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Ho DT, Kim N, Lee Y, Yun D, Sung M, Mansour EM, Pradhan PK, Sood N, Kim WS, Park CI, Kim KH, Kim DH. Development of a rapid and sensitive real-time diagnostic assay to detect and quantify Aphanomyces invadans, the causative agent of epizootic ulcerative syndrome. PLoS One 2023; 18:e0286553. [PMID: 37319186 PMCID: PMC10270590 DOI: 10.1371/journal.pone.0286553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
The oomycete Aphanomyces invadans causes epizootic ulcerative syndrome (EUS), a World Organization for Animal Health (WOAH)-listed disease that has seriously impacted a wide range of fish worldwide. Currently, only three conventional polymerase chain reaction (PCR) assays are recommended for the detection of A. invadans. The robust quantitative PCR (qPCR) assay has recently become more important due to its highly accurate nature and the applicability of qPCR-based environmental DNA (eDNA) detection in the monitoring of pathogens in aquatic environments. Therefore, in this study, we developed a novel TaqMan probe-based qPCR method to sensitively and quantitatively detect A. invadans. The assay limit of detection was determined using 10-fold serial dilutions of linearized A. invadans plasmid. Assay sensitivity was assessed in the presence of interfering substances and compared to three WOAH-listed primers using the mycelia and zoospores of A. invadans with and without fish muscle tissue. The assay specificity was also theoretically and experimentally assessed against other oomycetes, fish muscle tissue, and water samples. The assay's repeatability and reproducibility were determined. In this study, the limit of detection of the developed assay was 7.24 copies of A. invadans genomic DNA per reaction (95% confidence interval (CI): 2.75 to 19.05 copies/reaction). The assay showed the same sensitivity in the presence of other substances. Compared to the WOAH-recommended PCR assays, this assay had 10-times higher sensitivity for all tested samples. There were no cross-reactions with other closely related oomycetes, fish muscle, or water samples, indicating that the assay was highly specific for A. invadans. The repeatability and reproducibility tests showed little variation, ranging from 0.1-0.9% and 0.04-1.1%, respectively, indicating the high consistency, repeatability, and reliability of the developed assay. This highly rapid, sensitive, specific, and consistent EUS qPCR assay would be of importance in transboundary disease management and the monitoring of pathogens in aquatic environments.
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Affiliation(s)
- Diem Tho Ho
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Nameun Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Dongbin Yun
- PCR Reagent Development Group, Bioneer Corporation, Daejeon, Republic of Korea
| | - MinJi Sung
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - El-Matbouli Mansour
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - P. K. Pradhan
- Fish Health Management and Exotics, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Neeraj Sood
- Fish Health Management and Exotics, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Wi-Sik Kim
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Republic of Korea
| | - Chan-Il Park
- Department of Marine Biology & Aquaculture, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Ki Hong Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
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2
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Ahmed W, Bivins A, Payyappat S, Cassidy M, Harrison N, Besley C. Distribution of human fecal marker genes and their association with pathogenic viruses in untreated wastewater determined using quantitative PCR. WATER RESEARCH 2022; 226:119093. [PMID: 36252296 DOI: 10.1016/j.watres.2022.119093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/21/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Quantitative microbial risk assessment (QMRA) of human health risks using human fecal marker genes (HFMGs) is an useful water quality management tool. To inform accurate QMRA analysis, generation of probability distribution functions for HFMGs, and reference pathogenic viruses can be improved by input of correlation and ratios based upon measurement of HFMGs and gene copies (GC) of pathogenic viruses in untreated wastewater. The concentrations of four HFMGs (Bacteroides HF183, Lachnospiraceae Lachno3, CrAssphage and pepper mild mottle virus (PMMoV)), and GC of three reference pathogenic viruses human adenovirus 40/41 (HAdV 40/41), human norovirus GI + GII HNoV GI + GII and enterovirus (EV) were measured in untreated wastewater samples collected over a period of 12 months from two wastewater treatment plants in Sydney, Australia using quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR). Over the course of the study, the GC of potential pathogenic viruses were 3-5 orders of magnitude lower than HFMGs in untreated wastewater. The GC of pathogenic viruses were highly variable over the course of the study, which contrasted with the concentrations of HFMGs that were quite stable with little variation observed within and between WWTPs. Among the HFMGs, HF183, CrAssphage and PMMoV correlated well with pathogenic virus GC, whereas weak or negative correlations were observed between Lachno3 and pathogenic virus GC. While the two assessed WWTPs had dissimilar population service sizes, the ratios between log10 transformed pathogenic virus GC and HFMGs demonstrated similar central tendency and variability for the same combinations between WWTP A and WWTP B with no difference between the WWTPs. This suggests the widespread presence of these HFMGs in both populations serviced by these two WWTPs. The observed correlation and ratios of HFMGs and GC of reference pathogenic viruses can contribute to improved QMRA of human health risks in environmental waters subject to fresh sewer overflows.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Nathan Harrison
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
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3
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Sivaganesan M, Willis JR, Karim M, Babatola A, Catoe D, Boehm AB, Wilder M, Green H, Lobos A, Harwood VJ, Hertel S, Klepikow R, Howard MF, Laksanalamai P, Roundtree A, Mattioli M, Eytcheson S, Molina M, Lane M, Rediske R, Ronan A, D'Souza N, Rose JB, Shrestha A, Hoar C, Silverman AI, Faulkner W, Wickman K, Kralj JG, Servetas SL, Hunter ME, Jackson SA, Shanks OC. Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917. WATER RESEARCH 2022; 225:119162. [PMID: 36191524 PMCID: PMC9932931 DOI: 10.1016/j.watres.2022.119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material® 2917 (NIST SRM® 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n = 1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mohammad Karim
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - Akin Babatola
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - David Catoe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Maxwell Wilder
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Hyatt Green
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Aldo Lobos
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Stephanie Hertel
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Regina Klepikow
- U.S. Environmental Protection Agency, Region 7 Laboratory, Kansas City, KS, USA
| | | | | | - Alexis Roundtree
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie Eytcheson
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Molly Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Richard Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Amanda Ronan
- U.S. Environmental Protection Agency, Region 2 Laboratory, Edison, NJ, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | | | | | - Jason G Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
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4
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Willis JR, Sivaganesan M, Haugland RA, Kralj J, Servetas S, Hunter ME, Jackson SA, Shanks OC. Performance of NIST SRM® 2917 with 13 recreational water quality monitoring qPCR assays. WATER RESEARCH 2022; 212:118114. [PMID: 35091220 PMCID: PMC10786215 DOI: 10.1016/j.watres.2022.118114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Fecal pollution remains a significant challenge for recreational water quality management worldwide. In response, there is a growing interest in the use of real-time quantitative PCR (qPCR) methods to achieve same-day notification of recreational water quality and associated public health risk as well as to characterize fecal pollution sources for targeted mitigation. However, successful widespread implementation of these technologies requires the development of and access to a high-quality standard control material. Here, we report a single laboratory qPCR performance assessment of the National Institute of Standards and Technology Standard Reference Material 2917 (NIST SRM® 2917), a linearized plasmid DNA construct that functions with 13 recreational water quality qPCR assays. Performance experiments indicate the generation of standard curves with amplification efficiencies ranging from 0.95 ± 0.006 to 0.99 ± 0.008 and coefficient of determination values (R2) ≥ 0.980. Regardless of qPCR assay, variability in repeated measurements at each dilution level were very low (quantification threshold standard deviations ≤ 0.657) and exhibited a heteroscedastic trend characteristic of qPCR standard curves. The influence of a yeast carrier tRNA added to the standard control material buffer was also investigated. Findings demonstrated that NIST SRM® 2917 functions with all qPCR methods and suggests that the future use of this control material by scientists and water quality managers should help reduce variability in concentration estimates and make results more consistent between laboratories.
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Affiliation(s)
- Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jason Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
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5
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Basili M, Campanelli A, Frapiccini E, Luna GM, Quero GM. Occurrence and distribution of microbial pollutants in coastal areas of the Adriatic Sea influenced by river discharge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117672. [PMID: 34380232 DOI: 10.1016/j.envpol.2021.117672] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The transport of a variety of pollutants from agricultural, industrial and urbanised areas makes rivers major contributors to the contamination of coastal marine environments. Too little is known of their role in carrying pathogens to the coast. We used DNA-based metabarcoding data to describe the microbial community composition in seawater and sediment collected in front of the estuary of the Tronto, the Chienti and the Esino, three Italian rivers with different pollution levels that empty into the north-central Adriatic Sea, and to detect and measure within these communities the relative abundance of microbial pollutants, including traditional faecal indicators and alternative faecal and sewage-associated pollutants. We then applied the FORENSIC algorithm to distinguish human from non-human sources of microbial pollution and FAPROTAX to map prokaryotic clades to established metabolic or other ecologically relevant functions. Finally, we searched the dataset for other common pathogenic taxa. Seawater and sediment contained numerous potentially pathogenic bacteria, mainly faecal and sewage-associated. The samples collected in front of the Tronto estuary showed the highest level of contamination, likely sewage-associated. The pathogenic signature showed a weak but positive correlation with some nutrients and strong correlations with some polycyclic aromatic hydrocarbons. This study confirms that rivers transport pathogenic bacteria to the coastal sea and highlights the value of expanding the use of HTS data, source tracking and functional identification tools to detect microbial pollutants and identify their sources with a view to gaining a better understanding of the pathways of sewage-associated discharges to the sea.
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Affiliation(s)
- Marco Basili
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Alessandra Campanelli
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Emanuela Frapiccini
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Gian Marco Luna
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Grazia Marina Quero
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy.
