, this aspect has mostly been neglected so far, although it is conceivable that these mechanisms have a similar impact. The present study was therefore dedicated to investigate possible matrix effects on results of water quality analysis. Field testing in an aquatic environment with pronounced chemo-physical gradients [total suspended solids (TSS), inorganic turbidity, total organic carbon (TOC), and conductivity] indicated a negative association between DNA extractability (using a standard phenol/chloroform extraction procedure) and turbidity (spearman ρ = −0.72, p < 0.001, n = 21). Further detailed laboratory experiments on sediment suspensions confirmed the hypothesis of inorganic turbidity being the main driver for reduced DNA extractability. The observed effects, as known from soil samples, were also indicated to result from competitive effects for free charges on clay minerals, leading to adsorption of DNA to these inorganic particles. A protocol modification by supplementing the extraction buffer with salmon sperm DNA, to coat charged surfaces prior to cell lysis, was then applied on environmental water samples and compared to the standard protocol. At sites characterized by high inorganic turbidity, DNA extractability was significantly improved or made possible in the first place by applying the adapted protocol. This became apparent from intestinal enterococci and microbial source tracking (MST)-marker levels measured by quantitative polymerase chain reaction (qPCR) (100 to 10,000-fold median increase in target concentrations). The present study emphasizes the need to consider inorganic turbidity as a potential loss factor in DNA extraction from water-matrices. Negligence of these effects can lead to a massive bias, by up to several orders of magnitude, in the results of molecular MST and fecal pollution diagnostics.
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Affiliation(s)
- Rita B Linke
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Sibel Zeki
- Department of Marine Environment, Institute of Marine Sciences and Management, Istanbul University, Istanbul, Turkey
| | - René Mayer
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katharina Keiblinger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Domenico Savio
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Alexander K T Kirschner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Georg H Reischer
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Research Area Molecular Diagnostics, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria
| | - Robert L Mach
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Regina Sommer
- Unit of Water Microbiology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Andreas H Farnleitner
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
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5
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Holcomb DA, Knee J, Capone D, Sumner T, Adriano Z, Nalá R, Cumming O, Brown J, Stewart JR. Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11667-11679. [PMID: 34382777 PMCID: PMC8429117 DOI: 10.1021/acs.est.1c01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two nonspecific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique, participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced Escherichia coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide the implementation of effective interventions to safeguard health.
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Affiliation(s)
- David A. Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Drew Capone
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jill R. Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
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6
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Li D, Van De Werfhorst LC, Rugh MB, Feraud M, Hung WC, Jay J, Cao Y, Parker EA, Grant SB, Holden PA. Limited Bacterial Removal in Full-Scale Stormwater Biofilters as Evidenced by Community Sequencing Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9199-9208. [PMID: 34106689 DOI: 10.1021/acs.est.1c00510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In urban areas, untreated stormwater runoff can pollute downstream surface waters. To intercept and treat runoff, low-impact or "green infrastructure" approaches such as using biofilters are adopted. Yet, actual biofilter pollutant removal is poorly understood; removal is often studied in laboratory columns, with variable removal of viable and culturable microbial cell numbers including pathogens. Here, to assess bacterial pollutant removal in full-scale planted biofilters, stormwater was applied, unspiked or spiked with untreated sewage, in simulated storm events under transient flow conditions, during which biofilter influents versus effluents were compared. Based on microbial biomass, sequences of bacterial community genes encoding 16S rRNA, and gene copies of the human fecal marker HF183 and of the Enterococcus spp. marker Entero1A, removal of bacterial pollutants in biofilters was limited. Dominant bacterial taxa were similar for influent versus effluent aqueous samples within each inflow treatment of either spiked or unspiked stormwater. Bacterial pollutants in soil were gradually washed out, albeit incompletely, during simulated storm flushing events. In post-storm biofilter soil cores, retained influent bacteria were concentrated in the top layers (0-10 cm), indicating that the removal of bacterial pollutants was spatially limited to surface soils. To the extent that plant-associated processes are responsible for this spatial pattern, treatment performance might be enhanced by biofilter designs that maximize influent contact with the rhizosphere.
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Affiliation(s)
- Dong Li
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Laurie C Van De Werfhorst
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Megyn B Rugh
- Department of Civil and Environmental Engineering, UCLA Los Angeles, 420 Westwood Plaza, 5731 Boelter Hall, Los Angeles, California 90095, United States
| | - Marina Feraud
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Wei-Cheng Hung
- Department of Civil and Environmental Engineering, UCLA Los Angeles, 420 Westwood Plaza, 5731 Boelter Hall, Los Angeles, California 90095, United States
| | - Jennifer Jay
- Department of Civil and Environmental Engineering, UCLA Los Angeles, 420 Westwood Plaza, 5731 Boelter Hall, Los Angeles, California 90095, United States
| | - Yiping Cao
- Source Molecular Corporation, 15280 NW 79th Court, St 107, Miami Lakes, Florida 33016, United States
- Santa Ana Regional Water Quality Control Board, 3737 Main Street, St 500, Riverside, California 92501, United States
| | - Emily A Parker
- Occoquan Watershed Monitoring Laboratory, Department of Civil and Environmental Engineering, Virginia Tech, 9408 Prince William Street, Manassas, Virginia 20110, United States
| | - Stanley B Grant
- Occoquan Watershed Monitoring Laboratory, Department of Civil and Environmental Engineering, Virginia Tech, 9408 Prince William Street, Manassas, Virginia 20110, United States
- Center for Coastal Studies, Virginia Tech, 1068A Derring Hall (0420), Blacksburg, Virginia 24061, United States
| | - Patricia A Holden
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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7
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Li D, Van De Werfhorst LC, Steets B, Ervin J, Murray JLS, Devarajan N, Holden PA. Bather Shedding as a Source of Human Fecal Markers to a Recreational Beach. Front Microbiol 2021; 12:673190. [PMID: 34248883 PMCID: PMC8269448 DOI: 10.3389/fmicb.2021.673190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/30/2021] [Indexed: 11/24/2022] Open
Abstract
Microbial source tracking (MST) can identify and locate surf zone fecal indicator bacteria (FIB) sources. However, DNA-based fecal marker results may raise new questions, since FIB and DNA marker sources can differ. Here, during 2 years of summertime (dry season) MST for a Goleta, California recreational beach, surf zone FIB were mainly from gulls, yet low level human-associated DNA-based fecal marker (HF183) was detected in 25 and 14% of surf zone water samples, respectively. Watershed sources were hypothesized because dry weather creek waters had elevated FIB, and runoff-generating rain events mobilized human (and dog) fecal markers and Salmonella spp. into creeks, with human marker HF183 detected in 40 and 50% of creek water samples, dog markers detected in 70 and 50% of samples, and Salmonella spp. in 40 and 33.3% of samples, respectively over 2 years. However, the dry weather estuary outlet was bermed in the first study year; simultaneously, creek fecal markers and pathogens were lower or similar to surf zone results. Although the berm breached in the second year, surf zone fecal markers stayed low. Watershed sediments, intertidal beach sands, and nearshore sediments were devoid of HF183 and dog-associated DNA markers. Based on dye tests and groundwater sampling, beach sanitary sewers were not leaking; groundwater was also devoid of HF183. Offshore sources appeared unlikely, since FIB and fecal markers decreased along a spatial gradient from the surf zone toward nearshore and offshore ocean waters. Further, like other regional beaches, surf zone HF183 corresponded significantly to bather counts, especially in the afternoons when there were more swimmers. However, morning detections of surf zone HF183 when there were few swimmers raised the possibility that the wastewater treatment plant (WWTP) offshore outfall discharged HF183 overnight which transported to the surf zone. These findings support that there may be lowest achievable limits of surf zone HF183 owing to several chronic and permanent, perhaps diurnal, low concentration sources.
