1
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Keely SP, Brinkman NE, Wheaton EA, Jahne MA, Siefring SD, Varma M, Hill RA, Leibowitz SG, Martin RW, Garland JL, Haugland RA. Geospatial Patterns of Antimicrobial Resistance Genes in the US EPA National Rivers and Streams Assessment Survey. Environ Sci Technol 2022; 56:14960-14971. [PMID: 35737903 PMCID: PMC9632466 DOI: 10.1021/acs.est.2c00813] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antimicrobial resistance (AR) is a serious global problem due to the overuse of antimicrobials in human, animal, and agriculture sectors. There is intense research to control the dissemination of AR, but little is known regarding the environmental drivers influencing its spread. Although AR genes (ARGs) are detected in many different environments, the risk associated with the spread of these genes to microbial pathogens is unknown. Recreational microbial exposure risks are likely to be greater in water bodies receiving discharge from human and animal waste in comparison to less disturbed aquatic environments. Given this scenario, research practitioners are encouraged to consider an ecological context to assess the effect of environmental ARGs on public health. Here, we use a stratified, probabilistic survey of nearly 2000 sites to determine national patterns of the anthropogenic indicator class I integron Integrase gene (intI1) and several ARGs in 1.2 million kilometers of United States (US) rivers and streams. Gene concentrations were greater in eastern than in western regions and in rivers and streams in poor condition. These first of their kind findings on the national distribution of intI1 and ARGs provide new information to aid risk assessment and implement mitigation strategies to protect public health.
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Affiliation(s)
- Scott P. Keely
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Nichole E. Brinkman
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Emily A. Wheaton
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Michael A. Jahne
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Shawn D. Siefring
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Manju Varma
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Ryan A. Hill
- Center
for Public Health and Environmental Assessment, US Environmental Protection Agency, Corvallis, Oregon 97333, United States
| | - Scott G. Leibowitz
- Center
for Public Health and Environmental Assessment, US Environmental Protection Agency, Corvallis, Oregon 97333, United States
| | - Roy W. Martin
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Jay L. Garland
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
| | - Richard A. Haugland
- Center
for Environmental Measurement and Modeling and Center for Environmental Solutions
and Emergency Response, US Environmental
Protection Agency, Cincinnati, Ohio 45268, United States
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2
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Willis JR, Sivaganesan M, Haugland RA, Kralj J, Servetas S, Hunter ME, Jackson SA, Shanks OC. Corrigendum to Performance of NIST SRM® 2917 with 13 recreational water quality monitoring qPCR assays [Water Research 212 (2022) 118114/WR66550R1]. Water Res 2022; 223:119031. [PMID: 36067601 DOI: 10.1016/j.watres.2022.119031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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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3
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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 Res 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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Chern EC, Wymer L, Brenner K, Oshima K, Haugland RA. Persistence of fecal indicator bacteria and associated genetic markers from wastewater treatment plant effluents in freshwater microcosms. J Water Health 2022; 20:205-215. [PMID: 35100168 PMCID: PMC9000909 DOI: 10.2166/wh.2021.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Limited information exists on the environmental persistence of genetic markers for fecal indicator bacteria (FIB) in treated wastewaters. Here, the decay rate constants of culturable cells and genetic markers for four diverse groups of FIBs, such as enterococci, Clostridium, Escherichia coli, and Bacteroides, were investigated in freshwater microcosms seeded with disinfected and non-disinfected secondary-treated wastewaters. Decay rate constants of genetic markers and culturable cells varied significantly among the different FIB groups. Water temperatures (winter vs. fall/spring/summer) significantly affected the decay of all genetic marker and cell types; however, genetic marker decay were not found to be significantly different in disinfected (chlorination/ultraviolet) and non-disinfected wastewater-seeded microcosms or, for example, lake- and river-receiving waters. No evidence was seen that decay rate constants of FIB genetic markers from treated wastewater were substantially different from those observed in similar, previously reported microcosm studies using raw sewage. Unexpected relationships between decay rate constants of genetic markers and culturable cells of Bacteroides were observed. Results suggest that decay rate constants of FIB genetic markers determined from other studies may be applicable to treated wastewaters. Results of this study should be informative for ongoing efforts to determine the persistence of FIB genetic markers relative to surviving pathogens after wastewater treatment.
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Affiliation(s)
- Eunice C Chern
- U.S. Environmental Protection Agency, Region 10 Laboratory, 7411 Beach Dr. E., Port Orchard, WA 98366, USA E-mail:
| | - Larry Wymer
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Kristen Brenner
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
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Haugland RA, Vesper SJ, Harmon SM. Phylogenetic relationships ofMemnoniellaandStachybotrysspecies and evaluation of morphological features forMemnoniellaspecies identification. Mycologia 2019. [DOI: 10.1080/00275514.2001.12061279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Richard A. Haugland
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268
| | - Stephen J. Vesper
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268
| | - Stephen M. Harmon
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268
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6
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McMinn BR, Klemm S, Korajkic A, Wyatt KM, Herrmann MP, Haugland RA, Lu J, Villegas EN, Frye C. A Constructed Wetland for Treatment of an Impacted Waterway and the Influence of Native Waterfowl on its Perceived Effectiveness. Ecol Eng 2019; 128:48-56. [PMID: 31631948 PMCID: PMC6800712 DOI: 10.1016/j.ecoleng.2018.11.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A constructed, variable-flow treatment wetland was evaluated for its ability to reduce microbial loads from the Banklick Creek, an impacted recreational waterway in Northern Kentucky. For this study, levels of traditional (Escherichia coli and enterococci measured by culture and molecular techniques) and alternative fecal indicators (infectious somatic and F+ coliphage, Clostridium spp. and Clostridium perfringens by culture), potential pathogens (molecular signal of Campylobacter spp.) as well as various microbial source tracking (MST) markers (human fecal marker HF183 and avian fecal marker GFD) were monitored during the summer and early fall through five treatment stages within the Banklick Creek Wetland. No difference in concentrations of traditional or alternative fecal indicators were observed in any of the sites monitored. Microbial source tracking markers were employed to identify sources of fecal contamination within the wetland. Human marker HF183 concentrations at beginning stages of treatment were found to be significantly higher (P value range: 0.0016-0.0003) than levels at later stages. Conversely, at later stages of treatment where frequent bird activity was observed, Campylobacter and avian marker (GFD) signals were detected at significantly higher frequencies (P value range: 0.024 to <0.0001), and both signals were strongly correlated (P = 0.0001). Our study suggests constructed wetlands are an effective means for removal of microbial contamination in ambient waters, but reliance on general fecal indicators is not ideal for determining system efficacy or assessing appropriate remediation efforts.