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6
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Sangkaew W, Kongprajug A, Chyerochana N, Ahmed W, Rattanakul S, Denpetkul T, Mongkolsuk S, Sirikanchana K. Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand. WATER RESEARCH 2021; 190:116706. [PMID: 33310444 DOI: 10.1016/j.watres.2020.116706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log10 copies/100 mL), crAssphage (5.28-7.38 log10 copies/100 mL), and HPyVs (3.66-6.53 log10 copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log10 copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log10 copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log10 copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log10 copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.
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Affiliation(s)
- Watsawan Sangkaew
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Thammanitchpol Denpetkul
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, 272 Rama 6 Road, Ratchathevi, Bangkok, 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, 272 Rama 6 Road, Ratchathevi, Bangkok, 10400, Thailand.
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7
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Agrawal S, Weissbrodt DG, Annavajhala M, Jensen MM, Arroyo JMC, Wells G, Chandran K, Vlaeminck SE, Terada A, Smets BF, Lackner S. Time to act-assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems. WATER RESEARCH 2021; 190:116604. [PMID: 33279744 DOI: 10.1016/j.watres.2020.116604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg-1 wet biomass. The variability among the qPCR abundance data of different labs was very high (1-7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3-7 log fold), followed by the primers (1-3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.
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Affiliation(s)
- Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany.
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Medini Annavajhala
- Department of Earth and Environmental Engineering, Columbia University, New York, USA
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Microbial Ecology & Technology Laboratory, Technical University of Denmark, Bygningtorvet, Bldg 115, DK-2800, Lyngby, Denmark
| | | | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, USA
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, New York, USA
| | - Siegfried E Vlaeminck
- Department of Bioscience Engineering, Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Akihiko Terada
- Institute of Global Innovation Research and Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo 184-8588, Japan
| | - Barth F Smets
- Department of Environmental Engineering, Microbial Ecology & Technology Laboratory, Technical University of Denmark, Bygningtorvet, Bldg 115, DK-2800, Lyngby, Denmark
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
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8
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Nieuwkerk DM, Korajkic A, Valdespino EL, Herrmann MP, Harwood VJ. Critical review of methods for isothermal amplification of nucleic acids for environmental analysis. J Microbiol Methods 2020; 179:106099. [PMID: 33159993 DOI: 10.1016/j.mimet.2020.106099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
The past 30 years have seen the emergence and proliferation of isothermal amplification methods (IAMs) for rapid, sensitive detection and quantification of nucleic acids in a variety of sample types. These methods share dependence on primers and probes with quantitative PCR, but they differ in the specific enzymes and instruments employed, and are frequently conducted in a binary, rather than quantitative format. IAMs typically rely on simpler instruments than PCR analyses due to the maintenance of a single temperature throughout the amplification reaction, which could facilitate deployment of IAMs in a variety of environmental and field settings. This review summarizes the mechanisms of the most common IAM methods and their use in studies of pathogens, harmful algae and fecal indicators in environmental waters, feces, wastewater, reclaimed water, and tissues of aquatic animals. Performance metrics of sensitivity, specificity and limit of detection are highlighted, and the potential for use in monitoring and regulatory contexts is discussed.
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Affiliation(s)
- Dana M Nieuwkerk
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asja Korajkic
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erika L Valdespino
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Michael P Herrmann
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Valerie J Harwood
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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Ahmed W, Payyappat S, Cassidy M, Harrison N, Besley C. Interlaboratory accuracy and precision among results of three sewage-associated marker genes in urban environmental estuarine waters and freshwater streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140071. [PMID: 32887015 DOI: 10.1016/j.scitotenv.2020.140071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/06/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
The application of quantitative polymerase chain reaction (qPCR) based microbial source tracking (MST) marker genes are increasingly being used to identify contaminating sources and inform management decisions. In this study, we assessed interlaboratory agreement on duplicate environmental water samples collected from estuarine and freshwater locations, by comparing results of qPCR based testing for Bacteroides HF183, crAssphage CPQ_056, and pepper mild mottle virus (PMMoV). The overall agreements (co-detection and non-co-detection) between CSIRO Land and Water (CLW) laboratory and Sydney Water (SW) laboratory for the HF183, crAssphage CPQ_056 and PMMoV marker genes for duplicate water samples were 74, 75 and 74%, respectively. Cohene's kappa (k) revealed fair to moderate agreements and acceptable relative percent difference (RPD) values of <15% for duplicate samples. The pooled mean abundances of HF183, CPQ_056, and PMMoV in measurable samples at the CLW laboratory were 5.19 ± 0.93, 5.12 ± 0.82, and 4.42 ± 0.65 log10 copies/L, respectively. However, the pooled mean abundances were significantly lower at the SW laboratory, HF183 (4.58 ± 0.84 log10 copies/L), crAssphage CPQ_056 (4.20 ± 0.63 log10 copies/L), and PMMoV (3.89 ± 0.41 log10 copies/L). At individual sample level, most of the paired samples had <1 log10 difference. Significant positive Spearman rank correlations were obtained between two laboratories for the HF183 (Rs = 0.65; p < 0.05), CPQ_056 (Rs = 0.79; p < 0.05), and PMMoV (Rs = 0.54; p < 0.05) marker genes. Several factors such as standards, qPCR platforms, PCR inhibitors, nucleic acid extraction efficiency and low levels of targets in some samples may have contributed to the observed discrepancies. Results presented in this study highlight the importance of standardized protocol, laboratory equipment (such as digital PCR), sample processing strategies and appropriate quality controls that may need implementation to further improve accuracy and precision of results between laboratories.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Nathan Harrison
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
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10
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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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11
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Nakano S, Tomaru Y, Kubota T, Takase H, Mochizuki M, Shimizu N, Sugita S. Multiplex Solid-Phase Real-Time Polymerase Chain Reaction without DNA Extraction: A Rapid Intraoperative Diagnosis Using Microvolumes. Ophthalmology 2020; 128:729-739. [PMID: 32987046 DOI: 10.1016/j.ophtha.2020.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/17/2020] [Accepted: 09/22/2020] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Current polymerase chain reaction (PCR) methods for the diagnosis of infections are time consuming and require large sample volume and skilled technicians. We developed a novel, easy-to-use, and rapid (processing time, 1 minute; total time, 33 minutes) multiplex real-time PCR test (Direct Strip PCR) that did not require DNA extraction to detect 9 pathogens that could cause uveitis in 20-μl samples. DESIGN Multicenter prospective evaluation of a diagnostic PCR test. PARTICIPANTS A total of 511 participants (patients with infectious uveitis and controls) were examined at 18 institutes worldwide. METHODS After validation, intraocular fluid samples were subjected to etiologic or exclusive diagnosis, including intraoperative rapid diagnosis. MAIN OUTCOME MEASURES The concordance and correlations between Direct Strip PCR and quantitative PCR (qPCR) results. RESULTS Direct Strip PCR exhibited rapid detection, good repeatability and specificity, long storage stability, and detection ability equal to that of qPCR. It also showed low interinstitutional variability compared with qPCR, even when PCR beginners used various real-time PCR machines. The Direct Strip PCR for 9 pathogens exhibited high concordance against the qPCR (positive concordance rate, 98.8%-100%; negative concordance rate, 99.8%-100%; κ coefficient, 0.969-1.000; P < 0.001-0.031). Additionally, results obtained using Direct Strip PCR and qPCR were highly correlated (ρ = 0.748; P < 0.001). This assay was used for rapid intraoperative diagnosis. CONCLUSIONS The Direct Strip PCR test may improve the prognosis of various infectious diseases because it facilitates rapid etiologic evaluation at the first hospital visit and can be used for intraoperative diagnosis.
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Affiliation(s)
- Satoko Nakano
- Department of Ophthalmology, Oita University, Yufu, Japan
| | - Yasuhiro Tomaru
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Hiroshi Takase
- Department of Ophthalmology & Visual Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Manabu Mochizuki
- Department of Ophthalmology & Visual Science, Tokyo Medical and Dental University, Tokyo, Japan; Miyata Eye Hospital, Miyakonojo, Japan
| | - Norio Shimizu
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sunao Sugita
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
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12
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Kongprajug A, Chyerochana N, Mongkolsuk S, Sirikanchana K. Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8232-8244. [PMID: 32484662 DOI: 10.1021/acs.est.0c01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log10 copies/g and 0.41 log10 copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log10 copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.
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Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
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Rudko SP, Reimink RL, Peter B, White J, Hanington PC. Democratizing water monitoring: Implementation of a community-based qPCR monitoring program for recreational water hazards. PLoS One 2020; 15:e0229701. [PMID: 32401786 PMCID: PMC7219769 DOI: 10.1371/journal.pone.0229701] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/23/2020] [Indexed: 12/21/2022] Open
Abstract
Recreational water monitoring can be challenging due to the highly variable nature of pathogens and indicator concentrations, the myriad of potential biological hazards to measure for, and numerous access points, both official and unofficial, that are used for recreation. The aim of this study was to develop, deploy, and assess the effectiveness of a quantitative polymerase chain reaction (qPCR) community-based monitoring (CBM) program for the assessment of bacterial and parasitic hazards in recreational water. This study developed methodologies for performing qPCR ‘in the field,’ then engaged with water management and monitoring groups and tested the method in a real-world implementation study to evaluate the accuracy of CBM using qPCR both quantitatively and qualitatively. This study found high reproducibility between qPCR results performed by non-expert field users and expert laboratory results, suggesting that qPCR as a methodology could be amenable to a CBM program.