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Affiliation(s)
- Dong Li
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Laurie C. Van De Werfhorst
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | | | - Jared Ervin
- Geosyntec Consultants, Santa Barbara, CA, United States
| | - Jill L. S. Murray
- Creeks Division, Department of Parks and Recreation, Santa Barbara, CA, United States
| | - Naresh Devarajan
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Patricia A. Holden
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
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8
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Lane MJ, Rediske RR, McNair JN, Briggs S, Rhodes G, Dreelin E, Sivy T, Flood M, Scull B, Szlag D, Southwell B, Isaacs NM, Pike S. A comparison of E. coli concentration estimates quantified by the EPA and a Michigan laboratory network using EPA Draft Method C. J Microbiol Methods 2020; 179:106086. [PMID: 33058947 DOI: 10.1016/j.mimet.2020.106086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 01/15/2023]
Abstract
We evaluated data from 10 laboratories that analyzed water samples from 82 recreational water sites across the state of Michigan between 2016 and 2018. Water sample replicates were analyzed by experienced U.S. Environmental Protection Agency (EPA) analysts and Michigan laboratories personnel, many of whom were newly trained, using EPA Draft Method C-a rapid quantitative polymerase chain reaction (qPCR) technique that provides same day Escherichia coli (E. coli) concentration results. Beach management decisions (i.e. remain open or issue an advisory or closure) based on E. coli concentration estimates obtained by Michigan labs and by the EPA were compared; the beach management decision agreed in 94% of the samples analyzed. We used the Wilcoxon one-sample signed rank test and nonparametric quantile regression to assess (1) the degree of agreement between E. coli concentrations quantified by Michigan labs versus the EPA and (2) Michigan lab E. coli measurement precision, relative to EPA results, in different years and water body types. The median quantile regression curve for Michigan labs versus EPA approximated the 1:1 line of perfect agreement more closely as years progressed. Similarly, Michigan lab E. coli estimates precision also demonstrated yearly improvements. No meaningful difference was observed in the degree of association between Michigan lab and EPA E. coli concentration estimates for inland lake and Great Lakes samples (median regression curve average slopes 0.93 and 0.95, respectively). Overall, our study shows that properly trained laboratory personnel can perform Draft Method C to a degree comparable with experienced EPA analysts. This allows health departments that oversee recreational water quality monitoring to be confident in qPCR results generated by the local laboratories responsible for analyzing the water samples.
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Affiliation(s)
- Molly J Lane
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - Richard R Rediske
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - James N McNair
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA.
| | - Geoff Rhodes
- Michigan Department of Environment, Great Lakes and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA.
| | - Erin Dreelin
- Michigan State University, Department of Fisheries and Wildlife, Natural Resource Building, 420 Wilson Rd, Room 13, East Lansing, MI 48824, USA.
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI 48710, USA.
| | - Matthew Flood
- Michigan State University, Department of Fisheries and Wildlife, Natural Resource Building, 420 Wilson Rd, Room 13, East Lansing, MI 48824, USA.
| | - Brian Scull
- Annis Water Resources Institute, Grand Valley State University, 1 Campus Dr., Allendale, MI 49401, USA.
| | - David Szlag
- Oakland University, Department of Chemistry, 146 Library Dr., Rochester, MI 48309, USA.
| | - Benjamin Southwell
- Lake Superior State University, 650 W Easterday Ave., Sault Ste Marie, MI 49783, USA.
| | - Natasha M Isaacs
- U.S. Geological Survey (USGS), Upper Midwest Water Science Center, 5840 Enterprise Dr., Lansing, MI 48911, USA.
| | - Schuyler Pike
- Ferris State University, Shimadzu Core Laboratory for Academic and Research Excellence, 820 Campus Dr., Big Rapids, MI 49307, USA.
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9
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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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10
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Li D, Van De Werfhorst LC, Dunne T, Devarajan N, Ayala TG, Holden PA. Surf zone microbiological water quality following emergency beach nourishment using sediments from a catastrophic debris flow. WATER RESEARCH 2020; 176:115733. [PMID: 32234606 DOI: 10.1016/j.watres.2020.115733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
Urban disaster response requires disposal of complex wastes. This study regards a case wherein high intensity rainfall fell over a remote mountainous area previously burned by wildfire, generating debris flows that devastated a downstream town. Sanitary sewers and homes with septic systems were damaged, releasing human waste into the debris flow field. Contaminated sediments, with their high fecal indicator bacteria (FIB) concentrations, were cleared from public rights-of-way and creek channels by local authorities, then disposed onto distant Goleta Beach for beach nourishment, causing immediate surf zone microbiological water quality exceedances. To determine potential public health threats, disposed sediments and surf zone waters were sampled and analyzed-relative to reference samples of mountain soil and raw sewage-for FIB, pathogens, human (HF183) and other host- (Gull2 TaqMan, and DogBact) associated DNA-based fecal markers, and bacterial community 16S rRNA gene sequences. Approximately 20% of disposed sediment samples contained the HF183 marker; sequencing suggested that all samples were contaminated by sewage. In an initial sediment disposal period, surf zone waters harbored intestinal bacterial sequences that were shared with disposed sediments and sewage. Yet surf zone bacterial communities returned to mostly marine clades within weeks. Taken together, multiple conventional and DNA-based analyses informed this forensic assessment of human waste contamination. In the future, similar analyses could be used earlier in disaster response to guide sediment disposal decisions towards continuously protecting beachgoer health.
