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Nappier SP, Ichida A, Jaglo K, Haugland R, Jones KR. Advancements in mitigating interference in quantitative polymerase chain reaction (qPCR) for microbial water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:732-740. [PMID: 30939326 PMCID: PMC6555561 DOI: 10.1016/j.scitotenv.2019.03.242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/13/2019] [Accepted: 03/15/2019] [Indexed: 05/31/2023]
Abstract
The United States Environmental Protection Agency's (EPA)1 2012 Recreational Water Quality Criteria included an Enterococcus spp. quantitative polymerase chain reaction (qPCR) method as a supplemental indicator-method. In 2012, performance of qPCR for beach monitoring remained limited, specifically with addressing interference. A systematic literature search of peer-reviewed publications was conducted to identify where Enterococcus spp. and E. coli qPCR methods have been applied in ambient waters. In the present study, we evaluated interference rates, contributing factors resulting in increased interference in these methods, and method improvements that reduced interference. Information on qPCR methods of interest and interference controls were reported in 16 papers for Enterococcus spp. and 13 papers for E. coli. Of the Enterococcus spp. qPCR methods assessed in this effort, the lowest frequencies of interference were reported in samples using Method 1609. Low frequencies of sample interference were also reported EPA's modified E. coli qPCR method, which incorporates the same reagents and interference controls as Method 1609. The literature indicates that more work is needed to demonstrate the utility of E. coli qPCR for widespread beach monitoring purposes, whereas more broad use of Method 1609 for Enterococcus spp. is appropriate when the required and suggested controls are employed.
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Affiliation(s)
- Sharon P Nappier
- U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, 1200 Pennsylvania Avenue, NW, Washington, DC 20460, USA.
| | | | | | - Rich Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, USA
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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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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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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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Paar J, Doolittle MM, Varma M, Siefring S, Oshima K, Haugland RA. Development and evaluation of a culture-independent method for source determination of fecal wastes in surface and storm waters using reverse transcriptase-PCR detection of FRNA coliphage genogroup gene sequences. J Microbiol Methods 2015; 112:28-35. [PMID: 25744574 DOI: 10.1016/j.mimet.2015.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/28/2015] [Accepted: 02/28/2015] [Indexed: 10/23/2022]
Abstract
A method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for detecting interferences in RNA recovery and analysis, was developed for the direct, culture-independent detection of genetic markers from FRNA coliphage genogroups I, II & IV in water samples. Results were obtained from an initial evaluation of the performance of this method in analyses of waste water, ambient surface water and stormwater drain and outfall samples from predominantly urban locations. The evaluation also included a comparison of the occurrence of the FRNA genetic markers with genetic markers from general and human-related bacterial fecal indicators determined by current or pending EPA-validated qPCR methods. Strong associations were observed between the occurrence of the putatively human related FRNA genogroup II marker and the densities of the bacterial markers in the stormwater drain and outfall samples. However fewer samples were positive for FRNA coliphage compared to either the general bacterial fecal indicator or the human-related bacterial fecal indicator markers particularly for ambient water samples. Together, these methods show promise as complementary tools for the identification of contaminated storm water drainage systems as well as the determination of human and non-human sources of contamination.
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Affiliation(s)
- Jack Paar
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA, USA
| | - Mark M Doolittle
- ESAT Contractor-TechLaw, Inc., EPA New England Regional Laboratory, North Chelmsford, MA, USA
| | - Manju Varma
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH, USA
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH, 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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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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