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Affiliation(s)
- Sydney P. Rudko
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Ronald L. Reimink
- Office of Campus Ministries, Hope College, Holland, Michigan, United States of America
- Freshwater Solutions, LLC, Traverse City, Michigan, United States of America
| | - Bradley Peter
- Alberta Lake Management Society, Edmonton, Alberta, Canada
| | - Jay White
- Aquality Environmental Consulting Ltd., Edmonton, Alberta, Canada
| | - Patrick C. Hanington
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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14
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Lane MJ, McNair JN, Rediske RR, Briggs S, Sivaganesan M, Haugland R. Simplified Analysis of Measurement Data from A Rapid E. coli qPCR Method (EPA Draft Method C) Using A Standardized Excel Workbook. WATER 2020; 12:1-775. [PMID: 32461809 PMCID: PMC7252523 DOI: 10.3390/w12030775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Draft method C is a standardized method for quantifying E. coli densities in recreational waters using quantitative polymerase chain reaction (qPCR). The method includes a Microsoft Excel workbook that automatically screens for poor-quality data using a set of previously proposed acceptance criteria, generates weighted linear regression (WLR) composite standard curves, and calculates E. coli target gene copies in test samples. We compared standard curve parameter values and test sample results calculated with the WLR model to those from a Bayesian master standard curve (MSC) model using data from a previous multi-lab study. The two models' mean intercept and slope estimates from twenty labs' standard curves were within each other's 95% credible or confidence intervals for all labs. E. coli gene copy estimates of six water samples analyzed by eight labs were highly overlapping among labs when quantified with the WLR and MSC models. Finally, we compared multiple labs' 2016-2018 composite curves, comprised of data from individual curves where acceptance criteria were not used, to their corresponding composite curves with passing acceptance criteria. Composite curves developed from passing individual curves had intercept and slope 95% confidence intervals that were often narrower than without screening and an analysis of covariance test was passed more often. The Excel workbook WLR calculation and acceptance criteria will help laboratories implement draft method C for recreational water analysis in an efficient, cost-effective, and reliable manner.
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Affiliation(s)
- Molly J. Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
| | - James N. McNair
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
| | - Richard R. Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
- Correspondence:
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes, and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA
| | - Mano Sivaganesan
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. EPA, Cincinnati, OH 45268, USA
| | - Richard Haugland
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. EPA, Cincinnati, OH 45268, USA
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15
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Zhang Q, Gallard J, Wu B, Harwood VJ, Sadowsky MJ, Hamilton KA, Ahmed W. Synergy between quantitative microbial source tracking (qMST) and quantitative microbial risk assessment (QMRA): A review and prospectus. ENVIRONMENT INTERNATIONAL 2019; 130:104703. [PMID: 31295713 DOI: 10.1016/j.envint.2019.03.051] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 05/20/2023]
Abstract
The use of microbial source tracking (MST) marker genes has grown in recent years due to the need to attribute point and non-point fecal contamination to specific sources. Quantitative microbial risk assessment (QMRA) is a modeling approach used to estimate health risks from exposure to feces-contaminated water and associated pathogens. A combination of these approaches [quantitative MST (qMST) and QMRA] can provide additional pathogen-related information for prioritizing and addressing health risks, compared to reliance on conventional fecal indicator bacteria (FIB). To inform expansion of this approach, a review of published qMST-QMRA studies was conducted to summarize the state of the science and to identify research needs. The reviewed studies primarily aimed to identify what levels of MST marker genes in hypothetical recreational waterbodies would exceed the United States Environmental Protection Agency (USEPA) risk benchmarks for primary contact recreators. The QMRA models calculated relationships between MST marker gene(s) and reference pathogens based on published data in the literature. The development of a robust, accurate relationship was identified as an urgent research gap for qMST-QMRA. This metric requires additional knowledge to quantify the relationship between MST marker genes and the degree of variability in decay of pathogens as a dynamic function of environmental conditions and combinations of fecal sources at multiple spatial and temporal scales. Improved characterization of host shedding rates of host-associated microorganisms (i.e., MST marker genes), as well as fate and transport of these microorganisms and their nucleic acids, would facilitate expansion of this approach to other exposure pathways. Incorporation of information regarding the recovery efficiency, and host-specificity of MST marker genes into QMRA model parameters, and the sensitivity analysis, would greatly improve risk management and site-specific water monitoring criteria.
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Affiliation(s)
- Qian Zhang
- BioTechnology Institute, University of Minnesota, 1479 Gortner Ave, St. Paul, MN 55108, USA
| | - Javier Gallard
- Department of Integrative Biology, SCA 110, University of South Florida, 4202 East Fowler Ave, Tampa, FL 33620, USA
| | - Baolei Wu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, Shaanxi 710055, PR China
| | - Valerie J Harwood
- Department of Integrative Biology, SCA 110, University of South Florida, 4202 East Fowler Ave, Tampa, FL 33620, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 1479 Gortner Ave, St. Paul, MN 55108, USA; Department of Soil, Water & Climate and Department of Plant & Microbial Biology, University of Minnesota, 1991 Upper Buford Ave, St. Paul, MN 55108, USA
| | - Kerry A Hamilton
- School for Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA; The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
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16
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Nshimyimana JP, Cruz MC, Wuertz S, Thompson JR. Variably improved microbial source tracking with digital droplet PCR. WATER RESEARCH 2019; 159:192-202. [PMID: 31096066 DOI: 10.1016/j.watres.2019.04.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 05/05/2023]
Abstract
This study addressed whether digital droplet PCR (ddPCR) could improve sensitivity and specificity of human-associated Bacteroidales genetic markers, BacHum and B. theta, and their quantification in environmental and fecal composite samples. Human markers were quantified by qPCR and ddPCR platforms obtained from the same manufacturer. A total of 180 samples were evaluated by each platform including human and animal feces, sewage, and environmental water. The sensitivity of ddPCR and qPCR marker assays in sewage and human stool was 0.85-1.00 with marginal reduction in human stool by ddPCR relative to qPCR (<10%). The prevalence and distribution of markers across complex sample types was similar (74-100% agreement) by both platforms with qPCR showing higher sensitivity for markers in environmental and composite samples and ddPCR showing greater reproducibility for marker detection in fecal composites. Determination of BacHum prevalence in fecal samples by ddPCR increased specificity relative to qPCR (from 0.58 to 0.88) and accuracy (from 0.77 to 0.94), while the B. theta assay performed similarly on both platforms (specificity = 0.98). In silico analysis indicated higher specificity of ddPCR for BacHum was not solely attributed to reduced sensitivity relative to qPCR. Marker concentrations measured by ddPCR for all sample types were consistently lower than those measured by qPCR, by a factor of 2.6 ± 2.8 for B. theta and 18.7 ± 10.0 for BacHum. We suggest that differences in assay performance on ddPCR and qPCR platforms may be linked to the characteristics of the assay targets (that is, genes with multiple versus single copies and encoding proteins versus ribosomal RNA) however further work is needed to validate these ideas. We conclude that ddPCR is a suitable tool for microbial source tracking, however, other factors such as cost-effectiveness and assay-specific performance should be considered.
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Affiliation(s)
- Jean Pierre Nshimyimana
- School of Civil and Environmental Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering, NTU, 60 Nanyang Dr., Singapore, 637551, Singapore; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Mercedes C Cruz
- Singapore Centre for Environmental Life Sciences Engineering, NTU, 60 Nanyang Dr., Singapore, 637551, Singapore
| | - Stefan Wuertz
- School of Civil and Environmental Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering, NTU, 60 Nanyang Dr., Singapore, 637551, Singapore
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA, 02139, USA; Centre for Environmental Sensing and Modeling, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Singapore, 138602, Singapore.
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17
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Aw TG, Sivaganesan M, 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. Evaluation of multiple laboratory performance and variability in analysis of recreational freshwaters by a rapid Escherichia coli qPCR method (Draft Method C). WATER RESEARCH 2019; 156:465-474. [PMID: 30953844 PMCID: PMC9994418 DOI: 10.1016/j.watres.2019.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 06/01/2023]
Abstract
There is interest in the application of rapid quantitative polymerase chain reaction (qPCR) methods for recreational freshwater quality monitoring of the fecal indicator bacteria Escherichia coli (E. coli). In this study we determined the performance of 21 laboratories in meeting proposed, standardized data quality acceptance (QA) criteria and the variability of target gene copy estimates from these laboratories in analyses of 18 shared surface water samples by a draft qPCR method developed by the U.S. Environmental Protection Agency (EPA) for E. coli. The participating laboratories ranged from academic and government laboratories with more extensive qPCR experience to "new" water quality and public health laboratories with relatively little previous experience in most cases. Failures to meet QA criteria for the method were observed in 24% of the total 376 test sample analyses. Of these failures, 39% came from two of the "new" laboratories. Likely factors contributing to QA failures included deviations in recommended procedures for the storage and preparation of reference and control materials. A master standard curve calibration model was also found to give lower overall variability in log10 target gene copy estimates than the delta-delta Ct (ΔΔCt) calibration model used in previous EPA qPCR methods. However, differences between the mean estimates from the two models were not significant and variability between laboratories was the greatest contributor to overall method variability in either case. Study findings demonstrate the technical feasibility of multiple laboratories implementing this or other qPCR water quality monitoring methods with similar data quality acceptance criteria but suggest that additional practice and/or assistance may be valuable, even for some more generally experienced qPCR laboratories. Special attention should be placed on providing and following explicit guidance on the preparation, storage and handling of reference and control materials.