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Affiliation(s)
- Dong Li
- Bren School of Environmental Science & Management, and the Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Laurie C Van De Werfhorst
- Bren School of Environmental Science & Management, and the Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Thomas Dunne
- Bren School of Environmental Science & Management, and the Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Naresh Devarajan
- Bren School of Environmental Science & Management, and the Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Tania Gomez Ayala
- Bren School of Environmental Science & Management, and the Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Patricia A Holden
- Bren School of Environmental Science & Management, and the Earth Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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11
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Holcomb DA, Knee J, Sumner T, Adriano Z, de Bruijn E, Nalá R, Cumming O, Brown J, Stewart JR. Human fecal contamination of water, soil, and surfaces in households sharing poor-quality sanitation facilities in Maputo, Mozambique. Int J Hyg Environ Health 2020; 226:113496. [PMID: 32135507 PMCID: PMC7174141 DOI: 10.1016/j.ijheh.2020.113496] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/09/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Identifying the origin of fecal contamination can support more effective interventions to interrupt enteric pathogen transmission. Microbial source tracking (MST) assays may help to identify environmental routes of pathogen transmission although these assays have performed poorly in highly contaminated domestic settings, highlighting the importance of both diagnostic validation and understanding the context-specific ecological, physical, and sociodemographic factors driving the spread of fecal contamination. We assessed fecal contamination of compounds (clusters of 2-10 households that share sanitation facilities) in low-income neighborhoods of urban Maputo, Mozambique, using a set of MST assays that were validated with animal stool and latrine sludge from study compounds. We sampled five environmental compartments involved in fecal microbe transmission and exposure: compound water source, household stored water and food preparation surfaces, and soil from the entrance to the compound latrine and the entrances to each household. Each sample was analyzed by culture for the general fecal indicator Escherichia coli (cEC) and by real-time PCR for the E. coli molecular marker EC23S857, human-associated markers HF183/BacR287 and Mnif, and GFD, an avian-associated marker. We collected 366 samples from 94 households in 58 compounds. At least one microbial target (indicator organism or marker gene) was detected in 96% of samples (353/366), with both E. coli targets present in the majority of samples (78%). Human targets were frequently detected in soils (59%) and occasionally in stored water (17%) but seldom in source water or on food surfaces. The avian target GFD was rarely detected in any sample type but was most common in soils (4%). To identify risk factors of fecal contamination, we estimated associations with sociodemographic, meteorological, and physical sample characteristics for each microbial target and sample type combination using Bayesian censored regression for target concentration responses and Bayesian logistic regression for target detection status. Associations with risk factors were generally weak and often differed in direction between different targets and sample types, though relationships were somewhat more consistent for physical sample characteristics. Wet soils were associated with elevated concentrations of cEC and EC23S857 and odds of detecting HF183. Water storage container characteristics that expose the contents to potential contact with hands and other objects were weakly associated with human target detection. Our results describe a setting impacted by pervasive domestic fecal contamination, including from human sources, that was largely disconnected from the observed variation in socioeconomic and sanitary conditions. This pattern suggests that in such highly contaminated settings, transformational changes to the community environment may be required before meaningful impacts on fecal contamination can be realized.
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Affiliation(s)
- David A Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Zaida Adriano
- We Consult, Maputo, Mozambique; Departamento de Geografia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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12
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Chen L, Zhang X, Zhi X, Dai Y, Zhang P, Xiao Y, Shen Z. Tracking faecal microorganisms using the qPCR method in a typical urban catchment in China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:158. [PMID: 32016573 DOI: 10.1007/s10661-020-8130-8] [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: 07/17/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Faecal microorganisms represent a key threat to human health. Potential origins of faecal microbial contamination in a typical urban-representative micro-scale were evaluated. The quantitative polymerase chain reaction (qPCR) method was used in this study. The Bacteroidetes is selected as the indicative microorganism in runoff samples that are collected during four representative stormwater events in north China. The principal component analysis (PCA) method indicated the distribution feature of the environmental factors. The largest contributor is dog, followed by bird and human to the faecal pollution in stormwater runoff. The output of human and dog faecal pollutants in response to the first flush effect of nonpoint source pollution while the transmit time of bird faecal pollutant is relatively longer. In addition, the number of antecedent drying days represents the key factor for dog faecal pollution, while human faecal pollution is impacted by more factors. The results of this study will provide sound evidence for the tracking and management of nonpoint source faecal pollution in urban catchment areas.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiaoyue Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiaosha Zhi
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Satellite Environment Centre, Ministry of Environmental Protection, Beijing, 100094, People's Republic of China
| | - Ying Dai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Pu Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Yuechen Xiao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
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13
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Zhang C, Sun G, Senapati S, Chang HC. A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification. LAB ON A CHIP 2019; 19:3853-3861. [PMID: 31621762 PMCID: PMC6982425 DOI: 10.1039/c9lc00818g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
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Affiliation(s)
- Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA and Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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14
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Nappier SP, Ichida A, Jaglo K, Haugland R, Jones KR. Advancements in mitigating interference in quantitative polymerase chain reaction (qPCR) for microbial water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:732-740. [PMID: 30939326 PMCID: PMC6555561 DOI: 10.1016/j.scitotenv.2019.03.242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/13/2019] [Accepted: 03/15/2019] [Indexed: 05/31/2023]
Abstract
The United States Environmental Protection Agency's (EPA)1 2012 Recreational Water Quality Criteria included an Enterococcus spp. quantitative polymerase chain reaction (qPCR) method as a supplemental indicator-method. In 2012, performance of qPCR for beach monitoring remained limited, specifically with addressing interference. A systematic literature search of peer-reviewed publications was conducted to identify where Enterococcus spp. and E. coli qPCR methods have been applied in ambient waters. In the present study, we evaluated interference rates, contributing factors resulting in increased interference in these methods, and method improvements that reduced interference. Information on qPCR methods of interest and interference controls were reported in 16 papers for Enterococcus spp. and 13 papers for E. coli. Of the Enterococcus spp. qPCR methods assessed in this effort, the lowest frequencies of interference were reported in samples using Method 1609. Low frequencies of sample interference were also reported EPA's modified E. coli qPCR method, which incorporates the same reagents and interference controls as Method 1609. The literature indicates that more work is needed to demonstrate the utility of E. coli qPCR for widespread beach monitoring purposes, whereas more broad use of Method 1609 for Enterococcus spp. is appropriate when the required and suggested controls are employed.