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Affiliation(s)
- Brian R. McMinn
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Sara Klemm
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Asja Korajkic
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Kimberly M. Wyatt
- Thomas More College 33 Thomas More Parkway Crestview Hills, Kentucky 41017
| | - Michael P. Herrmann
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Richard A. Haugland
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Jingrang Lu
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Eric N. Villegas
- National Exposure Research Laboratory Office of Research and Development United States Environmental Protection Laboratory 26 West Martin Luther King Drive Cincinnati, OH 45268 United States
| | - Craig Frye
- Sanitation District No.1 1045 Eaton Drive Fort Wright, Kentucky 41017
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7
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Shanks OC, Kelty CA, Oshiro R, Haugland RA, Madi T, Brooks L, Field KG, Sivaganesan M. Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods. Appl Environ Microbiol 2016; 82:2773-2782. [PMID: 26921430 PMCID: PMC4836407 DOI: 10.1128/aem.03661-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (no-template and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria proposed in this study should help scientists, managers, reviewers, and the public evaluate the technical quality of future findings against an established benchmark.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
| | - Catherine A Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
| | - Robin Oshiro
- U.S. Environmental Protection Agency, Office of Water, Washington DC, USA
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
| | - Tania Madi
- Source Molecular Corporation, Miami, Florida, USA
| | - Lauren Brooks
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Katharine G Field
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, Ohio, USA
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Sivaganesan M, Siefring S, Varma M, Haugland RA. Corrigendum to “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 101 (2014) 9–17]. J Microbiol Methods 2015. [DOI: 10.1016/j.mimet.2015.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Neely AN, Gallardo V, Barth E, Haugland RA, Warden GD, Vesper SJ. Rapid Monitoring by Quantitative Polymerase Chain Reaction for Pathogenic Aspergillus During Carpet Removal From a Hospital. Infect Control Hosp Epidemiol 2015; 25:350-2. [PMID: 15108736 DOI: 10.1086/502405] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractMonitoring for pathogenic Aspergillus species using a rapid, highly sensitive, quantitative polymerase chain reaction technique during carpet removal in a burn unit provided data that allowed patients to be safely returned to the refloored area sooner than if only conventional culture monitoring had been used.
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Affiliation(s)
- Alice N Neely
- Shriners Burns Hospital, Cincinnati, OH 45229-3095, USA
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Heaney CD, Exum NG, Dufour AP, Brenner KP, Haugland RA, Chern E, Schwab KJ, Love DC, Serre ML, Noble R, Wade TJ. Water quality, weather and environmental factors associated with fecal indicator organism density in beach sand at two recreational marine beaches. Sci Total Environ 2014; 497-498:440-447. [PMID: 25150738 PMCID: PMC4523396 DOI: 10.1016/j.scitotenv.2014.07.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/23/2014] [Accepted: 07/29/2014] [Indexed: 05/25/2023]
Abstract
Recent studies showing an association between fecal indicator organisms (FIOs) in sand and gastrointestinal (GI) illness among beachgoers with sand contact have important public health implications because of the large numbers of people who recreate at beaches and engage in sand contact activities. Yet, factors that influence fecal pollution in beach sand remain unclear. During the 2007 National Epidemiological and Environmental Assessment of Recreational (NEEAR) Water Study, sand samples were collected at three locations (60 m apart) on weekend days (Sat, Sun) and holidays between June and September at two marine beaches - Fairhope Beach, AL and Goddard Beach, RI - with nearby publicly-owned treatment works (POTWs) outfalls. F(+) coliphage, enterococci, Bacteroidales, fecal Bacteroides spp., and Clostridium spp. were measured in sand using culture and qPCR-based calibrator-cell equivalent methods. Water samples were also collected on the same days, times and transects as the 144 sand samples and were assayed using the same FIO measurements. Weather and environmental data were collected at the time of sample collection. Mean FIO concentrations in sand varied over time, but not space. Enterococci CFU and CCE densities in sand were not correlated, although other FIOs in sand were. The strongest correlation between FIO density in sand and water was fecal Bacteroides CCE, followed by enterococci CFU, Clostridium spp. CCE, and Bacteroidales CCE. Overall, the factors associated with FIO concentrations in sand were related to the sand-water interface (i.e., sand-wetting) and included daily average densities of FIOs in water, rainfall, and wave height. Targeted monitoring that focuses on daily trends of sand FIO variability, combined with information about specific water quality, weather, and environmental factors may inform beach monitoring and management decisions to reduce microbial burdens in beach sand. The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency.
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Affiliation(s)
- Christopher D Heaney
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA.
| | - Natalie G Exum
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA
| | - Alfred P Dufour
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Kristen P Brenner
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Richard A Haugland
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Eunice Chern
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, OH 45268-1593, USA
| | - Kellogg J Schwab
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA
| | - David C Love
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA
| | - Marc L Serre
- Department of Environmental Sciences and Engineering, CB# 7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431, USA
| | - Rachel Noble
- Institute of Marine Sciences, CB# 3301, University of North Carolina at Chapel Hill, Morehead City, NC 28557-3301, USA
| | - Timothy J Wade
- Epidemiology Branch, Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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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] [What about the content of this article? (0)] [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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13
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Chern EC, Brenner K, Wymer L, Haugland RA. Influence of wastewater disinfection on densities of culturable fecal indicator bacteria and genetic markers. J Water Health 2014; 12:410-417. [PMID: 25252344 DOI: 10.2166/wh.2013.179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The US Environmental Protection Agency has proposed the use of quantitative polymerase chain reaction (qPCR) as a rapid alternative analytical method for monitoring recreational water quality at beaches. For qPCR to be considered for other Clean Water Act purposes, such as inclusion in discharge permits and use in Total Maximum Daily Load calculations, it is necessary to understand how qPCR detectable genetic markers are influenced by wastewater disinfection. This study investigated genetic markers for Escherichia coli, Enterococcus, Clostridium spp., Bacteroides, total Bacteroidales, as well as the human-associated Bacteroides markers, HF183 and HumM2, to determine which, if any, were influenced by disinfection (chlorination or ultraviolet light) of effluents from secondary wastewater treatment in different seasons. The effects of disinfection on culturable enterococci, E. coli, Bacteroides, and C. perfringens were also compared to their associated genetic markers. Disinfection of secondary treatment effluents significantly reduced culturable fecal indicator bacteria (FIB) but not genetic marker densities. No significant differences were observed in the responses of FIB culture and genetic marker densities to type of disinfection (chlorination vs UV) or season. Results of this study provide evidence that qPCR may not be suitable for monitoring efficacy of wastewater disinfection on the inactivation of bacterial pathogens.
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Affiliation(s)
- Eunice C Chern
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Kristen Brenner
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Larry Wymer
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
| | - Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA E-mail:
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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] [What about the content of this article? (0)] [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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15
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Cao Y, Sivaganesan M, Kinzelman J, Blackwood AD, Noble RT, Haugland RA, Griffith JF, Weisberg SB. Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods. Water Res 2013; 47:233-241. [PMID: 23123048 DOI: 10.1016/j.watres.2012.09.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 08/28/2012] [Accepted: 09/28/2012] [Indexed: 06/01/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is increasingly being used for the quantitative detection of fecal indicator bacteria in beach water. QPCR allows for same-day health warnings, and its application is being considered as an option for recreational water quality testing in the United States (USEPA, 2011. EPA-OW-2011-0466, FRL-9609-3, Notice of Availability of Draft Recreational Water Quality Criteria and Request for Scientific Views). However, transition of qPCR from a research tool to routine water quality testing requires information on how various method variations affect target enumeration. Here we compared qPCR performance and enumeration of enterococci in spiked and environmental water samples using three qPCR platforms (Applied Biosystem StepOnePlus™, the BioRad iQ™5 and the Cepheid SmartCycler(®) II), two reference materials (lyophilized cells and frozen cells on filters) and two comparative CT quantification models (ΔCT and ΔΔCT). Reference materials exerted the biggest influence, consistently affecting results by approximately 0.5 log(10) unit. Platform had the smallest effect, generally exerting <0.1 log(10) unit difference in final results. Quantification model led to small differences (0.04-0.2 log(10) unit) in this study with relatively uninhibited samples, but has the potential to cause as much as 8-fold (0.9 log(10) unit) difference in potentially inhibitory samples. Our findings indicate the need for a certified and centralized source of reference materials and additional studies to assess applicability of the quantification models in analyses of PCR inhibitory samples.
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA.