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Affiliation(s)
- 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
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, 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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18
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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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19
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Ahmed W, Payyappat S, Cassidy M, Besley C. A duplex PCR assay for the simultaneous quantification of Bacteroides HF183 and crAssphage CPQ_056 marker genes in untreated sewage and stormwater. ENVIRONMENT INTERNATIONAL 2019; 126:252-259. [PMID: 30822654 DOI: 10.1016/j.envint.2019.01.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/13/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
Abstract
The HF183 marker gene, derived from the 16S rRNA gene of Bacteroides dorei, has been widely used to identify sewage pollution in environmental waters. CrAssphages are recently discovered DNA bacteriophages that are highly abundant in untreated sewage and have shown promises for tracking sewage contamination in environmental waters. In this paper, we report the development of a duplex quantitative PCR (qPCR) assay for simultaneous quantification of HF183 and crAssphage CPQ_056 marker genes in untreated sewage and sewage impacted stormwater. Same primer and probe sequences were used in the duplex qPCR assay as used in published simplex qPCR assays. The performance characteristics of the duplex qPCR assay were similar to its simplex counterparts. We validated the performance of the duplex assay in a collaborative laboratory study with the aim to evaluate reproducibility, sensitivity and concordance for field study. The concordance values between the simplex vs. duplex qPCR assays for HF183 and crAssphage CPQ_056 marker genes ranged from 96.7 to 100% and the mean concentrations of HF183 and CPQ_056 in environmental water samples were remarkably similar or in some cases slightly greater for the duplex qPCR assay suggesting the reliability of this assay for monitoring HF183 and CPQ_056 simultaneously. The newly developed duplex qPCR assay will be a valuable addition to the MST toolbox for sewage pollution monitoring and would allow rapid and comparative sample analysis.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
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20
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Searcy RT, Taggart M, Gold M, Boehm AB. Implementation of an automated beach water quality nowcast system at ten California oceanic beaches. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 223:633-643. [PMID: 29975890 DOI: 10.1016/j.jenvman.2018.06.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/12/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Fecal indicator bacteria like Escherichia coli and entercococci are monitored at beaches around the world to reduce incidence of recreational waterborne illness. Measurements are usually made weekly, but FIB concentrations can exhibit extreme variability, fluctuating at shorter periods. The result is that water quality has likely changed by the time data are provided to beachgoers. Here, we present an automated water quality prediction system (called the nowcast system) that is capable of providing daily predictions of water quality for numerous beaches. We created nowcast models for 10 California beaches using weather, oceanographic, and other environmental variables as input to tuned regression models to predict if FIB concentrations were above single sample water quality standards. Rainfall was used as a variable in nearly every model. The models were calibrated and validated using historical data. Subsequently, models were implemented during the 2017 swim season in collaboration with local beach managers. During the 2017 swim season, the median sensitivity of the nowcast models was 0.5 compared to 0 for the current method of using day-to-week old measurements to make beach posting decisions. Model specificity was also high (median of 0.87). During the implementation phase, nowcast models provided an average of 140 additional days per beach of updated water quality information to managers when water quality measurements were not made. The work presented herein emphasizes that a one-size-fits all approach to nowcast modeling, even when beaches are in close proximity, is infeasible. Flexibility in modeling approaches and adaptive responses to modeling and data challenges are required when implementing nowcast models for beach management.
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Affiliation(s)
- Ryan T Searcy
- Heal the Bay, 1444 9th Street, Santa Monica, CA 90401, USA
| | - Mitzy Taggart
- Heal the Bay, 1444 9th Street, Santa Monica, CA 90401, USA
| | - Mark Gold
- UCLA, 2248 Murphy Hall, 410 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA, 94305, USA.
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21
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Kelly EA, Feng Z, Gidley ML, Sinigalliano CD, Kumar N, Donahue AG, Reniers AJHM, Solo-Gabriele HM. Effect of beach management policies on recreational water quality. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 212:266-277. [PMID: 29448181 PMCID: PMC5844856 DOI: 10.1016/j.jenvman.2018.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/19/2017] [Accepted: 02/02/2018] [Indexed: 05/30/2023]
Abstract
When beach water monitoring programs identify poor water quality, the causes are frequently unknown. We hypothesize that management policies play an important role in the frequency of fecal indicator bacteria (FIB) exceedances (enterococci and fecal coliform) at recreational beaches. To test this hypothesis we implemented an innovative approach utilizing large amounts of monitoring data (n > 150,000 measurements per FIB) to determine associations between the frequency of contaminant exceedances and beach management practices. The large FIB database was augmented with results from a survey designed to assess management policies for 316 beaches throughout the state of Florida. The FIB and survey data were analyzed using t-tests, ANOVA, factor analysis, and linear regression. Results show that beach geomorphology (beach type) was highly associated with exceedance of regulatory standards. Low enterococci exceedances were associated with open coast beaches (n = 211) that have sparse human densities, no homeless populations, low densities of dogs and birds, bird management policies, low densities of seaweed, beach renourishment, charge access fees, employ lifeguards, without nearby marinas, and those that manage storm water. Factor analysis and a linear regression confirmed beach type as the predominant factor with secondary influences from grooming activities (including seaweed densities and beach renourishment) and beach access (including charging fees, employing lifeguards, and without nearby marinas). Our results were observable primarily because of the very large public FIB database available for analyses; similar approaches can be adopted at other beaches. The findings of this research have important policy implications because the selected beach management practices that were associated with low levels of FIB can be implemented in other parts of the US and around the world to improve recreational beach water quality.
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Affiliation(s)
- Elizabeth A Kelly
- University of Miami, Leonard and Jayne Abess Center for Ecosystem Science and Policy, Coral Gables, FL, USA; NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; University of Miami, College of Engineering, Department of Civil, Architectural, and Environmental Engineering, USA
| | - Zhixuan Feng
- NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Maribeth L Gidley
- NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; University of Miami Cooperative Institute for Marine and Atmospheric Studies, Key Biscayne, FL, USA; NOAA Atlantic Oceanographic and Meteorological Laboratory, Key Biscayne, FL, USA
| | - Christopher D Sinigalliano
- NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; NOAA Atlantic Oceanographic and Meteorological Laboratory, Key Biscayne, FL, USA
| | - Naresh Kumar
- University of Miami Department of Public Health Sciences, Division of Environment & Public Health, Miami, FL, USA
| | - Allison G Donahue
- NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; University of Miami, Department of Biology, Coral Gables, FL, USA
| | - Adrianus J H M Reniers
- NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; Delft University of Technology, Department of Hydraulic Engineering, Delft, The Netherlands
| | - Helena M Solo-Gabriele
- University of Miami, Leonard and Jayne Abess Center for Ecosystem Science and Policy, Coral Gables, FL, USA; NSF NIEHS Oceans and Human Health Center, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Key Biscayne, FL, USA; University of Miami, College of Engineering, Department of Civil, Architectural, and Environmental Engineering, USA.
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22
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Cao Y, Raith MR, Griffith JF. Testing of General and Human-Associated Fecal Contamination in Waters. Methods Mol Biol 2018; 1768:127-140. [PMID: 29717441 DOI: 10.1007/978-1-4939-7778-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
qPCR has become increasingly popular for microbial water quality testing because it is faster, more specific, and more flexible than culture-based methods. However, qPCR method limitations such as quantification bias introduced by reliance on standards and susceptibility to PCR inhibitors are major obstacles for implementation in water testing. This is because water testing requires accurate quantification of rare targets and because environmental waters often contain PCR inhibitors. Digital PCR offers the opportunity to maintain qPCR's advantages over culture-based methods while ameliorating two of qPCR's major limitations: the necessity to run standard curves and high susceptibility to inhibition. Here we describe a complete method for simultaneous testing for a general microbial water quality indicator (Enterococcus spp.) and a human-associated fecal marker in environmental waters. The complete method includes water sampling and filtration to capture bacteria, DNA extraction from bacteria captured on the filter, and droplet digital PCR to quantify the genetic markers from bacteria indicative of general and human-associated fecal contamination.
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Affiliation(s)
- Yiping Cao
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA.
- Source Molecular Corporation, Miami, FL, USA.
| | - Meredith R Raith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA
| | - John F Griffith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA
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23
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Brown KI, Graham KE, Soller JA, Boehm AB. Estimating the probability of illness due to swimming in recreational water with a mixture of human- and gull-associated microbial source tracking markers. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:1528-1541. [PMID: 29114693 DOI: 10.1039/c7em00316a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Beaches often receive fecal contamination from more than one source. Human sources include untreated sewage as well as treated wastewater effluent, and animal sources include wildlife such as gulls. Different contamination sources are expected to pose different health risks to swimmers. Genetic microbial source tracking (MST) markers can be used to detect bacteria that are associated with different animal sources, but the health risks associated with a mixture of MST markers are unknown. This study presents a method for predicting these health risks, using human- and gull-associated markers as an example. Quantitative Microbial Risk Assessment (QMRA) is conducted with MST markers as indicators. We find that risks associated with exposure to a specific concentration of a human-associated MST marker (HF) are greater if the HF source is untreated sewage rather than treated wastewater effluent. We also provide a risk-based threshold of HF from untreated sewage at a beach, to stay below a predicted illness risk of 3 per 100 swimmers, that is a function of gull-associated MST marker (CAT) concentration.
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Affiliation(s)
- Kendra I Brown
- Department of Civil and Environmental Engineering, Environmental Engineering and Science, Stanford University, 94305-4020, USA.