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Affiliation(s)
- Sharon P Nappier
- U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, 1200 Pennsylvania Avenue, NW, Washington, DC 20460, USA.
| | | | | | - Rich Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, USA
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15
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Sivaganesan M, Aw TG, Briggs S, Dreelin E, Aslan A, Dorevitch S, Shrestha A, Isaacs N, Kinzelman J, Kleinheinz G, Noble R, Rediske R, Scull B, Rosenberg S, Weberman B, Sivy T, Southwell B, Siefring S, Oshima K, Haugland R. Standardized data quality acceptance criteria for a rapid Escherichia coli qPCR method (Draft Method C) for water quality monitoring at recreational beaches. WATER RESEARCH 2019; 156:456-464. [PMID: 30952079 PMCID: PMC9943056 DOI: 10.1016/j.watres.2019.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 05/31/2023]
Abstract
There is growing interest in the application of rapid quantitative polymerase chain reaction (qPCR) and other PCR-based methods for recreational water quality monitoring and management programs. This interest has strengthened given the publication of U.S. Environmental Protection Agency (EPA)-validated qPCR methods for enterococci fecal indicator bacteria (FIB) and has extended to similar methods for Escherichia coli (E. coli) FIB. Implementation of qPCR-based methods in monitoring programs can be facilitated by confidence in the quality of the data produced by these methods. Data quality can be determined through the establishment of a series of specifications that should reflect good laboratory practice. Ideally, these specifications will also account for the typical variability of data coming from multiple users of the method. This study developed proposed standardized data quality acceptance criteria that were established for important calibration model parameters and/or controls from a new qPCR method for E. coli (EPA Draft Method C) based upon data that was generated by 21 laboratories. Each laboratory followed a standardized protocol utilizing the same prescribed reagents and reference and control materials. After removal of outliers, statistical modeling based on a hierarchical Bayesian method was used to establish metrics for assay standard curve slope, intercept and lower limit of quantification that included between-laboratory, replicate testing within laboratory, and random error variability. A nested analysis of variance (ANOVA) was used to establish metrics for calibrator/positive control, negative control, and replicate sample analysis data. These data acceptance criteria should help those who may evaluate the technical quality of future findings from the method, as well as those who might use the method in the future. Furthermore, these benchmarks and the approaches described for determining them may be helpful to method users seeking to establish comparable laboratory-specific criteria if changes in the reference and/or control materials must be made.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Shannon Briggs
- Water Resources Division, Michigan Department of Environmental Quality, P. O. Box 30458, 525 West Allegan Street, Lansing, MI, 48909, USA
| | - Erin Dreelin
- Center for Water Sciences, Michigan State University, 1405 South Harrison Road, East Lansing, MI, 48823, USA
| | - Asli Aslan
- Georgia Southern University, Department of Environmental Health Sciences, 501 Forest Drive, Statesboro, GA, 30458, USA
| | - Samuel Dorevitch
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Abhilasha Shrestha
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Natasha Isaacs
- U.S. Geological Survey, Upper Midwest Water Science Center, 6520 Mercantile Way, Ste 5, Lansing, MI, 48911, USA
| | - Julie Kinzelman
- City of Racine Public Health Department, 730 Washington Ave, Racine, WI, 53403, USA
| | - Greg Kleinheinz
- University of Wisconsin-Oshkosh, Environmental Research Laboratory, 800 Algoma Boulevard, Oshkosh, WI, 54901, USA
| | - Rachel Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC, 28557, USA
| | - Rick Rediske
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Brian Scull
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Susan Rosenberg
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Barbara Weberman
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI, 48710, USA
| | - Ben Southwell
- Lake Superior State University, Environmental Analysis Laboratory, 650 W. Easterday Ave, Sault Ste Marie, MI, 49783, USA
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA.
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16
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de Bruin OM, Chiefari A, Wroblewski D, Egan C, Kelly-Cirino CD. A novel chemical lysis method for maximum release of DNA from difficult-to-lyse bacteria. Microb Pathog 2018; 126:292-297. [PMID: 30414838 DOI: 10.1016/j.micpath.2018.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
Molecular detection of microorganisms requires releasing DNA from cells. However, since certain microbial organisms are refractory to lysis by chemical or enzymatic methods, mechanical lysis by bead-beating is typically employed to disrupt difficult-to-lyse microbes. A newly developed chemical lysis method called sporeLYSE enables release of DNA from difficult-to-lyse microbes without bead-beating. The sporeLYSE method was compared to bead-beating and an alkaline/detergent lysis solution for releasing DNA from microbes grown in vitro, including surrogates of Category A bioterrorism agents. sporeLYSE released 83% to 100% of DNA from Mycobacterium smegmatis, Francisella philomiragia, Yersinia enterocolitica, Bacillus thuringiensis, Pseudomonas aeruginosa, Moraxella catarrhalis and Klebsiella pneumoniae. qPCR results indicated that sporeLYSE extracted an equal or greater amount of DNA than either bead-beating or alkaline/detergent lysis from Gram-positive and Gram-negative bacteria. When sporeLYSE was used to extract DNA from saliva and sputum spiked with M. smegmatis and M. tuberculosis, respectively, the qPCR Ct values were 4-8 cycles lower than those for extractions via alkaline/detergent lysis and heat. Mean Ct values for sporesLYSE extractions from spores of Clostridium difficile and C. botulinum were approximately two cycles lower than those of MagNA Pure DNA extractions. Our results suggest that sporeLYSE is an easy-to-use liquid reagent that can efficiently release large amounts of DNA from a variety of bacteria, including spores.
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Affiliation(s)
- Olle M de Bruin
- DNA Genotek Inc., 3000 - 500 Palladium Drive, Ottawa, ON, K2V 1C2, Canada.
| | - Amy Chiefari
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Danielle Wroblewski
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Christina Egan
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
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17
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Al-Hunaiti A, Arar S, Täubel M, Wraith D, Maragkidou A, Hyvärinen A, Hussein T. Floor dust bacteria and fungi and their coexistence with PAHs in Jordanian indoor environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 601-602:940-945. [PMID: 28582739 DOI: 10.1016/j.scitotenv.2017.05.211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 05/09/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
Floor dust samples were collected from Jordanian indoor environments (eight dwellings and an educational building) in Amman. Quantitative PCR (qPCR) analyses of selected fungal and bacterial groups were performed. The bacterial and fungal concentrations were also correlated with PAHs concentrations, which were previously measured in the same samples by using GC-MS. The bacterial and fungal concentrations varied significantly among and within the tested indoor environments. Based on the collected samples in the entrance area of the dwellings, the largest variation was found in Gram-negative bacteria and total fungi concentration. The lowest bacterial and fungal concentrations were found in the dwelling that was least occupied and the most recently built. At the educational building, the Gram-positive bacteria concentrations were lower than those observed in the dwellings. Unlike for bacteria, we observed significant negative correlation with some polycyclic aromatic hydrocarbons (PAHs). This calls for further studies investigating biodegradation of PAHs in house dust and presence of potentially health hazardous PAH metabolites. Since biocontamination in floor dust has been given relatively little to no attention in the MENA region we recommend that more extensive measurements be conducted in the future with chemical and biological analysis of floor dust contaminants and their exposure indoors.