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16
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Haugland RA, Siefring S, Lavender J, Varma M. Influences of sample interference and interference controls on quantification of enterococci fecal indicator bacteria in surface water samples by the qPCR method. Water Res 2012; 46:5989-6001. [PMID: 22981586 DOI: 10.1016/j.watres.2012.08.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 08/03/2012] [Accepted: 08/14/2012] [Indexed: 05/18/2023]
Abstract
A quantitative polymerase chain reaction (qPCR) method for the detection of enterococci fecal indicator bacteria has been shown to be generally applicable for the analysis of temperate fresh (Great Lakes) and marine coastal waters and for providing risk-based determinations of water quality at recreational beaches. In this study we further examined the applicability of the method for analyses of diverse inland waters as well as tropical marine waters from Puerto Rico based on the frequencies of samples showing presumptive PCR interference. Interference was assessed by salmon DNA sample processing control (SPC) and internal amplification control (IAC) assay analysis results and pre-established acceptance criteria of <3.0 and <1.5 cycle threshold (Ct) offsets from control samples, respectively. SPC assay results were accepted in analyses of 93% of the inland water samples whereas the criterion was met at frequencies of 60% and 97% in analyses of samples from Puerto Rico in two different years of sampling. The functionality of the control assays and their acceptance criteria was assessed on the basis of relative recovery estimates of spiked enterococci target organisms extracted in the presence of water sample filters and sample-free control filters and was supported by observations that recovery estimates from the water sample and control filters were substantially different for samples that failed these criteria. Through the combined use of the SPC and IAC assays, two presumptive types of interference were identified. One type, observed in the tropical marine water samples, appeared to primarily affect the availability of the DNA templates for detection. The second type, observed in river water samples, appeared to primarily affect PCR amplification efficiency. In the presence of DNA template interference, adjustments from SPC assay results by the ΔΔCt comparative Ct calculation method decreased the variability of spiked enterococci recovery estimates and increased the similarity with control filters as compared to unadjusted recovery estimates obtained by the ΔCt calculation method. Use of a higher salmon DNA concentration in the extraction buffer also reduced this type of interference. The effects of amplification interference were largely reversed by dilution of the DNA extracts and even more effectively by the use of an alternative, commercial PCR reagent, designed for the analysis of environmental samples.
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Affiliation(s)
- Richard A Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA.
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17
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Sivaganensan M, Varma M, Haugland RA. Comparison of Enterococcus quantitative polymerase chain reaction analysis results from fresh and marine waters on two real-time instruments. Anal Biochem 2012; 430:68-74. [DOI: 10.1016/j.ab.2012.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 07/18/2012] [Accepted: 07/19/2012] [Indexed: 10/28/2022]
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18
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Converse RR, Kinzelman JL, Sams EA, Hudgens E, Dufour AP, Ryu H, Santo-Domingo JW, Kelty CA, Shanks OC, Siefring SD, Haugland RA, Wade TJ. Dramatic improvements in beach water quality following gull removal. Environ Sci Technol 2012; 46:10206-13. [PMID: 22913457 DOI: 10.1021/es302306b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Gulls are often cited as important contributors of fecal contamination to surface waters, and some recreational beaches have used gull control measures to improve microbial water quality. In this study, gulls were chased from a Lake Michigan beach using specially trained dogs, and water quality improvements were quantified. Fecal indicator bacteria and potentially pathogenic bacteria were measured before and during gull control using culture methods and quantitative polymerase chain reaction (qPCR). Harassment by dogs was an effective method of gull control: average daily gull populations fell from 665 before to 17 during intervention; and a significant reduction in the density of a gull-associated marker was observed (p < 0.001). Enterococcus spp. and Escherichia coli densities were also significantly reduced during gull control (p < 0.001 and p = 0.012, respectively for culture methods; p = 0.012 and p = 0.034, respectively for qPCR). Linear regression results indicate that a 50% reduction in gulls was associated with a 38% and 29% decrease in Enterococcus spp. and E. coli densities, respectively. Potentially human pathogenic bacteria were detected on 64% of days prior to gull control and absent during gull intervention, a significant reduction (p = 0.005). This study demonstrates that gull removal can be a highly successful beach remedial action to improve microbial water quality.
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Affiliation(s)
- Reagan R Converse
- US Environmental Protection Agency, Chapel Hill, North Carolina 27514, United States.
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19
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Shanks OC, Sivaganesan M, Peed L, Kelty CA, Blackwood AD, Greene MR, Noble RT, Bushon RN, Stelzer EA, Kinzelman J, Anan'eva T, Sinigalliano C, Wanless D, Griffith J, Cao Y, Weisberg S, Harwood VJ, Staley C, Oshima KH, Varma M, Haugland RA. Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria. Environ Sci Technol 2012; 46:945-53. [PMID: 22133009 DOI: 10.1021/es2031455] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized protocol requires information on the reproducibility and sources of variation associated with qPCR methodology across laboratories. This study examines interlaboratory variability in the measurement of enterococci and Bacteroidales concentrations from standardized, spiked, and environmental sources of DNA using the Entero1a and GenBac3 qPCR methods, respectively. Comparisons are based on data generated from eight different research facilities. Special attention was placed on the influence of the DNA isolation step and effect of simplex and multiplex amplification approaches on interlaboratory variability. Results suggest that a crude lysate is sufficient for DNA isolation unless environmental samples contain substances that can inhibit qPCR amplification. No appreciable difference was observed between simplex and multiplex amplification approaches. Overall, interlaboratory variability levels remained low (<10% coefficient of variation) regardless of qPCR protocol.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio, United States.
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20
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Heaney CD, Sams E, Dufour AP, Brenner KP, Haugland RA, Chern E, Wing S, Marshall S, Love DC, Serre M, Noble R, Wade TJ. Fecal indicators in sand, sand contact, and risk of enteric illness among beachgoers. Epidemiology 2012; 23:95-106. [PMID: 22157306 PMCID: PMC3240855 DOI: 10.1097/ede.0b013e31823b504c] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Beach sand can harbor fecal indicator organisms and pathogens, but enteric illness risk associated with sand contact remains unclear. METHODS In 2007, visitors at 2 recreational marine beaches were asked on the day of their visit about sand contact. Ten to 12 days later, participants answered questions about health symptoms since the visit. F+ coliphage, Enterococcus, Bacteroidales, fecal Bacteroides, and Clostridium spp. in wet sand were measured using culture and molecular methods. RESULTS We analyzed 144 wet sand samples and completed 4999 interviews. Adjusted odds ratios (aORs) were computed, comparing those in the highest tertile of fecal indicator exposure with those who reported no sand contact. Among those digging in sand compared with those not digging in sand, a molecular measure of Enterococcus spp. (calibrator cell equivalents/g) in sand was positively associated with gastrointestinal (GI) illness (aOR = 2.0 [95% confidence interval (CI) = 1.2-3.2]) and diarrhea (2.4 [1.4-4.2]). Among those buried in sand, point estimates were greater for GI illness (3.3 [1.3-7.9]) and diarrhea (4.9 [1.8-13]). Positive associations were also observed for culture-based Enterococcus (colony-forming units/g) with GI illness (aOR digging = 1.7 [1.1-2.7]) and diarrhea (2.1 [1.3-3.4]). Associations were not found among nonswimmers with sand exposure. CONCLUSIONS We observed a positive relationship between sand-contact activities and enteric illness as a function of concentrations of fecal microbial pollution in beach sand.
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Affiliation(s)
- Christopher D Heaney
- Department of Epidemiology, University of North Carolina at Chapel Hill, NC, USA.