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24
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Jastrow A, Gordon DA, Auger KM, Punska EC, Arcaro KF, Keteles K, Winkelman D, Lattier D, Biales A, Lazorchak JM. Tools to minimize interlaboratory variability in vitellogenin gene expression monitoring programs. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017. [PMID: 28631833 PMCID: PMC5894818 DOI: 10.1002/etc.3885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The egg yolk precursor protein vitellogenin is widely used as a biomarker of estrogen exposure in male fish. However, standardized methodology is lacking and little is known regarding the reproducibility of results among laboratories using different equipment, reagents, protocols, and data analysis programs. To address this data gap we tested the reproducibility across laboratories to evaluate vitellogenin gene (vtg) expression and assessed the value of using a freely available software data analysis program. Samples collected from studies of male fathead minnows (Pimephales promelas) exposed to 17α-ethinylestradiol (EE2) and minnows exposed to processed wastewater effluent were evaluated for vtg expression in 4 laboratories. Our results indicate reasonable consistency among laboratories if the free software for expression analysis LinRegPCR is used, with 3 of 4 laboratories detecting vtg in fish exposed to 5 ng/L EE2 (n = 5). All 4 laboratories detected significantly increased vtg levels in 15 male fish exposed to wastewater effluent compared with 15 male fish held in a control stream. Finally, we were able to determine that the source of high interlaboratory variability from complementary deoxyribonucleic acid (cDNA) to quantitative polymerase chain reaction (qPCR) analyses was the expression analysis software unique to each real-time qPCR machine. We successfully eliminated the interlaboratory variability by reanalyzing raw fluorescence data with independent freeware, which yielded cycle thresholds and polymerase chain reaction (PCR) efficiencies that calculated results independently of proprietary software. Our results suggest that laboratories engaged in monitoring programs should validate their PCR protocols and analyze their gene expression data following the guidelines established in the present study for all gene expression biomarkers. Environ Toxicol Chem 2017;36:3102-3107. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
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Affiliation(s)
- Aaron Jastrow
- Region 5 Laboratory, US Environmental Protection Agency, Chicago, Illinois, USA
| | - Denise A Gordon
- National Exposure Research Laboratory, US Environmental Protection Agency Office of Research and Development, Cincinnati, Ohio, USA
| | - Kasie M Auger
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Elizabeth C Punska
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kathleen F Arcaro
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kristen Keteles
- National Enforcement Investigations Center, US Environmental Protection Agency, Denver, Colorado, USA
| | - Dana Winkelman
- US Geological Survey, Colorado Cooperative Fish and Wildlife Research Unit, Colorado State University, Fort Collins, Colorado, USA
| | - David Lattier
- National Exposure Research Laboratory, US Environmental Protection Agency Office of Research and Development, Cincinnati, Ohio, USA
| | - Adam Biales
- National Exposure Research Laboratory, US Environmental Protection Agency Office of Research and Development, Cincinnati, Ohio, USA
| | - James M Lazorchak
- National Exposure Research Laboratory, US Environmental Protection Agency Office of Research and Development, Cincinnati, Ohio, USA
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25
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Napier MD, Haugland R, Poole C, Dufour AP, Stewart JR, Weber DJ, Varma M, Lavender JS, Wade TJ. Exposure to human-associated fecal indicators and self-reported illness among swimmers at recreational beaches: a cohort study. Environ Health 2017; 16:103. [PMID: 28969670 PMCID: PMC5625766 DOI: 10.1186/s12940-017-0308-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/18/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Fecal indicator bacteria used to assess illness risks in recreational waters (e.g., Escherichia coli, Enterococci) cannot discriminate among pollution sources. To address this limitation, human-associated Bacteroides markers have been proposed, but the risk of illness associated with the presence of these markers in recreational waters is unclear. Our objective was to estimate associations between human-associated Bacteroides markers in water and self-reported illness among swimmers at 6 U.S. beaches spanning 2003-2007. METHODS We used data from a prospectively-enrolled cohort of 12,060 swimmers surveyed about beach activities and water exposure on the day of their beach visit. Ten to twelve days later, participants reported gastroinestinal, diarrheal, and respiratory illnesses experienced since the visit. Daily water samples were analyzed for the presence of human-associated Bacteroides genetic markers: HF183, BsteriF1, BuniF2, HumM2. We used model-based standardization to estimate risk differences (RD) and 95% confidence intervals (CI). We assessed whether the presence of Bacteroides markers were modifiers of the association between general Enterococcus and illness among swimmers using interaction contrast. RESULTS Overall we observed inconsistent associations between the presence of Bacteroides markers and illness. There was a pattern of increased risks of gastrointestinal (RD = 1.9%; 95% CI: 0.1%, 3.7%), diarrheal (RD = 1.3%; 95% CI: -0.2%, 2.7%), and respiratory illnesses (RD = 1.1%; 95% CI: -0.2%, 2.5%) associated with BsteriF1. There was no evidence that Bacteroides markers acted as modifiers of Enterococcus and illness. Patterns were similar when stratified by water matrix. CONCLUSIONS Quantitative measures of fecal pollution using Bacteroides, rather than presence-absence indicators, may be necessary to accurately assess human risk specific to the presence of human fecal pollution.
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Affiliation(s)
- Melanie D. Napier
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, 135 Dauer Drive, 2101 McGavran-Greenberg Hall, CB #7435, Chapel Hill, NC 27599 USA
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH USA
| | - Charles Poole
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, 135 Dauer Drive, 2101 McGavran-Greenberg Hall, CB #7435, Chapel Hill, NC 27599 USA
| | - Alfred P. Dufour
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH USA
| | - Jill R. Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, 135 Dauer Drive, 166 Rosenau Hall, CB #7431, Chapel Hill, NC 27599 USA
| | - David J. Weber
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, 135 Dauer Drive, 2101 McGavran-Greenberg Hall, CB #7435, Chapel Hill, NC 27599 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Health Care, Bioinformatics Building, 130 Mason Farm Road, 2nd Floor, CB#7030, Chapel Hill, NC 27599 USA
| | - Manju Varma
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH USA
| | - Jennifer S. Lavender
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH USA
| | - Timothy J. Wade
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC 27709 USA
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26
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Real-time PCR assay for Aquimarina macrocephali subsp. homaria and its distribution in shell disease lesions of Homarus americanus, Milne-Edwards, 1837, and environmental samples. J Microbiol Methods 2017; 139:61-67. [PMID: 28385456 DOI: 10.1016/j.mimet.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/23/2017] [Accepted: 04/02/2017] [Indexed: 11/21/2022]
Abstract
Epizootic shell disease (ESD) is causing major losses to the lobster fishery in southern New England. Potential pathogens have been identified in lesion communities, but there are currently no efficient means of detecting and quantifying their presence. A qPCR assay was developed for a key potential pathogen, Aquimarina macrocephali subsp. homaria found to be ubiquitous in ESD lesions but not the unaffected integument. Application of the assay to various samples demonstrated that A. macrocephali subsp. homaria is ubiquitous and abundant in lobster lesions, commonly associated with healthy surfaces of crabs and is scarce in water and sediment samples from southern New England suggesting the affinity of this microorganism to the Arthropod integument. The qPCR assay developed here can be applied in future in vivo and in vitro studies to better understand the ecology and role of A. macrocephali subsp.homaria. in shell disease.
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27
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Mattioli MC, Sassoubre LM, Russell TL, Boehm AB. Decay of sewage-sourced microbial source tracking markers and fecal indicator bacteria in marine waters. WATER RESEARCH 2017; 108:106-114. [PMID: 27855952 DOI: 10.1016/j.watres.2016.10.066] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 05/20/2023]
Abstract
The decay of sewage-sourced enterococci, Escherichia coli, three human-associated microbial source tracking (MST) markers, Salmonella, Campylobacter, and norovirus GII was measured in situ in coastal, marine waters. Experiments examined the effects of sunlight intensity and season on decay. Seawater was seeded with untreated sewage, placed into permeable dialysis bags, and deployed in the coastal ocean near the water surface, and at 18 cm, and 99 cm depths, to vary solar intensity, during winter and summer seasons. Microbial decay was modeled using a log-linear or shoulder log-linear decay model. Pathogen levels were too low in sewage to obtain kinetic parameters. Human-associated MST markers all decayed with approximately the same rate constant (k ∼ 1.5 d-1) in all experimental treatments, suggesting markers could be detectable up to ∼6 days after a raw sewage spill. E. coli and enterococci (culturable and molecular marker) k significantly varied with season and depth; enterococci decayed faster at shallow depths and during the summer, while E. coli decayed faster at shallow depths and during the winter. Rate constants for MST markers and culturable FIB diverged except at the deepest depth in the water column potentially complicating the use of MST marker concentrations to allocate sources of FIB contamination.
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Affiliation(s)
- Mia Catharine Mattioli
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, United States
| | - Lauren M Sassoubre
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, United States
| | - Todd L Russell
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, United States
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, United States.
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28
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Wanjugi P, Sivaganesan M, Korajkic A, Kelty CA, McMinn B, Ulrich R, Harwood VJ, Shanks OC. Differential decomposition of bacterial and viral fecal indicators in common human pollution types. WATER RESEARCH 2016; 105:591-601. [PMID: 27693971 PMCID: PMC7440646 DOI: 10.1016/j.watres.2016.09.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 05/19/2023]
Abstract
Understanding the decomposition of microorganisms associated with different human fecal pollution types is necessary for proper implementation of many water quality management practices, as well as predicting associated public health risks. Here, the decomposition of select cultivated and molecular indicators of fecal pollution originating from fresh human feces, septage, and primary effluent sewage in a subtropical marine environment was assessed over a six day period with an emphasis on the influence of ambient sunlight and indigenous microbiota. Ambient water mixed with each fecal pollution type was placed in dialysis bags and incubated in situ in a submersible aquatic mesocosm. Genetic and cultivated fecal indicators including fecal indicator bacteria (enterococci, E. coli, and Bacteroidales), coliphage (somatic and F+), Bacteroides fragilis phage (GB-124), and human-associated genetic indicators (HF183/BacR287 and HumM2) were measured in each sample. Simple linear regression assessing treatment trends in each pollution type over time showed significant decay (p ≤ 0.05) in most treatments for feces and sewage (27/28 and 32/40, respectively), compared to septage (6/26). A two-way analysis of variance of log10 reduction values for sewage and feces experiments indicated that treatments differentially impact survival of cultivated bacteria, cultivated phage, and genetic indicators. Findings suggest that sunlight is critical for phage decay, and indigenous microbiota play a lesser role. For bacterial cultivated and genetic indicators, the influence of indigenous microbiota varied by pollution type. This study offers new insights on the decomposition of common human fecal pollution types in a subtropical marine environment with important implications for water quality management applications.