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Affiliation(s)
| | - Sharif Arar
- The University of Jordan, Department of Chemistry, Amman 11942, Jordan
| | - Martin Täubel
- National Institute for Health and Welfare (THL), Department of Health Protection Living Environment and Health Unit, PL 95, FI -70701 Kuopio, Finland
| | - Darren Wraith
- Queensland University of Technology, Institute of Health and Biomedical Innovation (IHBI), Victoria Park Road, Kelvin Grove 4059, Queensland, Australia
| | - Androniki Maragkidou
- University of Helsinki, Division of Atmospheric Sciences, PL 48, FI 00014, Helsinki, Finland
| | - Anne Hyvärinen
- National Institute for Health and Welfare (THL), Department of Health Protection Living Environment and Health Unit, PL 95, FI -70701 Kuopio, Finland
| | - Tareq Hussein
- The University of Jordan, Department of Physics, Amman 11942, Jordan.
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18
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Shanks OC, Kelty CA, Oshiro R, Haugland RA, Madi T, Brooks L, Field KG, Sivaganesan M. Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods. Appl Environ Microbiol 2016; 82:2773-2782. [PMID: 26921430 PMCID: PMC4836407 DOI: 10.1128/aem.03661-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (no-template and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria proposed in this study should help scientists, managers, reviewers, and the public evaluate the technical quality of future findings against an established benchmark.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
| | - Catherine A Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
| | - Robin Oshiro
- U.S. Environmental Protection Agency, Office of Water, Washington DC, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
| | - Tania Madi
- Source Molecular Corporation, Miami, Florida, USA
| | - Lauren Brooks
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Katharine G Field
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
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Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters. J Microbiol Methods 2016; 123:114-25. [DOI: 10.1016/j.mimet.2016.01.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/31/2016] [Accepted: 01/31/2016] [Indexed: 11/22/2022]
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20
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The Evaluation of Magnetic Polymethacrylate-based Microspheres Used for Solid Phase DNA Micro-Extraction. CHROMATOGRAPHY 2015. [DOI: 10.3390/chromatography2020156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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A novel triplex quantitative PCR strategy for quantification of toxigenic and nontoxigenic Vibrio cholerae in aquatic environments. Appl Environ Microbiol 2015; 81:3077-85. [PMID: 25724966 DOI: 10.1128/aem.03516-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/13/2015] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is a severe human pathogen and a frequent member of aquatic ecosystems. Quantification of V. cholerae in environmental water samples is therefore fundamental for ecological studies and health risk assessment. Beside time-consuming cultivation techniques, quantitative PCR (qPCR) has the potential to provide reliable quantitative data and offers the opportunity to quantify multiple targets simultaneously. A novel triplex qPCR strategy was developed in order to simultaneously quantify toxigenic and nontoxigenic V. cholerae in environmental water samples. To obtain quality-controlled PCR results, an internal amplification control was included. The qPCR assay was specific, highly sensitive, and quantitative across the tested 5-log dynamic range down to a method detection limit of 5 copies per reaction. Repeatability and reproducibility were high for all three tested target genes. For environmental application, global DNA recovery (GR) rates were assessed for drinking water, river water, and water from different lakes. GR rates ranged from 1.6% to 76.4% and were dependent on the environmental background. Uncorrected and GR-corrected V. cholerae abundances were determined in two lakes with extremely high turbidity. Uncorrected abundances ranged from 4.6×10(2) to 2.3×10(4) cell equivalents liter(-1), whereas GR-corrected abundances ranged from 4.7×10(3) to 1.6×10(6) cell equivalents liter(-1). GR-corrected qPCR results were in good agreement with an independent cell-based direct detection method but were up to 1.6 log higher than cultivation-based abundances. We recommend the newly developed triplex qPCR strategy as a powerful tool to simultaneously quantify toxigenic and nontoxigenic V. cholerae in various aquatic environments for ecological studies as well as for risk assessment programs.
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Gensberger ET, Polt M, Konrad-Köszler M, Kinner P, Sessitsch A, Kostić T. Evaluation of quantitative PCR combined with PMA treatment for molecular assessment of microbial water quality. WATER RESEARCH 2014; 67:367-76. [PMID: 25459225 DOI: 10.1016/j.watres.2014.09.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/05/2014] [Accepted: 09/16/2014] [Indexed: 05/15/2023]
Abstract
Microbial water quality assessment currently relies on cultivation-based methods. Nucleic acid-based techniques such as quantitative PCR (qPCR) enable more rapid and specific detection of target organisms and propidium monoazide (PMA) treatment facilitates the exclusion of false positive results caused by DNA from dead cells. Established molecular assays (qPCR and PMA-qPCR) for legally defined microbial quality parameters (Escherichia coli, Enterococcus spp. and Pseudomonas aeruginosa) and indicator organism group of coliforms (implemented on the molecular detection of Enterobacteriaceae) were comparatively evaluated to conventional microbiological methods. The evaluation of an extended set of drinking and process water samples showed that PMA-qPCR for E. coli, Enterococcus spp. and P. aeruginosa resulted in higher specificity because substantial or complete reduction of false positive signals in comparison to qPCR were obtained. Complete compliance to reference method was achieved for E. coli PMA-qPCR and 100% specificity for Enterococcus spp. and P. aeruginosa in the evaluation of process water samples. A major challenge remained in sensitivity of the assays, exhibited through false negative results (7-23%), which is presumably due to insufficient sample preparation (i.e. concentration of bacteria and DNA extraction), rather than the qPCR limit of detection. For the detection of the indicator group of coliforms, the evaluation study revealed that the utilization of alternative molecular assays based on the taxonomic group of Enterobacteriaceae was not adequate. Given the careful optimization of the sensitivity, the highly specific PMA-qPCR could be a valuable tool for rapid detection of hygienic parameters such as E. coli, Enterococcus spp. and P. aeruginosa.