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21
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Abstract
Genetic markers from Bacteroides and other faecal bacteria are being tested for inclusion in regulations to quantify aquatic faecal contamination and estimate public health risk. For the method to be used quantitatively across environments, persistence and decay of markers must be understood. We measured concentrations of contaminant molecular markers targeting Enterococcus and Bacteroides spp. in marine and freshwater microcosms spiked with human sewage and exposed to either sunlight or dark treatments. We used Bayesian statistics with a delayed Chick-Watson model to estimate kinetic parameters for target decay. DNA- and RNA-based targets decayed at approximately the same rate. Molecular markers persisted (could be detected) longer in marine water. Sunlight increased the decay rates of cultured indicators more than those of molecular markers; sunlight also limited persistence of molecular markers. Within each treatment, Bacteroides markers had similar decay profiles, but some Bacteroides markers significantly differed in decay rates. The role of extracellular DNA in persistence appeared unimportant in the microcosms. Because conditions were controlled, microcosms allowed the effects of specific environmental variables on marker persistence and decay to be measured. While marker decay profiles in more complex environments would be expected to vary from those observed here, the differences we measured suggest that water matrix is an important factor affecting quantitative source tracking and microbial risk assessment applications.
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Affiliation(s)
- Hyatt C Green
- Dept. of Microbiology, Oregon State University, Corvallis, OR 97331, USA
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22
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Chern EC, Siefring S, Paar J, Doolittle M, Haugland RA. Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes. Lett Appl Microbiol 2011; 52:298-306. [PMID: 21204885 DOI: 10.1111/j.1472-765x.2010.03001.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Compare specificity and sensitivity of quantitative PCR (qPCR) assays targeting single and multi-copy gene regions of Escherichia coli. METHODS AND RESULTS A previously reported assay targeting the uidA gene (uidA405) was used as the basis for comparing the taxonomic specificity and sensitivity of qPCR assays targeting the rodA gene (rodA984) and two regions of the multi-copy 23S ribosomal RNA gene (EC23S and EC23S857). Experimental analyses of 28 culture collection strains representing E. coli and 21 related non-target species indicated that the uidA405 and rodA984 assays were both 100% specific for E. coli while the EC23S assay was only 29% specific. The EC23S857 assay was only 95% specific due to detection of E. fergusonii. The uidA405, rodA984, EC23S and EC23S857 assays were 85%, 85%, 100% and 86% sensitive, respectively, in detecting 175 presumptive E. coli culture isolates from fresh, marine and waste water samples. In analyses of DNA extracts from 32 fresh, marine and waste water samples, the rodA984, EC23S and EC23S857 assays detected mean densities of target sequences at ratios of approximately 1:1, 243:1 and 6:1 compared with the mean densities detected by the uidA405 assay. CONCLUSIONS The EC23S assay was less specific for E. coli, whereas the rodA984 and EC23S857 assay taxonomic specificities and sensitivities were similar to those of the uidA405 gene assay. SIGNIFICANCE AND IMPACT The EC23S857 assay has a lower limit of detection for E. coli cells than the uidA405 and rodA984 assays due to its multi-copy gene target and therefore provides greater analytical sensitivity in monitoring for these faecal pollution indicators in environmental waters by qPCR methods.
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Affiliation(s)
- E C Chern
- US Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH 45268, USA
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Sivaganesan M, Haugland RA, Chern EC, Shanks OC. Improved strategies and optimization of calibration models for real-time PCR absolute quantification. Water Res 2010; 44:4726-35. [PMID: 20701947 DOI: 10.1016/j.watres.2010.07.066] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 07/07/2010] [Accepted: 07/20/2010] [Indexed: 05/23/2023]
Abstract
Real-time PCR absolute quantification applications are becoming more common in the recreational and drinking water quality industries. Many methods rely on the use of standard curves to make estimates of DNA target concentrations in unknown samples. Traditional absolute quantification approaches dictate that a standard curve must accompany each experimental run. However, the generation of a standard curve for each qPCR experiment set-up can be expensive and time consuming, especially for studies with large numbers of unknown samples. As a result, many researchers have adopted a master calibration strategy where a single curve is derived from DNA standard measurements generated from multiple instrument runs. However, a master curve can inflate uncertainty associated with intercept and slope parameters and decrease the accuracy of unknown sample DNA target concentration estimates. Here we report two alternative strategies termed 'pooled' and 'mixed' for the generation of calibration equations from absolute standard curves which can help reduce the cost and time of laboratory testing, as well as the uncertainty in calibration model parameter estimates. In this study, four different strategies for generating calibration models were compared based on a series of repeated experiments for two different qPCR assays using a Monte Carlo Markov Chain method. The hierarchical Bayesian approach allowed for the comparison of uncertainty in intercept and slope model parameters and the optimization of experiment design. Data suggests that the 'pooled' model can reduce uncertainty in both slope and intercept parameter estimates compared to the traditional single curve approach. In addition, the 'mixed' model achieved uncertainty estimates similar to the 'single' model while increasing the number of available reaction wells per instrument run.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
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24
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Shanks OC, White K, Kelty CA, Sivaganesan M, Blannon J, Meckes M, Varma M, Haugland RA. Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples. Environ Sci Technol 2010; 44:6281-8. [PMID: 20704227 DOI: 10.1021/es100311n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
There are numerous PCR-based assays available to characterize human fecal pollution in ambient waters. Each assay employs distinct oligonucleotides and many target different genes and microorganisms leading to potential variations in assay performance. Performance comparisons utilizing feces and raw sewage samples are needed to determine which assays are best suited for expensive and time-consuming field validation, fate, transport, and epidemiology studies. We report the assessment of five end-point PCR and 10 real-time quantitative PCR (qPCR) assays that target genes from presumptive Bacteroidales microorganisms reported to be associated with human feces. Each assay was tested against a reference collection of 54 primary influent sewage samples collected from different geographical locations across the United States and 174 fecal DNA extracts from 23 different animal sources. Experiments indicate that human-associated genetic markers are distributed across a broad range of human populations but show substantial differences in specificity for human feces suggesting that particular assays may be more suitable than others depending on the abundance of genetic marker required for detection and the animal sources impacting a particular watershed or beach of interest.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, USA.
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25
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Whitman RL, Ge Z, Nevers MB, Boehm AB, Chern EC, Haugland RA, Lukasik AM, Molina M, Przybyla-Kelly K, Shively DA, White EM, Zepp RG, Byappanahalli MN. Relationship and variation of qPCR and culturable Enterococci estimates in ambient surface waters are predictable. Environ Sci Technol 2010; 44:5049-54. [PMID: 20527919 DOI: 10.1021/es9028974] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based methods, the U.S. Environmental Protection Agency is currently considering its use as a basis for revised ambient water quality criteria. In anticipation of this possibility, we sought to examine the relationship between qPCR-based and culture-based estimates of enterococci in surface waters. Using data from several research groups, we compared enterococci estimates by the two methods in water samples collected from 37 sites across the United States. A consistent linear pattern in the relationship between cell equivalents (CCE), based on the qPCR method, and colony-forming units (CFU), based on the traditional culturable method, was significant (P < 0.05) at most sites. A linearly decreasing variance of CCE with increasing CFU levels was significant (P < 0.05) or evident for all sites. Both marine and freshwater sites under continuous influence of point-source contamination tended to reveal a relatively constant proportion of CCE to CFU. The consistency in the mean and variance patterns of CCE versus CFU indicates that the relationship of results based on these two methods is more predictable at high CFU levels (e.g., log(10)CFU > 2.0/100 mL) while uncertainty increases at lower CFU values. It was further noted that the relative error in replicated qPCR estimates was generally higher than that in replicated culture counts even at relatively high target levels, suggesting a greater need for replicated analyses in the qPCR method to reduce relative error. Further studies evaluating the relationship between culture and qPCR should take into account analytical uncertainty as well as potential differences in results of these methods that may arise from sample variability, different sources of pollution, and environmental factors.
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Affiliation(s)
- Richard L Whitman
- Lake Michigan Ecological Research Station, Great Lakes Science Center, United States Geological Survey, Porter, Indiana 46304, USA.