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Affiliation(s)
- Pauline Wanjugi
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Asja Korajkic
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Catherine A Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Brian McMinn
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls. Appl Environ Microbiol 2016; 82:6357-6366. [PMID: 27542934 DOI: 10.1128/aem.01675-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 12/26/2022] Open
Abstract
Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log10 CFU/100 ml, and 7.65 log10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. IMPORTANCE Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination.
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Staley ZR, Edge TA. Comparative microbial source tracking methods for identification of fecal contamination sources at Sunnyside Beach in the Toronto region area of concern. JOURNAL OF WATER AND HEALTH 2016; 14:839-850. [PMID: 27740549 DOI: 10.2166/wh.2016.296] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Several beaches within the Toronto region area of concern have persistent issues with fecal contamination, causing a beach beneficial use impairment (BUI). In this study, Escherichia coli, including ampicillin-resistant strains, were enumerated via culturable and quantitative polymerase chain reaction (qPCR) methods. Microbial source tracking (MST) markers (for general Bacteroidales, human, ruminant/cow, gull, and dog) were detected and enumerated via PCR and qPCR to identify sources of fecal contamination at Sunnyside Beach and in the Humber River. Human, cow, and dog markers had good host-specificity, while gull markers sometimes amplified a few other bird species. The ruminant endpoint PCR marker amplified a variety of other animal species rendering it less useful. Both human and gull fecal contamination were prevalent in the Humber River, while Sunnyside Beach was predominantly impacted by gull fecal contamination. Human sewage impacts were more prevalent in the lower Humber River, particularly in Black Creek. However, to reduce Sunnyside beach postings, reducing bird fecal contamination in the river and at the beach would be necessary. When there are high levels of E. coli throughout a beachshed, an MST toolbox approach can add value to discriminate source(s) of E. coli contamination and guide decisions relating to public health risk and remediation strategies.
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Affiliation(s)
- Zachery R Staley
- Environment Canada, Water Science and Technology Directorate, 867 Lakeshore Road, Burlington, Ontario L7R 4A6, Canada E-mail:
| | - Thomas A Edge
- Environment Canada, Water Science and Technology Directorate, 867 Lakeshore Road, Burlington, Ontario L7R 4A6, Canada E-mail:
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31
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Wang D, Yamahara KM, Cao Y, Boehm AB. Absolute Quantification of Enterococcal 23S rRNA Gene Using Digital PCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3399-408. [PMID: 26903207 DOI: 10.1021/acs.est.5b05747] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We evaluated the ability of chip-based digital PCR (dPCR) to quantify enterococci, the fecal indicator recommended by the United States Environmental Protection Agency (USEPA) for water-quality monitoring. dPCR uses Poisson statistics to estimate the number of DNA fragments in a sample with a specific sequence. Underestimation may occur when a gene is redundantly encoded in the genome and multiple copies of that gene are on one DNA fragment. When genomic DNA (gDNA) was extracted using two commercial DNA extraction kits, we confirmed that dPCR could discern individual copies of the redundant 23s rRNA gene in the enterococcal genome. dPCR quantification was accurate when compared to the nominal concentration inferred from fluorometer measurements (linear regression slope = 0.98, intercept = 0.03, R(2) = 0.99, and p value <0.0001). dPCR quantification was also consistent with quantitative PCR (qPCR) measurements as well as cell counts for BioBall reference standard and 24 environmental water samples. qPCR and dPCR quantification of enterococci in the 24 environmental samples were significantly correlated (linear regression slope =1.08, R(2) of 0.96, and p value <0.0001); the group mean of the qPCR measurements was 0.19 log units higher than that of the dPCR measurements. At environmentally relevant concentrations, dPCR quantification was more precise (i.e., had narrower 95% confidence intervals than qPCR quantification). We observed that humic acid caused a similar level of inhibition in both dPCR and qPCR, but calcium inhibited dPCR to a lesser degree than qPCR. Inhibition of dPCR was partially relieved when the number of thermal cycles was increased. Based on these results, we conclude that dPCR is a viable option for enumerating enterococci in ambient water.
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Affiliation(s)
- Dan Wang
- Environmental and Water Studies, Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Kevan M Yamahara
- Environmental and Water Studies, Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Yiping Cao
- Southern California Coastal Water Research Project Authority , Costa Mesa, California 92626, United States
| | - Alexandria B Boehm
- Environmental and Water Studies, Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
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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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Mayer RE, Bofill-Mas S, Egle L, Reischer GH, Schade M, Fernandez-Cassi X, Fuchs W, Mach RL, Lindner G, Kirschner A, Gaisbauer M, Piringer H, Blaschke AP, Girones R, Zessner M, Sommer R, Farnleitner AH. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution. WATER RESEARCH 2016; 90:265-276. [PMID: 26745175 PMCID: PMC4884448 DOI: 10.1016/j.watres.2015.12.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 12/13/2015] [Accepted: 12/17/2015] [Indexed: 05/19/2023]
Abstract
This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml(-1)) and biologically treated wastewater samples (median log10 6.2-6.5 ME 100 ml(-1)), irrespective of plant size, type and time of the season (n = 53-65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3-3.0) and treated wastewater (s* = 3.7-4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support if highly specific markers are needed.
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Affiliation(s)
- R E Mayer
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - L Egle
- Institute for Water Quality Resources and Waste Management, Vienna University of Technology, Karlsplatz 13/226, 1040, Vienna, Austria; Center of Water Resource Systems, Vienna University of Technology, Karlsplatz 13/222, 1040, Vienna, Austria
| | - G H Reischer
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| | - M Schade
- Bavarian Environment Agency, Bürgermeister-Ulrich-Straße 160, 86179, Augsburg, Germany
| | - X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - W Fuchs
- Department of Environmental Biotechnology at IFA, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - R L Mach
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
| | - G Lindner
- InterUniversity Cooperation Centre for Water and Health, Austria; Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - A Kirschner
- InterUniversity Cooperation Centre for Water and Health, Austria; Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090, Vienna, Austria
| | - M Gaisbauer
- Schreiber-AWATEC Umwelttechnik GmbH, Bergmillergasse 3/1, 1140, Vienna, Austria
| | - H Piringer
- VRVis Research Center, Donau-City-Strasse 1, 1220, Vienna, Austria
| | - A P Blaschke
- InterUniversity Cooperation Centre for Water and Health, Austria; Center of Water Resource Systems, Vienna University of Technology, Karlsplatz 13/222, 1040, Vienna, Austria
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - M Zessner
- Institute for Water Quality Resources and Waste Management, Vienna University of Technology, Karlsplatz 13/226, 1040, Vienna, Austria; Center of Water Resource Systems, Vienna University of Technology, Karlsplatz 13/222, 1040, Vienna, Austria
| | - R Sommer
- InterUniversity Cooperation Centre for Water and Health, Austria; Medical University Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090, Vienna, Austria.
| | - A H Farnleitner
- Institute of Chemical Engineering, Research Division Biotechnology and Microbiology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Gumpendorfer Straße 1a/166-5-2, A-1060, Vienna, Austria; InterUniversity Cooperation Centre for Water and Health, Austria
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34
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Staley ZR, Robinson C, Edge TA. Comparison of the occurrence and survival of fecal indicator bacteria in recreational sand between urban beach, playground and sandbox settings in Toronto, Ontario. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 541:520-527. [PMID: 26432162 DOI: 10.1016/j.scitotenv.2015.09.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
While beach sands are increasingly being studied as a reservoir of fecal indicator bacteria (FIB), less is known about the occurrence of FIB in other recreational sands (i.e., sandboxes and playgrounds). In this study, different culture-based FIB enumeration techniques were compared and microbial source tracking assays were conducted on recreational sand samples from beaches, playgrounds and sandboxes around Toronto, ON. FIB were detected in every sand sample (n=104) with concentrations not changing significantly over the five month sampling period. Concentrations of FIB and a gull-specific DNA marker were significantly higher in foreshore beach sands, and indicated these were a more significant reservoir of FIB contamination than sandbox or playground sands. Human- and dog-specific contamination markers were not detected. All culture-based FIB enumeration techniques were consistent in identifying the elevated FIB concentrations associated with foreshore beach sands. However, significant differences between differential agar media, IDEXX and Aquagenx Compartment Bag Test were observed, with DC media and Enterolert being the most sensitive methods to detect Escherichia coli and enterococci, respectively. To better understand the elevated occurrence of E. coli in foreshore sands, microcosm survival experiments were conducted at two different temperatures (15 °C and 28 °C) using non-sterile saturated foreshore beach sands collected from two urban freshwater beaches with different sand type (fine grain and sand-cobble). Microcosms were inoculated with a mixture of eight sand-derived E. coli strains and sampled over a 28-day period. E. coli levels were found to decline in all microcosms, although survival was significantly greater in the finer sand and at the cooler temperature (15 °C). These results indicate that FIB can be widespread in any type of recreational sand and, while E. coli can survive for many weeks, it is most likely to accumulate in cooler fine-grain sand as occurs below the foreshore sand surface.