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Affiliation(s)
- Eva Theres Gensberger
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria.
| | - Marlies Polt
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Marianne Konrad-Köszler
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Paul Kinner
- AIT Austrian Institute of Technology GmbH, Environmental Resources & Technologies Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
| | - Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln, Austria
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23
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Haugland RA, Siefring SD, Varma M, Dufour AP, Brenner KP, Wade TJ, Sams E, Cochran S, Braun S, Sivaganensan M. Standardization of enterococci density estimates by EPA qPCR methods and comparison of beach action value exceedances in river waters with culture methods. J Microbiol Methods 2014; 105:59-66. [DOI: 10.1016/j.mimet.2014.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/03/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
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24
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Sivaganensan M, Siefring S, Varma M, Haugland RA. Comparison of Enterococcus quantitative polymerase chain reaction analysis results from Midwest U.S. river samples using EPA Method 1611 and Method 1609 PCR reagents. J Microbiol Methods 2014; 101:9-17. [DOI: 10.1016/j.mimet.2014.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/15/2014] [Accepted: 03/16/2014] [Indexed: 11/24/2022]
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25
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Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the upper Mississippi river. Appl Environ Microbiol 2014; 80:3952-61. [PMID: 24747902 DOI: 10.1128/aem.00388-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The sanitary quality of recreational waters that may be impacted by sewage is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); these organisms are found in the gastrointestinal tracts of humans and many other animals, and hence their presence provides no information about the pollution source. Microbial source tracking (MST) methods can discriminate between different pollution sources, providing critical information to water quality managers, but relatively little is known about factors influencing the decay of FIB and MST genetic markers following release into aquatic environments. An in situ mesocosm was deployed at a temperate recreational beach in the Mississippi River to evaluate the effects of ambient sunlight and biotic interactions (predation, competition, and viral lysis) on the decay of culture-based FIB, as well as molecularly based FIB (Entero1a and GenBac3) and human-associated MST genetic markers (HF183 and HumM2) measured by quantitative real-time PCR (qPCR). In general, culturable FIB decayed the fastest, while molecularly based FIB and human-associated genetic markers decayed more slowly. There was a strong correlation between the decay of molecularly based FIB and that of human-associated genetic markers (r(2), 0.96 to 0.98; P < 0.0001) but not between culturable FIB and any qPCR measurement. Overall, exposure to ambient sunlight may be an important factor in the early-stage decay dynamics but generally was not after continued exposure (i.e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence.
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Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples. Appl Environ Microbiol 2014; 80:3086-94. [PMID: 24610857 DOI: 10.1128/aem.04137-13] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative real-time PCR (qPCR) assays that target the human-associated HF183 bacterial cluster within members of the genus Bacteroides are among the most widely used methods for the characterization of human fecal pollution in ambient surface waters. In this study, we show that a current TaqMan HF183 qPCR assay (HF183/BFDrev) routinely forms nonspecific amplification products and introduce a modified TaqMan assay (HF183/BacR287) that alleviates this problem. The performance of each qPCR assay was compared in head-to-head experiments investigating limits of detection, analytical precision, predicted hybridization to 16S rRNA gene sequences from a reference database, and relative marker concentrations in fecal and sewage samples. The performance of the modified HF183/BacR287 assay is equal to or improves upon that of the original HF183/BFDrev assay. In addition, a qPCR chemistry designed to combat amplification inhibition and a multiplexed internal amplification control are included. In light of the expanding use of PCR-based methods that rely on the detection of extremely low concentrations of DNA template, such as qPCR and digital PCR, the new TaqMan HF183/BacR287 assay should provide more accurate estimations of human-derived fecal contaminants in ambient surface waters.
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27
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Sabino R, Rodrigues R, Costa I, Carneiro C, Cunha M, Duarte A, Faria N, Ferreira FC, Gargaté MJ, Júlio C, Martins ML, Nevers MB, Oleastro M, Solo-Gabriele H, Veríssimo C, Viegas C, Whitman RL, Brandão J. Routine screening of harmful microorganisms in beach sands: implications to public health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 472:1062-1069. [PMID: 24355396 DOI: 10.1016/j.scitotenv.2013.11.091] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/29/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Beaches worldwide provide recreational opportunities to hundreds of millions of people and serve as important components of coastal economies. Beach water is often monitored for microbiological quality to detect the presence of indicators of human sewage contamination so as to prevent public health outbreaks associated with water contact. However, growing evidence suggests that beach sand can harbor microbes harmful to human health, often in concentrations greater than the beach water. Currently, there are no standards for monitoring, sampling, analyzing, or managing beach sand quality. In addition to indicator microbes, growing evidence has identified pathogenic bacteria, viruses, and fungi in a variety of beach sands worldwide. The public health threat associated with these populations through direct and indirect contact is unknown because so little research has been conducted relating to health outcomes associated with sand quality. In this manuscript, we present the consensus findings of a workshop of experts convened in Lisbon, Portugal to discuss the current state of knowledge on beach sand microbiological quality and to develop suggestions for standardizing the evaluation of sand at coastal beaches. The expert group at the "Microareias 2012" workshop recommends that 1) beach sand should be screened for a variety of pathogens harmful to human health, and sand monitoring should then be initiated alongside regular water monitoring; 2) sampling and analysis protocols should be standardized to allow proper comparisons among beach locations; and 3) further studies are needed to estimate human health risk with exposure to contaminated beach sand. Much of the manuscript is focused on research specific to Portugal, but similar results have been found elsewhere, and the findings have worldwide implications.
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Affiliation(s)
- R Sabino
- Reference Unit for Systemic Infections and Zoonosis, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - R Rodrigues
- Microbiology Laboratory, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - I Costa
- Laboratory of Molecular Biology, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - C Carneiro
- REQUIMTE/Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal
| | - M Cunha
- Portuguese Environment Agency, Environment Reference Laboratory, Portugal
| | - A Duarte
- Faculty of Pharmacy, iMed.UL-Research Institute for Medicines and Pharmaceutical Sciences, University of Lisboa, Portugal
| | - N Faria
- Microbiology Laboratory, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - F C Ferreira
- Microbiology Laboratory, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - M J Gargaté
- Reference Unit for Systemic Infections and Zoonosis, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - C Júlio
- Reference Unit for Gastro-intestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - M L Martins
- Unit of Medical Microbiology, Instituto de Higiene e Medicina Tropical-Centro de Recursos Microbiológicos (CREM), Universidade Nova de Lisboa (UNL), Portugal
| | - M B Nevers
- United States Geological Survey, Great Lakes Science Center, Porter, IN, USA
| | - M Oleastro
- Laboratory of Molecular Biology, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - H Solo-Gabriele
- Department of Civil, Architectural, and Environmental Engineering, University of Miami, Coral Gables, FL, USA
| | - C Veríssimo
- Reference Unit for Systemic Infections and Zoonosis, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal
| | - C Viegas
- Lisbon School of Health Technology, Polytechnic Institute of Lisboa, Portugal
| | - R L Whitman
- United States Geological Survey, Great Lakes Science Center, Porter, IN, USA
| | - J Brandão
- Reference Unit for Systemic Infections and Zoonosis, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal.