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Cantrell MA, Haugland RA, Evans HJ. Construction of a Rhizobium japonicum gene bank and use in isolation of a hydrogen uptake gene. Proc Natl Acad Sci U S A 2010; 80:181-5. [PMID: 16593268 PMCID: PMC393335 DOI: 10.1073/pnas.80.1.181] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gene bank of Rhizobium japonicum DNA was constructed by using the broad host range conjugative cosmid pLAFR1. Eighty-three percent of the clones in the bank contained cosmids with insert DNA averaging 22.6 kilobase pairs in length. A series of cosmids containing a hydrogen uptake (hup) gene was identified by transferring the gene bank into a H(2) uptake-negative (Hup(-)) R. japonicum point mutant (PJ17nal) and screening tetracycline-resistant colonies for the ability to grow chemolithotrophically and to reduce methylene blue in a recently devised colony assay. Hup(+) transconjugants arose at a frequency of approximately 6 x 10(-3). Plasmid DNAs from II of the Hup(+) transconjugants were isolated and used to transform Escherichia coli. EcoRI digests of all plasmids isolated from Hup(+) transconjugants had three DNA fragments in common. Eight of the E. coli transformants containing hup gene cosmids were conjugated with PJ17nal and another Hup(-) point mutant, PJ18nal. All PJ17nal transconjugants were Hup(+). The frequency of Hup(+) transconjugants with PJ18nal was approximately 10(-3). The results indicate that the hup gene cosmids may contain one gene and a portion of another.
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Affiliation(s)
- M A Cantrell
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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27
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Ayanaba A, Haugland RA, Sadowsky MJ, Upchurch RG, Weiland KD, Zablotowicz RM. Rapid Colored-Nodule Assay for Assessing Root Exudate-Enhanced Competitiveness of Bradyrhizobium japonicum. Appl Environ Microbiol 2010; 52:847-51. [PMID: 16347177 PMCID: PMC239125 DOI: 10.1128/aem.52.4.847-851.1986] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of root exudate (RE) treatment on nodule occupancy by Bradyrhizobium japonicum were investigated by a rapid colored-nodule assay, which is based on the observation that B. japonicum L-110 and its antibiotically marked derivatives form dark-red nodules on certain soybean (Glycine max) cultivars, whereas other strains form beige nodules. The efficacy of the assay was confirmed by direct immunofluorescence and by antibiotic platings of nodule bacteria. Both logarithmic- and stationary-phase cultures of the reference strain, L-110Nal, were used in paired-competition studies with RE-treated or untreated cells of seven challenge strains. On the basis of field and greenhouse competition studies, these strains were placed into three competitiveness groups: high (AN-11, AN-16aStrRif, and AN-6), intermediate (AN-3 and 122SR), and low (I-110ARS and AN-18). Seedlings of G. max cv. Centennial were inoculated with two ratios of challenge to reference strain, 1:1 and 1:9, and nodule occupancy was determined after the V4 to V5 stage of ontogeny. Two of the strains showed increased occupancy in response to RE treatment at the 1:1 inoculation ratio. Logarithmic- and stationary-phase cultures of AN-6 showed increased occupancy, from 22 to 38% (P < 0.10) and from 23 59 39% (P < 0.05), respectively. While the maximum increase for stationary-phase cultures of AN-16aStrRif was from 34 to 47% (P < 0.05), logarithmic-phase cultures failed to respond to RE treatment. The results of these studies indicate that RE treatment increases the nodule occupancy of some, but not all, B. japonicum strains and that the colored-nodule assay could be rapidly and reliably used to determine the competitive ability of B. japonicum.
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Affiliation(s)
- A Ayanaba
- Allied-Signal Inc., Crop Science Laboratory, Solvay, New York 13209
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28
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Lambert GR, Harker AR, Cantrell MA, Hanus FJ, Russell SA, Haugland RA, Evans HJ. Symbiotic Expression of Cosmid-Borne Bradyrhizobium japonicum Hydrogenase Genes. Appl Environ Microbiol 2010; 53:422-8. [PMID: 16347291 PMCID: PMC203676 DOI: 10.1128/aem.53.2.422-428.1987] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expression of cosmid-borne Bradyrhizobium japonicum hydrogenase genes in alfalfa, clover, and soybean nodules harboring Rhizobium transconjugants was studied. Cosmid pHU52 conferred hydrogen uptake (Hup) activity in both free-living bacteria and in nodules on the different plant hosts, although in nodules the instability of the cosmid resulted in low levels of Hup activity. In contrast, cosmid pHU1, which does not confer Hup activity on free-living bacteria, gave a Hup phenotype in nodules on alfalfa and soybean. Nodules formed by B. japonicum USDA 123Spc(pHU1) recycled about 90% of nitrogenase-mediated hydrogen evolution. Both subunits of hydrogenase (30- and 60-kilodalton polypeptides) were detected in enzyme-linked immunosorbent assays of bacteroid preparations from nodules harboring B. japonicum strains with pHU1 or pHU52. Neither pHU53 nor pLAFR1 conferred detectable Hup activity in either nodules or free-living bacteria. Based on the physical maps of pHU1 and pHU52, it is suggested that a 5.5-kilobase EcoRI fragment unique to pHU52 contains a gene or part of a gene required for Hup activity in free-living bacteria but not in nodules. This conclusion is supported by the observation that two Tn5 insertions in the chromosome of B. japonicum USDA 122DES obtained by marker exchange with Tn5-mutagenized pHU1 abolished Hup activity in free-living bacteria but not in nodules.
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Affiliation(s)
- G R Lambert
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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29
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Haugland RA, Hanus FJ, Cantrell MA, Evans HJ. Rapid Colony Screening Method for Identifying Hydrogenase Activity in Rhizobium japonicum. Appl Environ Microbiol 2010; 45:892-7. [PMID: 16346252 PMCID: PMC242389 DOI: 10.1128/aem.45.3.892-897.1983] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A method has been developed for the rapid screening of Rhizobium japonicum colonies for hydrogenase activity based on their ability to reduce methylene blue in the presence of respiratory inhibitors and hydrogen. Hydrogen uptake-positive (Hup) colonies derepressed for hydrogenase activity were visualized by their localized decolorization of filter paper disks impregnated with the dye. Appropriate responses were seen with a number of Hup and Hup wild-type strains of R. japonicum as well as Hup mutants. Its specificity was further confirmed in selected strains on the basis of comparisons with chemolithotrophic growth and the presence of other genetic markers. Utilization of the method in identifying Hup colonies among 16,000 merodiploid derivatives of the Hup mutant strain PJ17nal containing cloned DNA fragments of the Hup strain 122 DES has demonstrated its applicability as a screening procedure in the genetic analysis of the R. japonicum hydrogen uptake system.
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Affiliation(s)
- R A Haugland
- Laboratory for Nitrogen Fixation Research, Oregon State University, Corvallis, Oregon 97331
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Siefring S, Varma M, Atikovic E, Wymer L, Haugland RA. Improved real-time PCR assays for the detection of fecal indicator bacteria in surface waters with different instrument and reagent systems. J Water Health 2008; 6:225-37. [PMID: 18209285 DOI: 10.2166/wh.2008.022] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Previously reported and redesigned primer and probe assays were evaluated for the quantitative analysis of the fecal indicator bacterial groups, Enterococcus and Bacteroidetes with three real-time PCR instrument and reagent systems. The efficiency and sensitivity of the original assays varied between systems in analyses of DNA extracts from pure cultures of Enterococcus faecalis and Bacteroides fragilis, whereas the modified assays gave more consistent results. Distinctions between original and modified assays also occurred in analyses of known spike levels of E. faecalis and B. fragilis cells on filters with diverse surface water retentates. Percentages of samples causing PCR failures due to inhibition were lower using the modified assays. The accuracy and precision of spiked bacteria measurements were also generally higher, although mean measurements of both target organisms were still significantly different between systems (p < 0.05). The accuracy and precision of spiked bacteria measurements by both modified assays were further improved using a new sample matrix control spike consisting of cultured Lactococcus lactis cells and a reference assay for this organism. Corrections provided by the L. lactis assay eliminated significant differences in E. faecalis measurements between all three systems and between two of the three systems in B. fragilis measurements.