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Affiliation(s)
- Zachery R Staley
- Department of Civil and Environmental Engineering, Western University, London, ON, Canada; Environment Canada, Canada Centre for Inland Waters, Burlington, ON, Canada.
| | - Clare Robinson
- Department of Civil and Environmental Engineering, Western University, London, ON, Canada
| | - Thomas A Edge
- Environment Canada, Canada Centre for Inland Waters, Burlington, ON, Canada
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35
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Cao Y, Griffith JF, Weisberg SB. The Next-Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR. Methods Mol Biol 2016; 1452:113-30. [PMID: 27460373 DOI: 10.1007/978-1-4939-3774-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Real-time quantitative PCR (qPCR) is increasingly being used for ambient water monitoring, but development of digital polymerase chain reaction (digital PCR) has the potential to further advance the use of molecular techniques in such applications. Digital PCR refines qPCR by partitioning the sample into thousands to millions of miniature reactions that are examined individually for binary endpoint results, with DNA density calculated from the fraction of positives using Poisson statistics. This direct quantification removes the need for standard curves, eliminating the labor and materials associated with creating and running standards with each batch, and removing biases associated with standard variability and mismatching amplification efficiency between standards and samples. Confining reactions and binary endpoint measurements to small partitions also leads to other performance advantages, including reduced susceptibility to inhibition, increased repeatability and reproducibility, and increased capacity to measure multiple targets in one analysis. As such, digital PCR is well suited for ambient water monitoring applications and is particularly advantageous as molecular methods move toward autonomous field application.
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA
| | - John F Griffith
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project Authority, 3535 Harbor Blvd, Costa Mesa, CA, 92626, USA.
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36
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Lin Y, Hamme AT. Gold Nanoparticle Labeling Based ICP-MS Detection/Measurement of Bacteria, and Their Quantitative Photothermal Destruction. J Mater Chem B 2015; 3:3573-3582. [PMID: 26417447 PMCID: PMC4582679 DOI: 10.1039/c5tb00223k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Bacteria such as Salmonella and E. coli present a great challenge in public health care in today's society. Protection of public safety against bacterial contamination and rapid diagnosis of infection require simple and fast assays for the detection and elimination of bacterial pathogens. After utilizing Salmonella DT104 as an example bacterial strain for our investigation, we report a rapid and sensitive assay for the qualitative and quantitative detection of bacteria by using antibody affinity binding, popcorn shaped gold nanoparticle (GNPOPs) labeling, surfance enchanced Raman spectroscopy (SERS), and inductively coupled plasma mass spectrometry (ICP-MS) detection. For qualitative analysis, our assay can detect Salmonella within 10 min by Raman spectroscopy; for quantitative analysis, our assay has the ability to measure as few as 100 Salmonella DT104 in a 1 mL sample (100 CFU/mL) within 40 min. Based on the quantitative detection, we investigated the quantitative destruction of Salmonella DT104, and the assay's photothermal efficiency in order to reduce the amount of GNPOPs in the assay to ultimately to eliminate any potential side effects/toxicity to the surrounding cells in vivo. Results suggest that our assay may serve as a promising candidate for qualitative and quantitative detection and elimination of a variety of bacterial pathogens.
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Affiliation(s)
- Yunfeng Lin
- Department of Chemistry and Biochemistry, Jackson State University, 1400 J R Lynch street, Jackson, MS 39217, USA
| | - Ashton T. Hamme
- Department of Chemistry and Biochemistry, Jackson State University, 1400 J R Lynch street, Jackson, MS 39217, USA
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37
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Cao Y, Raith MR, Griffith JF. Droplet digital PCR for simultaneous quantification of general and human-associated fecal indicators for water quality assessment. WATER RESEARCH 2015; 70:337-49. [PMID: 25543243 DOI: 10.1016/j.watres.2014.12.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/25/2014] [Accepted: 12/07/2014] [Indexed: 05/18/2023]
Abstract
Despite wide application to beach water monitoring and microbial source identification, results produced by quantitative PCR (qPCR) methods are subject to bias introduced by reliance on quantitative standards. Digital PCR technology provides direct, standards-free quantification and may potentially alleviate or greatly reduce other qPCR limitations such as difficulty in multiplexing and susceptibility to PCR inhibition. This study examined the efficacy of employing a duplex droplet digital PCR (ddPCR) assay that simultaneously quantifies Enterococcus spp. and the human fecal-associated HF183 marker for water quality assessment. Duplex ddPCR performance was evaluated side-by-side with qPCR and simplex ddPCR using reference material and 131 fecal and water samples. Results for fecal and water samples were highly correlated between ddPCR and simplex qPCR (coefficients > 0.93, p < 0.001). Duplexing Enterococcus and HF183 in qPCR led to competition and resulted in non-detection or underestimation of the target with low concentration relative to the other, while results produced by simplex and duplex ddPCR were consistent and often indistinguishable from one another. ddPCR showed greater tolerance for inhibition, with no discernable effect on quantification at inhibitor concentrations one to two orders of magnitude higher than that tolerated by qPCR. Overall, ddPCR also exhibited improved precision, higher run-to-run repeatability, similar diagnostic sensitivity and specificity on the HF183 marker, but a lower upper limit of quantification than qPCR. Digital PCR has the potential to become a reliable and economical alternative to qPCR for recreational water monitoring and fecal source identification. Findings from this study may also be of interest to other aspects of water research such as detection of pathogens and antibiotic resistance genes.
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Affiliation(s)
- Yiping Cao
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA.
| | - Meredith R Raith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA
| | - John F Griffith
- Southern California Costal Water Research Project Authority, Costa Mesa, CA, USA.
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Mendes Silva D, Domingues L. On the track for an efficient detection of Escherichia coli in water: A review on PCR-based methods. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 113:400-11. [PMID: 25540852 DOI: 10.1016/j.ecoenv.2014.12.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 05/11/2023]
Abstract
Ensuring water safety is an ongoing challenge to public health providers. Assessing the presence of fecal contamination indicators in water is essential to protect public health from diseases caused by waterborne pathogens. For this purpose, the bacteria Escherichia coli has been used as the most reliable indicator of fecal contamination in water. The methods currently in use for monitoring the microbiological safety of water are based on culturing the microorganisms. However, these methods are not the desirable solution to prevent outbreaks as they provide the results with a considerable delay, lacking on specificity and sensitivity. Moreover, viable but non-culturable microorganisms, which may be present as a result of environmental stress or water treatment processes, are not detected by culture-based methods and, thus, may result in false-negative assessments of E. coli in water samples. These limitations may place public health at significant risk, leading to substantial monetary losses in health care and, additionally, in costs related with a reduced productivity in the area affected by the outbreak, and in costs supported by the water quality control departments involved. Molecular methods, particularly polymerase chain reaction-based methods, have been studied as an alternative technology to overcome the current limitations, as they offer the possibility to reduce the assay time, to improve the detection sensitivity and specificity, and to identify multiple targets and pathogens, including new or emerging strains. The variety of techniques and applications available for PCR-based methods has increased considerably and the costs involved have been substantially reduced, which together have contributed to the potential standardization of these techniques. However, they still require further refinement in order to be standardized and applied to the variety of environmental waters and their specific characteristics. The PCR-based methods under development for monitoring the presence of E. coli in water are here discussed. Special emphasis is given to methodologies that avoid pre-enrichment during the water sample preparation process so that the assay time is reduced and the required legislated sensitivity is achieved. The advantages and limitations of these methods are also reviewed, contributing to a more comprehensive overview toward a more conscious research in identifying E. coli in water.
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Affiliation(s)
- Diana Mendes Silva
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Wan MT, Chou CC. Spreading of β-lactam resistance gene (mecA) and methicillin-resistant Staphylococcus aureus through municipal and swine slaughterhouse wastewaters. WATER RESEARCH 2014; 64:288-295. [PMID: 25086302 DOI: 10.1016/j.watres.2014.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 06/30/2014] [Accepted: 07/09/2014] [Indexed: 05/23/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a potential zoonotic agent. Municipal wastewater treatment plants (WWTPs) can be reservoirs for MRSA dissemination. It is unclear, however, whether MRSA and its β-lactam resistance gene (mecA) can be spread from WWTPs that treat the wastewater of swine auction markets. The aims of the study were to compare (1) the abundance of the mecA gene in one municipal (M-) and one swine (S-) WWTP and (2) the genotypic and phenotypic characteristics of MRSA isolates from these two types of WWTPs. The concentrations of mecA gene from 96 wastewater samples were quantified using real-time quantitative polymerase chain reaction (real-time qPCR). One hundred and thirteen MRSA isolates were recovered and were characterized by antimicrobial susceptibility testing, minimum inhibitory concentrations (MICs), and staphylococcal cassette chromosome mec (SCCmec) typing. The mecA gene could be detected in all the wastewater samples. A high abundance of recovered mecA gene (2.6 × 10(1) to 1.9 × 10(4) gene copies μg(-1) of total DNA) in swine slaughterhouse wastewater implied a correspondingly high transferring/receiving potential. All MRSA isolates were multidrug resistant (MDR) and showed high MICs to different antimicrobials. The M-WWTP MRSA isolates harbored SCCmec II-IV and VII, whereas those from the S-WWTP harbored SCCmec V and IX. In conclusion, wastewater from swine slaughterhouses can make these slaughterhouses potential hotspots for the dissemination of mecA gene and MRSA, and the high MICs of MRSA from both WWTP origins may pose a health risk not only to workers but also to the general public.
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Affiliation(s)
- Min Tao Wan
- School of Veterinary Medicine, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Chin Cheng Chou
- School of Veterinary Medicine, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
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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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Zimmerman BD, Ashbolt NJ, Garland JL, Keely S, Wendell D. Human mitochondrial DNA and endogenous bacterial surrogates for risk assessment of graywater reuse. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:7993-8002. [PMID: 24932937 DOI: 10.1021/es501659r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Previous graywater risk assessment studies have focused on fecal contamination, yet the low density of fecal indicators may not provide the most useful approach to assess pathogen removal during graywater treatment. In this study, we employed high throughput bacterial sequencing and qPCR to elucidate potential microbial surrogates in wastewater sourced from an industrial laundry. In addition, we explored human mitochondrial DNA (HmtDNA) as a new, potentially more reliable molecular marker, because it can be unambiguously sourced, has a high copy number per cell, and is persistent when released from cells with no self-replication in graywater. Pyrosequencing and qPCR revealed that laundry water microbiota was dominated by the skin-associated bacteria Staphylococcus, Corynebacterium, and Propionibacterium (6.5, 5.7, 5.4 log10 copies/100 mL, respectively). While HmtDNA was less abundant (2.8 log10 copies/100 mL), it showed a strong positive correlation with the opportunistic pathogen Staphylococcus aureus (r=0.54, P=3.2×10(-4)) and closely followed a first-order exponential decay model (R2=0.98), remaining detectable in stored laundry graywater for up to 6 days at 20 °C. Based on abundance and persistence, we propose HmtDNA and total Staphylococcus as future laundry graywater treatment surrogates to potentially assess a wide dynamic range of pathogen removal.