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28
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Gonzalez RA, Noble RT. Comparisons of statistical models to predict fecal indicator bacteria concentrations enumerated by qPCR- and culture-based methods. WATER RESEARCH 2014; 48:296-305. [PMID: 24139103 DOI: 10.1016/j.watres.2013.09.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 05/04/2023]
Abstract
Recently, the United States Environmental Protection Agency (USEPA) revised their recreational water quality criteria, in which adjustments were made by approving enterococci (ENT) quantitative PCR (qPCR) as an alternative, rapid method and advocating the use of predictive models for water quality management. The implementation of qPCR-based methods and prediction models are meant to decrease the time between sample collection and public advisories and notifications. To date, few studies have compared qPCR-based models to culture-based prediction models and none of these studies have been conducted in coastal estuarine systems. In this study, we created prediction models using qPCR-based fecal indicator bacteria (FIB) data in dual-use recreational and shellfish harvesting waters and compared them to published ENT and Escherichia coli (EC) culture-based prediction models in eastern North Carolina estuaries. Furthermore, an empirical statistical model was created to predict qPCR inhibition levels so that proper remediation techniques can be applied when it is a problem. Predictor variable selection in both qPCR- and culture-based ENT models was very similar; both models included 14-day rain total, dissolved oxygen, and salinity/conductivity, with 89 and 90% of qPCR and culture data described, respectively. Using ENT management action thresholds, qPCR- and culture-based models showed high accuracy in management decisions. The qPCR model had 92 and 96% accuracy using the 110 and 1000 cell equivalents (CE)/100 ml thresholds, respectively, and the culture model had 90% accuracy in management decisions with the 110 MPN/100 ml threshold. EC models for qPCR- and culture-based concentrations used similar independent variables (14-day humidity, salinity/conductivity, a rain/storm variable, and a measure of air temperature), with each model explaining 26 and 55% of the data variation, respectively. When using different thresholds that were logs apart for management decisions, the two EC models accurately predicted management decisions; qPCR models correctly predicted management decisions 96 and 77% of the time (using 31 and 320 CE/100 ml, respectively) while culture models correctly predicted management decisions 96 and 88% percent of the time (with 31 and 320 MPN/100 ml, respectively). Equivalency between models was shown in our non-point source impacted estuaries, with ENT models performing slightly better than EC models. In addition, inhibition of the qPCR was a major issue that had to be addressed. An inhibition model was created with easily obtained meteorological data and accounted for a high level of data variability (adjusted R(2) = 0.82).
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Affiliation(s)
- Raul A Gonzalez
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC 28557, USA
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Use of quantitative real-time PCR for direct detection of serratia marcescens in marine and other aquatic environments. Appl Environ Microbiol 2013; 80:1679-83. [PMID: 24375136 DOI: 10.1128/aem.02755-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Serratia marcescens is the etiological agent of acroporid serratiosis, a distinct form of white pox disease in the threatened coral Acropora palmata. The pathogen is commonly found in untreated human waste in the Florida Keys, which may contaminate both nearshore and offshore waters. Currently there is no direct method for detection of this bacterium in the aquatic or reef environment, and culture-based techniques may underestimate its abundance in marine waters. A quantitative real-time PCR assay was developed to detect S. marcescens directly from environmental samples, including marine water, coral mucus, sponge tissue, and wastewater. The assay targeted the luxS gene and was able to distinguish S. marcescens from other Serratia species with a reliable quantitative limit of detection of 10 cell equivalents (CE) per reaction. The method could routinely discern the presence of S. marcescens for as few as 3 CE per reaction, but it could not be reliably quantified at this level. The assay detected environmental S. marcescens in complex sewage influent samples at up to 761 CE ml(-1) and in septic system-impacted residential canals in the Florida Keys at up to 4.1 CE ml(-1). This detection assay provided rapid quantitative abilities and good sensitivity and specificity, which should offer an important tool for monitoring this ubiquitous pathogen that can potentially impact both human health and coral health.
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30
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Kapoor V, Smith C, Santo Domingo JW, Lu T, Wendell D. Correlative assessment of fecal indicators using human mitochondrial DNA as a direct marker. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:10485-10493. [PMID: 23919424 DOI: 10.1021/es4020458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Identifying the source of surface water fecal contamination is paramount to mitigating pollution and risk to human health. Fecal bacteria such as E. coli have been staple indicator organisms for over a century, however there remains uncertainty with E. coli-based metrics since these bacteria are abundant in the environment. The relationships between the presence of direct indicator of human waste (human mitochondrial DNA), human-specific Bacteroidales, and E. coli were studied for water samples taken from an urban creek system (Duck Creek Watershed, Cincinnati, OH) impacted by combined sewer overflows. Logistic regression analysis shows that human-specific Bacteroidales correlates much more closely to human mitochondrial DNA (R = 0.62) relative to E. coli (R = 0.33). We also examine the speciation of Bacteroidales within the Duck Creek Watershed using next-generation sequencing technology (Ion Torrent) and show the most numerous populations to be associated with sewage. Here we demonstrate that human-specific Bacteroidales closely follow the dynamics of human mitochondrial DNA concentration changes, indicating that these obligate anaerobes are more accurate than E. coli for fecal source tracking, lending further support to risk overestimation using coliforms, especially fecal coliforms and E. coli.