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Affiliation(s)
- S Siefring
- US Environmental Protection Agency (EPA), National Exposure Research Laboratory, Cincinnati, OH, USA
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Sivaganesan M, Seifring S, Varma M, Haugland RA, Shanks OC. A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinformatics 2008; 9:120. [PMID: 18298858 PMCID: PMC2292693 DOI: 10.1186/1471-2105-9-120] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Accepted: 02/25/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In real-time quantitative PCR studies using absolute plasmid DNA standards, a calibration curve is developed to estimate an unknown DNA concentration. However, potential differences in the amplification performance of plasmid DNA compared to genomic DNA standards are often ignored in calibration calculations and in some cases impossible to characterize. A flexible statistical method that can account for uncertainty between plasmid and genomic DNA targets, replicate testing, and experiment-to-experiment variability is needed to estimate calibration curve parameters such as intercept and slope. Here we report the use of a Bayesian approach to generate calibration curves for the enumeration of target DNA from genomic DNA samples using absolute plasmid DNA standards. RESULTS Instead of the two traditional methods (classical and inverse), a Monte Carlo Markov Chain (MCMC) estimation was used to generate single, master, and modified calibration curves. The mean and the percentiles of the posterior distribution were used as point and interval estimates of unknown parameters such as intercepts, slopes and DNA concentrations. The software WinBUGS was used to perform all simulations and to generate the posterior distributions of all the unknown parameters of interest. CONCLUSION The Bayesian approach defined in this study allowed for the estimation of DNA concentrations from environmental samples using absolute standard curves generated by real-time qPCR. The approach accounted for uncertainty from multiple sources such as experiment-to-experiment variation, variability between replicate measurements, as well as uncertainty introduced when employing calibration curves generated from absolute plasmid DNA standards.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA.
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Varughese EA, Wymer LJ, Haugland RA. An integrated culture and real-time PCR method to assess viability of disinfectant treated Bacillus spores using robotics and the MPN quantification method. J Microbiol Methods 2007; 71:66-70. [PMID: 17804100 DOI: 10.1016/j.mimet.2007.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 07/30/2007] [Accepted: 07/30/2007] [Indexed: 11/22/2022]
Abstract
Using robotics and the MPN technique, a 96-microwell method was developed to compare two procedures for enumeration of viable chlorine-treated B. atrophaeus spores: broth-culture enrichment followed by real-time polymerase chain reaction analysis; and filter plating on agar. Recoveries of chlorine-treated spores were improved by broth enrichment over filter plating, whereas recoveries of non-treated spores were not different in the two procedures.
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Affiliation(s)
- Eunice A Varughese
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, 26 W. Martin Luther King, Cincinnati, OH 45268, United States.
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Vesper SJ, Haugland RA, Rogers ME, Neely AN. Opportunistic Aspergillus pathogens measured in home and hospital tap water by quantitative PCR (QPCR). J Water Health 2007; 5:427-31. [PMID: 17878557 DOI: 10.2166/wh.2007.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Opportunistic fungal pathogens are a concern because of the increasing number of immunocompromised patients. The goal of this research was to test a simple extraction method and rapid quantitative PCR (QPCR) measurement of the occurrence of potential pathogens, Aspergillus fumigatus, A. flavus, A. terreus and A. niger, in home tap water and a hospital water supply. Water samples were taken from the kitchen tap in the homes of 60 patients who were diagnosed with legionellosis. Water samples were also taken from three locations in a hospital that generated all of its hot water by flash heating. Opportunistic infectious agents Aspergillus fumigatus, A. flavus, A. terreus and A. niger were measured using QPCR. Aspergillus terreus DNA was found in 16.7% and A. fumigatus DNA in 1.7% of the samples taken from the kitchen tap. None of the Aspergillus species were found in any of the hospital water samples.The development of a simple DNA extraction method along with QPCR analysis is suitable for rapid screening of tap water for opportunistic fungal pathogens. This simple method can be used to obtain pathogen occurrence results in about 3 h, instead of waiting days to weeks for culture data. Obtaining pathogen occurrence data in a timely manner could promote the elimination of the pathogens from the water supply of immunocompromised patients.
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Affiliation(s)
- S J Vesper
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH 45216, USA.
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Meklin T, Reponen T, McKinstry C, Cho SH, Grinshpun SA, Nevalainen A, Vepsäläinen A, Haugland RA, LeMasters G, Vesper SJ. Comparison of mold concentrations quantified by MSQPCR in indoor and outdoor air sampled simultaneously. Sci Total Environ 2007; 382:130-4. [PMID: 17467772 PMCID: PMC2233941 DOI: 10.1016/j.scitotenv.2007.03.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2006] [Revised: 03/19/2007] [Accepted: 03/22/2007] [Indexed: 05/07/2023]
Abstract
Mold specific quantitative PCR (MSQPCR) was used to measure the concentrations of the 36 mold species in indoor and outdoor air samples that were taken simultaneously for 48 h in and around 17 homes in Cincinnati, Ohio. The total spore concentrations of 353 per m(3) of indoor air and 827 per m(3) of outdoor air samples were significantly different (p<or=0.05). However, only the concentrations of Aspergillus penicillioides, Cladosporium cladosporioides types 1 and 2 and Cladosporium herbarum were correlated in indoor and outdoor air samples (p-value<or=0.05 and sufficient data for estimate and absolute value rho estimate >or=0.5). These results suggest that interpretation of the meaning of short-term (<48 h) mold measurements in indoor and outdoor air samples must be made with caution.
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Affiliation(s)
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Craig McKinstry
- Pacific Northwest National Laboratory, Statistical Sciences, Richland, WA, USA
| | - Seung-Hyun Cho
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Sergey A. Grinshpun
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Richard A. Haugland
- US Environmental Protection Agency, 26 W. Ml. L. King Drive, Cincinnati, Ohio, USA
| | - Grace LeMasters
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen J. Vesper
- US Environmental Protection Agency, 26 W. Ml. L. King Drive, Cincinnati, Ohio, USA
- *Corresponding author. Tel.: +1 513 569 7367, fax: +1 513 487 2512, E-mail address: (S.J. Vesper)
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Vesper SJ, McKinstry C, Yang C, Haugland RA, Kercsmar CM, Yike I, Schluchter MD, Kirchner HL, Sobolewski J, Allan TM, Dearborn DG. Specific molds associated with asthma in water-damaged homes. J Occup Environ Med 2007; 48:852-8. [PMID: 16902378 DOI: 10.1097/01.jom.0000224736.52780.2f] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We sought to determine if specific molds were found in significantly higher concentrations in the water-damaged homes of asthmatic children compared with homes with no visible water damage. METHODS The mold concentrations in the dust in asthmatic children's bedrooms in water-damaged homes (N = 60) and control homes (N = 22) were measured by mold-specific quantitative polymerase chain reaction. RESULTS Two molds, Scopulariopsis brevicaulis and Trichoderma viride, had significantly (P < 0.05) higher concentrations in asthmatics' homes compared with control homes and three other molds (Penicillium crustosum group, Stachybotrys chartarum, and Wallemia sebi) had P values <0.1. CONCLUSIONS A relative moldiness index was developed to predict the likely development of asthma in water-damaged homes in Cleveland.