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Affiliation(s)
- Brian D Zimmerman
- Department of Biomedical, Chemical and Environmental Engineering, University of Cincinnati , Cincinnati, Ohio 45221, United States
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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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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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Riedel TE, Zimmer-Faust AG, Thulsiraj V, Madi T, Hanley KT, Ebentier DL, Byappanahalli M, Layton B, Raith M, Boehm AB, Griffith JF, Holden PA, Shanks OC, Weisberg SB, Jay JA. Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2014; 136:112-20. [PMID: 24583609 DOI: 10.1016/j.jenvman.2014.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 05/04/2023]
Abstract
Some molecular methods for tracking fecal pollution in environmental waters have both PCR and quantitative PCR (qPCR) assays available for use. To assist managers in deciding whether to implement newer qPCR techniques in routine monitoring programs, we compared detection limits (LODs) and costs of PCR and qPCR assays with identical targets that are relevant to beach water quality assessment. For human-associated assays targeting Bacteroidales HF183 genetic marker, qPCR LODs were 70 times lower and there was no effect of target matrix (artificial freshwater, environmental creek water, and environmental marine water) on PCR or qPCR LODs. The PCR startup and annual costs were the lowest, while the per reaction cost was 62% lower than the Taqman based qPCR and 180% higher than the SYBR based qPCR. For gull-associated assays, there was no significant difference between PCR and qPCR LODs, target matrix did not effect PCR or qPCR LODs, and PCR startup, annual, and per reaction costs were lower. Upgrading to qPCR involves greater startup and annual costs, but this increase may be justified in the case of the human-associated assays with lower detection limits and reduced cost per sample.
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Affiliation(s)
- Timothy E Riedel
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
| | - Amity G Zimmer-Faust
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA; Institute of the Environment and Sustainability, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Vanessa Thulsiraj
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Tania Madi
- Source Molecular Corporation, Miami, FL 33155, USA
| | - Kaitlyn T Hanley
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Darcy L Ebentier
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Muruleedhara Byappanahalli
- U.S. Geological Survey, Great Lakes Science Center, Lake Michigan Ecological Research Station, Porter, IN 46304, USA
| | - Blythe Layton
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Meredith Raith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Alexandria B Boehm
- Environmental and Water Studies, Department of Civil and Environmental, Engineering, Stanford University, Stanford, CA 94305, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Patricia A Holden
- Bren School of Environmental Science & Management, and Earth Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, OH 45268, USA
| | - Stephen B Weisberg
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
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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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Oliver DM, van Niekerk M, Kay D, Heathwaite AL, Porter J, Fleming LE, Kinzelman JL, Connolly E, Cummins A, McPhail C, Rahman A, Thairs T, de Roda Husman AM, Hanley ND, Dunhill I, Globevnik L, Harwood VJ, Hodgson CJ, Lees DN, Nichols GL, Nocker A, Schets C, Quilliam RS. Opportunities and limitations of molecular methods for quantifying microbial compliance parameters in EU bathing waters. ENVIRONMENT INTERNATIONAL 2014; 64:124-8. [PMID: 24394589 DOI: 10.1016/j.envint.2013.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 12/17/2013] [Accepted: 12/18/2013] [Indexed: 05/11/2023]
Abstract
The debate over the suitability of molecular biological methods for the enumeration of regulatory microbial parameters (e.g. Faecal Indicator Organisms [FIOs]) in bathing waters versus the use of traditional culture-based methods is of current interest to regulators and the science community. Culture-based methods require a 24-48hour turn-around time from receipt at the laboratory to reporting, whilst quantitative molecular tools provide a more rapid assay (approximately 2-3h). Traditional culturing methods are therefore often viewed as slow and 'out-dated', although they still deliver an internationally 'accepted' evidence-base. In contrast, molecular tools have the potential for rapid analysis and their operational utility and associated limitations and uncertainties should be assessed in light of their use for regulatory monitoring. Here we report on the recommendations from a series of international workshops, chaired by a UK Working Group (WG) comprised of scientists, regulators, policy makers and other stakeholders, which explored and interrogated both molecular (principally quantitative polymerase chain reaction [qPCR]) and culture-based tools for FIO monitoring under the European Bathing Water Directive. Through detailed analysis of policy implications, regulatory barriers, stakeholder engagement, and the needs of the end-user, the WG identified a series of key concerns that require critical appraisal before a potential shift from culture-based approaches to the employment of molecular biological methods for bathing water regulation could be justified.
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Affiliation(s)
- David M Oliver
- Biological & Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK.
| | - Melanie van Niekerk
- Biological & Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - David Kay
- Centre for Research into Environment & Health, Aberystwyth University, Wales SA48 8HU, UK
| | | | - Jonathan Porter
- National Laboratory Service, Environment Agency, Starcross, Devon EX6 8FD, UK
| | - Lora E Fleming
- European Centre for Environment & Human Health, University of Exeter Medical School, Truro, Cornwall TR1 3HD, UK
| | - Julie L Kinzelman
- City of Racine Health Department Laboratory, 730 Washington Avenue, Racine, WI 53403, USA
| | - Elaine Connolly
- Department for Environment Food and Rural Affairs, Nobel House, London SW1P 3JR, UK
| | - Andy Cummins
- Surfers Against Sewage, Wheal Kitty Workshops, St Agnes, Cornwall TR5 0RD, UK
| | - Calum McPhail
- Scottish Environment Protection Agency, Eurocentral, North Lanarkshire ML1 4WQ, UK
| | - Amanna Rahman
- Environment Agency, Horizon House, Bristol BS1 5AH, UK
| | - Ted Thairs
- UK Water Industry Research Ltd, 1 Queen Anne's Gate, London SW1H 9BT, UK
| | - Ana Maria de Roda Husman
- Laboratory for Zoonoses & Environmental Microbiology, National Institute for Public Health (RIVM), Centre for Infectious Disease Control, 3720 BA Bilthoven, The Netherlands
| | - Nick D Hanley
- Department of Economics, University of Stirling, Stirling FK9 4LA, UK
| | - Ian Dunhill
- Environment Agency, Oving Road, Chichester, West Sussex PO20 2AG, UK
| | - Lidija Globevnik
- European Environment Agency, European Topic Center for Inland, Coastal and Marine Water, Institute for Water of Republic of Slovenia, Slovenia
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
| | - Chris J Hodgson
- Rothamsted Research, North Wyke, Okehampton, Devon EX20 2SB, UK
| | - David N Lees
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK
| | | | - Andreas Nocker
- Cranfield Water Science Institute, School of Applied Sciences, Cranfield University, MK43 0AL, UK
| | - Ciska Schets
- Laboratory for Zoonoses & Environmental Microbiology, National Institute for Public Health (RIVM), Centre for Infectious Disease Control, 3720 BA Bilthoven, The Netherlands
| | - Richard S Quilliam
- Biological & Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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Performance and specificity of the covalently linked immunomagnetic separation-ATP method for rapid detection and enumeration of enterococci in coastal environments. Appl Environ Microbiol 2014; 80:2705-14. [PMID: 24561583 DOI: 10.1128/aem.04096-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance and specificity of the covalently linked immunomagnetic separation-ATP (Cov-IMS/ATP) method for the detection and enumeration of enterococci was evaluated in recreational waters. Cov-IMS/ATP performance was compared with standard methods: defined substrate technology (Enterolert; IDEXX Laboratories), membrane filtration (EPA Method 1600), and an Enterococcus-specific quantitative PCR (qPCR) assay (EPA Method A). We extend previous studies by (i) analyzing the stability of the relationship between the Cov-IMS/ATP method and culture-based methods at different field sites, (ii) evaluating specificity of the assay for seven ATCC Enterococcus species, (iii) identifying cross-reacting organisms binding the antibody-bead complexes with 16S rRNA gene sequencing and evaluating specificity of the assay to five nonenterococcus species, and (iv) conducting preliminary tests of preabsorption as a means of improving the assay. Cov-IMS/ATP was found to perform consistently and with strong agreement rates (based on exceedance/compliance with regulatory limits) of between 83% and 100% compared to the culture-based Enterolert method at a variety of sites with complex inputs. The Cov-IMS/ATP method is specific to five of seven different Enterococcus spp. tested. However, there is potential for nontarget bacteria to bind the antibody, which may be reduced by purification of the IgG serum with preabsorption at problematic sites. The findings of this study help to validate the Cov-IMS/ATP method, suggesting a predictable relationship between the Cov-IMS/ATP method and traditional culture-based methods, which will allow for more widespread application of this rapid and field-portable method for coastal water quality assessment.
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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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49
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Tracking human sewage microbiome in a municipal wastewater treatment plant. Appl Microbiol Biotechnol 2013; 98:3317-26. [DOI: 10.1007/s00253-013-5402-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 10/25/2022]
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50
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Kim J, Lim J, Lee C. Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: Applications and considerations. Biotechnol Adv 2013; 31:1358-73. [DOI: 10.1016/j.biotechadv.2013.05.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/02/2013] [Accepted: 05/28/2013] [Indexed: 02/08/2023]
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