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Affiliation(s)
- Vikram Kapoor
- School of Energy, Environmental, Biological & Medical Engineering, University of Cincinnati , Cincinnati, Ohio 45221, United States
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Cox AM, Goodwin KD. Sample preparation methods for quantitative detection of DNA by molecular assays and marine biosensors. MARINE POLLUTION BULLETIN 2013; 73:47-56. [PMID: 23790450 DOI: 10.1016/j.marpolbul.2013.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 05/26/2013] [Accepted: 06/02/2013] [Indexed: 06/02/2023]
Abstract
The need for quantitative molecular methods is growing in environmental, food, and medical fields but is hindered by low and variable DNA extraction and by co-extraction of PCR inhibitors. DNA extracts from Enterococcus faecium, seawater, and seawater spiked with E. faecium and Vibrio parahaemolyticus were tested by qPCR for target recovery and inhibition. Conventional and novel methods were tested, including Synchronous Coefficient of Drag Alteration (SCODA) and lysis and purification systems used on an automated genetic sensor (the Environmental Sample Processor, ESP). Variable qPCR target recovery and inhibition were measured, significantly affecting target quantification. An aggressive lysis method that utilized chemical, enzymatic, and mechanical disruption enhanced target recovery compared to commercial kit protocols. SCODA purification did not show marked improvement over commercial spin columns. Overall, data suggested a general need to improve sample preparation and to accurately assess and account for DNA recovery and inhibition in qPCR applications.
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Affiliation(s)
- Annie M Cox
- National Oceanic & Atmospheric Administration (NOAA), Northwest Fisheries Science Center, La Jolla, CA 92037, USA
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32
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De Keuckelaere A, Stals A, Baert L, Uyttendaele M. Performance of Two Real-Time RT-PCR Assays for the Quantification of GI and GII Noroviruses and Hepatitis A Virus in Environmental Water Samples. FOOD ANAL METHOD 2013. [DOI: 10.1007/s12161-013-9647-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Ferretti JA, Tran HV, Peterson SJ, Loftin V. Rapid method demonstration project at four New Jersey marine beaches using real time quantitative Polymerase Chain Reaction (qPCR). MARINE POLLUTION BULLETIN 2013; 71:51-63. [PMID: 23623653 DOI: 10.1016/j.marpolbul.2013.03.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/22/2013] [Accepted: 03/28/2013] [Indexed: 05/15/2023]
Abstract
Real time quantitative Polymerase Chain Reaction (qPCR) was used at four marine bathing beaches in New Jersey as part of a demonstration project to evaluate the potential for use of qPCR as part of a routine beach monitoring program. Split sample analyses for Enterococcus spp. using membrane filtration (MF) and qPCR were performed for 11weeks during the summer of 2011 using swimming advisories based on qPCR results. Comparison of qPCR and MF results from split samples indicated that there was an 82% overall agreement rate between the two methods. Results from the qPCR tests were available by noon the same day of sample collection and swimming advisories were posted on a dedicated website. The qPCR method can be more labor intensive and requires a higher level of training to perform, however, qPCR was able to assess beach water quality in a timelier manner compared to conventional MF techniques.
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Affiliation(s)
- James A Ferretti
- Division of Environmental Science and Assessment, USEPA Region 2, 2890 Woodbridge Ave., Edison, NJ 08837, USA.
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Tracking the primary sources of fecal pollution in a tropical watershed in a one-year study. Appl Environ Microbiol 2013; 79:1689-96. [PMID: 23291547 DOI: 10.1128/aem.03070-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A study was conducted to determine the primary sources of fecal pollution in a subtropical watershed using host-specific assays developed in temperate regions. Water samples (n = 534) from 10 different sites along the Rio Grande de Arecibo (RGA) watershed were collected mostly on a weekly basis (54 sampling events) during 13 months. DNA extracts from water samples were used in PCR assays to determine the occurrence of fecal bacteria (Bacteroidales, Clostridium coccoides, and enterococci) and human-, cattle-, swine-, and chicken-specific fecal sources. Feces from 12 different animals (n = 340) and wastewater treatment samples (n = 16) were analyzed to determine the specificity and distribution of host-specific assays. The human-specific assay (HF183) was found to be highly specific, as it did not cross-react with nontarget samples. The cattle marker (CF128) cross-reacted to some extent with swine, chicken, and turkeys and was present in 64% of the cattle samples tested. The swine assays showed poor host specificity, while the three chicken assays showed poor host distribution. Differences in the detection of host-specific markers were noted per site. While human and cattle assays showed moderate average detection rates throughout the watershed, areas impacted by wastewater treatment plants and cattle exhibited the highest prevalence of these markers. When conditional probability for positive signals was determined for each of the markers, the results indicated higher confidence levels for the human assay and lower levels for all the other assays. Overall, the results from this study suggest that additional assays are needed, particularly to track cattle, chicken, and swine fecal pollution sources in the RGA watershed. The results also suggest that the geographic stability of genetic markers needs to be determined prior to conducting applied source tracking studies in tropical settings.
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Cao Y, Sivaganesan M, Kinzelman J, Blackwood AD, Noble RT, Haugland RA, Griffith JF, Weisberg SB. Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods. WATER RESEARCH 2013; 47:233-241. [PMID: 23123048 DOI: 10.1016/j.watres.2012.09.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 08/28/2012] [Accepted: 09/28/2012] [Indexed: 06/01/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is increasingly being used for the quantitative detection of fecal indicator bacteria in beach water. QPCR allows for same-day health warnings, and its application is being considered as an option for recreational water quality testing in the United States (USEPA, 2011. EPA-OW-2011-0466, FRL-9609-3, Notice of Availability of Draft Recreational Water Quality Criteria and Request for Scientific Views). However, transition of qPCR from a research tool to routine water quality testing requires information on how various method variations affect target enumeration. Here we compared qPCR performance and enumeration of enterococci in spiked and environmental water samples using three qPCR platforms (Applied Biosystem StepOnePlus™, the BioRad iQ™5 and the Cepheid SmartCycler(®) II), two reference materials (lyophilized cells and frozen cells on filters) and two comparative CT quantification models (ΔCT and ΔΔCT). Reference materials exerted the biggest influence, consistently affecting results by approximately 0.5 log(10) unit. Platform had the smallest effect, generally exerting <0.1 log(10) unit difference in final results. Quantification model led to small differences (0.04-0.2 log(10) unit) in this study with relatively uninhibited samples, but has the potential to cause as much as 8-fold (0.9 log(10) unit) difference in potentially inhibitory samples. Our findings indicate the need for a certified and centralized source of reference materials and additional studies to assess applicability of the quantification models in analyses of PCR inhibitory samples.
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA.
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Abstract
Culture-independent approaches, such as next-generation sequencing and microarray-based tools, provide insight into the identity and functional diversity of microbial communities. Although these approaches are potentially powerful tools in understanding microbial structure and function, there are a number of limitations that may bias conclusions. In order to mitigate these biases, an understanding of potential biases within each stage of the experimental process is necessary. This review focuses on the biases associated with sample collection, nucleic acid extraction, processing, sequencing analyses, and Chip technologies used in microbial ecology studies.
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Affiliation(s)
- Terry C Hazen
- Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States.
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