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Affiliation(s)
- Stephen J Vesper
- U.S. Environmental Protection Agency, Cincinnati, Ohio 45268, USA.
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Vesper SJ, McKinstry C, Haugland RA, Iossifova Y, Lemasters G, Levin L, Khurana Hershey GK, Villareal M, Bernstein DI, Lockey J, Reponen T. Relative moldiness index as predictor of childhood respiratory illness. J Expo Sci Environ Epidemiol 2007; 17:88-94. [PMID: 17033680 PMCID: PMC2233948 DOI: 10.1038/sj.jes.7500528] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The results of a traditional visual mold inspection were compared to a mold evaluation based on the Relative Moldiness Index (RMI). The RMI is calculated from mold-specific quantitative PCR (MSQPCR) measurements of the concentration of 36 species of molds in floor dust samples. These two prospective mold evaluations were used to classify the mold condition in 271 homes of infants. Later, the development of respiratory illness was measured in the infants living in these homes and the predictive value of each classification system was evaluated. The binary classification of homes as either moldy or non-moldy by on-site visual home inspection was not predictive of the development of respiratory illness (wheeze and/or rhinitis) (P=0.27). Conversely, a method developed and validated in this paper, using the RMI index fit to a logistic function, can be used to predict the occurrence of illness in homes and allows stake-holders the choice among various levels of risk.
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Vesper SJ, Wymer LJ, Meklin T, Varma M, Stott R, Richardson M, Haugland RA. Comparison of populations of mould species in homes in the UK and USA using mould-specific quantitative PCR. Lett Appl Microbiol 2005; 41:367-73. [PMID: 16162146 DOI: 10.1111/j.1472-765x.2005.01764.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To compare the populations of 81 mould species in homes in the USA and UK using mould-specific quantitative polymerase chain reaction (MSQPCR) technology. METHODS AND RESULTS Dust samples were obtained from randomly selected homes in the UK (n=11). The mould populations in British homes were compared with those found in typical homes (no visible mould) in the USA (in the state of Ohio, n=45). Only 13 of 81 species screened showed significantly different concentrations in these two sets of home. CONCLUSIONS Although only a small survey, the results suggest that typical mould profiles in the USA (Ohio) and British homes are very similar. Analysis of 26 mould indicator species revealed that the British homes fell into two clusters, tentatively identified as 'atypical' and 'typical' mould conditions. SIGNIFICANCE AND IMPACT OF THE STUDY MSQPCR analysis of dust samples can provide an objective measure of indoor moulds which could lead to better management of their health effects.
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Affiliation(s)
- S J Vesper
- US Environmental Protection Agency, Cincinnati, OH 45268, USA.
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Haugland RA, Siefring SC, Wymer LJ, Brenner KP, Dufour AP. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res 2005; 39:559-68. [PMID: 15707628 DOI: 10.1016/j.watres.2004.11.011] [Citation(s) in RCA: 327] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2004] [Revised: 10/05/2004] [Accepted: 11/17/2004] [Indexed: 05/03/2023]
Abstract
Cell densities of the fecal pollution indicator genus, Enterococcus, were determined by a rapid (3 h or less) quantitative polymerase chain reaction (QPCR) analysis method in 100 ml water samples collected from recreational beaches on Lake Michigan and Lake Erie during the summer of 2003. Measurements by this method were compared with counts of Enterococcus colony-forming units (CFU) determined by Method 1600 membrane filter (MF) analysis using mEI agar. The QPCR method had an estimated 95% confidence, minimum detection limit of 27 Enterococcus cells per sample in analyses of undiluted DNA extracts and quantitative analyses of multiple lake water samples, spiked with known numbers of these organisms, gave geometric mean results that were highly consistent with the spike levels. At both beaches, the geometric means of ambient Enterococcus concentrations in water samples, determined from multiple collection points during each sampling visit, showed approximately lognormal distributions over the study period using both QPCR and MF analyses. These geometric means ranged from 10 to 8548 cells by QPCR analysis and 1-2499 CFU by MF culture analysis in Lake Michigan (N=56) and from 8 to 8695 cells by QPCR and 3-1941 CFU by MF culture in Lake Erie (N=47). Regression analysis of these results showed a significant positive correlation between the two methods with an overall correlation coefficient (r) of 0.68.
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Affiliation(s)
- Richard A Haugland
- US Environmental Protection Agency, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH 45268-1314, USA.
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Vesper SJ, Varma M, Wymer LJ, Dearborn DG, Sobolewski J, Haugland RA. Quantitative polymerase chain reaction analysis of fungi in dust from homes of infants who developed idiopathic pulmonary hemorrhaging. J Occup Environ Med 2004; 46:596-601. [PMID: 15213523 DOI: 10.1097/01.jom.0000128160.17144.6e] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Fungal concentrations were measured in the dust of 6 homes in Cleveland, Ohio, where an infant developed pulmonary hemorrhage (pulmonary hemorrhage homes [PHH]) and 26 reference homes (RH) with no known fungal contamination. Quantitative polymerase chain reaction assays for 82 species (or assay groups) were used to identify and quantify fungal concentrations. The ratios of the geometric means of PHH to RH were >1 for 26 species (group I). However, the same ratios were <1 for 10 species (group II). Probit analysis of the sum of the logs of the concentrations of these 2 groups resulted in a 95% probability range for separating PHH from RH homes. The same 82 fungal species were also tested for hemolysin production on sheep's blood agar (incubated at 37 degree C). Hemolysins were more commonly produced by group I species (42%) compared with group II species (10%).
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Affiliation(s)
- Stephen J Vesper
- US Environmental Protection Agency, National Exposure Research Laboratory, Cincinnati, Ohio 45268, USA.
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Meklin T, Haugland RA, Reponen T, Varma M, Lummus Z, Bernstein D, Wymer LJ, Vesper SJ. Quantitative PCR analysis of house dust can reveal abnormal mold conditions. ACTA ACUST UNITED AC 2004; 6:615-20. [PMID: 15237292 PMCID: PMC2233939 DOI: 10.1039/b400250d] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Indoor mold concentrations were measured in the dust of moldy homes (MH) and reference homes (RH) by quantitative PCR (QPCR) assays for 82 species or related groups of species (assay groups). About 70% of the species and groups were never or only rarely detected. The ratios (MH geometric mean : RH geometric mean) for 6 commonly detected species (Aspergillus ochraceus, A. penicillioides, A. unguis, A. versicolor, Eurotium group, and Cladosporium sphaerospermum) were >1 (Group I). Logistic regression analysis of the sum of the logs of the concentrations of Group I species resulted in a 95% probability for separating MH from RH. These results suggest that it may be possible to evaluate whether a home has an abnormal mold condition by quantifying a limited number of mold species in a dust sample. Also, four common species of Aspergillus were quantified by standard culturing procedures and their concentrations compared to QPCR results. Culturing underestimated the concentrations of these four species by 2 to 3 orders of magnitude compared to QPCR.
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Affiliation(s)
- Teija Meklin
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH 45268, USA. E-mail: ; Fax: +1 (513)-487-2512; Tel: +1 (513)-569-7135
| | - Richard A. Haugland
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH 45268, USA. E-mail: ; Fax: +1 (513)-487-2512; Tel: +1 (513)-569-7135
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Manju Varma
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH 45268, USA. E-mail: ; Fax: +1 (513)-487-2512; Tel: +1 (513)-569-7135
| | - Zana Lummus
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - David Bernstein
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Larry J. Wymer
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH 45268, USA. E-mail: ; Fax: +1 (513)-487-2512; Tel: +1 (513)-569-7135
| | - Stephen J. Vesper
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH 45268, USA. E-mail: ; Fax: +1 (513)-487-2512; Tel: +1 (513)-569-7135
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Morrison J, Yang C, Lin KT, Haugland RA, Neely AN, Vesper SJ. Monitoring Aspergillus species by quantitative PCR during construction of a multi-storey hospital building. J Hosp Infect 2004; 57:85-7. [PMID: 15142721 DOI: 10.1016/j.jhin.2004.01.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Accepted: 01/28/2004] [Indexed: 11/30/2022]
Abstract
During the enlargement of an existing hospital, quantitative polymerase chain reaction (PCR) was used to monitor Aspergillus spp. populations within the construction site. The rapid availability of results meant that the construction schedule was largely uninterrupted, while assuring that the new construction was free from contamination by the targeted Aspergillus spp.
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Affiliation(s)
- J Morrison
- Boelter & Yates, Inc., Park Ridge, IL, USA
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Abstract
A total of 65 quantitative PCR (QPCR) assays, incorporating fluorigenic 5' nuclease (TaqMan) chemistry and directed at the nuclear ribosomal RNA operon, internal transcribed spacer regions (ITS1 or ITS2) was developed and tested for the detection of selected Aspergillus, Penicillium and Paecilomyces species. The assays varied in specificity from species or subspecies to closely related species groups, subject to the amount of nucleotide sequence variation in the different organisms. A generic assay for all target species of Aspergillus, Penicillium and Paecilomyces was also developed and tested. Using a previously reported DNA extraction method, estimated conidia detection limits for target species ranged from less than one to several hundred per sample for the different assays. Conidia detection limits for non-target species were at least 1,000 fold higher in nearly all instances. The assays were used to analyze ten HVAC dust samples from different sources around the US. Total quantities of Aspergillus, Penicillium and Paecilomyces conidia in the samples, determined by the generic assay and the summed totals from the specific assays, were in general agreement, suggesting that all of the numerically dominant species in the samples were accounted for by the specific assays. QPCR analyses of these samples after spiking them with selected target organisms indicated that the enumeration results were within approximately a one-half log range of the expected values 95% of the time. Evidence is provided that the commonly used practices of enumerating Aspergillus and Penicillium as a single group or only by genus can be misleading in understanding the indoor populations of these organisms and their potential health risks.
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Affiliation(s)
- Richard A Haugland
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, Ohio 45268, USA.
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Brinkman NE, Haugland RA, Wymer LJ, Byappanahalli M, Whitman RL, Vesper SJ. Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water. Appl Environ Microbiol 2003; 69:1775-82. [PMID: 12620869 PMCID: PMC150045 DOI: 10.1128/aem.69.3.1775-1782.2003] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative PCR (QPCR) technology, incorporating fluorigenic 5' nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C. lusitaniae) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target Candida species detected in these analyses and colony counts of Enterococcus organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic Candida species from drinking and recreational waters and may have applications in the detection of fecal pollution.
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Affiliation(s)
- Nichole E Brinkman
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA
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Abstract
A 16S rDNA real-time PCR method was developed to detect Enterococcus faecalis in water samples. The dynamic range for cell detection spanned five logs and the detection limit was determined to be 6 cfu/reaction. The assay was capable of detecting E. faecalis cells added to biofilms from a simulator of a water distribution system and in freshwater samples. Nucleic acid extraction was not required, permitting the detection of E. faecalis cells in less than 3 h.
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Affiliation(s)
- Jorge W Santo Domingo
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Microbial Exposure Research Branch, 26 W Martin Luther King Dr, Cincinnati, OH 45268, USA.
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Haugland RA, Brinkman N, Vesper SJ. Evaluation of rapid DNA extraction methods for the quantitative detection of fungi using real-time PCR analysis. J Microbiol Methods 2002; 50:319-23. [PMID: 12031583 DOI: 10.1016/s0167-7012(02)00037-4] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Three comparatively rapid methods for the extraction of DNA from fungal conidia and yeast cells in environmental (air, water and dust) samples were evaluated for use in real-time PCR (TaqMan) analyses. A simple bead milling method was developed to provide sensitive, accurate and precise quantification of target organisms in air and water (tap and surface) samples. However, quantitative analysis of dust samples required further purification of the extracted DNA by a streamlined silica adsorption procedure.
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Affiliation(s)
- Richard A Haugland
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, 26 W. M.L. King Drive, Cincinnati, OH 45268, USA.
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Abstract
Stachybotrys chartarum is a toxigenic fungus that has been associated with human health concerns, including pulmonary hemorrhage and hemosiderosis. This fungus produces a hemolysin, stachylysin, which in its apparent monomeric form has a molecular mass of 11,920 Da as determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry. However, it appears to form polydispersed aggregates, which confounds understanding of the actual hemolytically active form. Exhaustive dialysis or heat treatment at 60 degrees C for 30 min inactivated stachylysin. Stachylysin is composed of about 40% nonpolar amino acids and contains two cysteine residues. Purified stachylysin required more than 6 h to begin lysing sheep erythrocytes, but by 48 h, lysis was complete. Stachylysin also formed pores in sheep erythrocyte membranes.
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Affiliation(s)
- S J Vesper
- U.S. Environmental Protection Agency, National Environmental Research Laboratory, Cincinnati, Ohio 45268, USA. Vesper.Stephen@EPA/gov
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Roe JD, Haugland RA, Vesper SJ, Wymer LJ. Quantification of Stachybotrys chartarum conidia in indoor dust using real time, fluorescent probe-based detection of PCR products. J Expo Anal Environ Epidemiol 2001; 11:12-20. [PMID: 11246797 DOI: 10.1038/sj.jea.7500147] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Analyses of fungal spores or conidia in indoor dust samples can be useful for determining the contamination status of building interiors and in signaling instances where potentially harmful exposures of building occupants to these organisms may exist. A recently developed method for the quantification of Stachybotrys chartarum conidia, using real-time, fluorescence probe--based detection of PCR products (TaqMan system) was employed to analyze indoor dust samples for this toxigenic fungal species. Dust samples ofup to 10 mg were found to be amenable to DNA extraction and analysis. Quantitative estimates of S. chartarum conidia in composite dust samples, containing a four-log range of these cells, were within 25 -- 104% of the expected quantities in 95% of analyses performed by the method. Calibrator samples containing known numbers of S. chartarum conidia were used as standards for quantification. Conidia of an arbitrarily selected strain of Geotrichum candidum were added in equal numbers to both dust and calibrator samples before DNA extraction. Partial corrections for reductions in overall DNA yields from the dust samples compared to the calibrator samples were obtained by comparative analyses of rDNA sequence yields from these reference conidia in the two types of samples. Dust samples from two contaminated homes were determined to contain greater than 10(3) S. chartarum conidia per milligram in collection areas near the sites of contamination and greater than 10(2) conidia per milligram in several areas removed from these sites in analyses performed by the method. These measurements were within the predicted range of agreement with results obtained by direct microscopic enumeration of presumptive Stachybotrys conidia in the same samples.
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Affiliation(s)
- J D Roe
- US Army Center for Health Promotion and Preventative Medicine, Aberdeen Proving Ground, Maryland, USA
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Haugland RA, Vesper SJ, Harmon SM. Phylogenetic Relationships of Memnoniella and Stachybotrys Species and Evaluation of Morphological Features for Memnoniella Species Identification. Mycologia 2001. [DOI: 10.2307/3761605] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Vesper SJ, Dearborn DG, Elidemir O, Haugland RA. Quantification of siderophore and hemolysin from Stachybotrys chartarum strains, including a strain isolated from the lung of a child with pulmonary hemorrhage and hemosiderosis. Appl Environ Microbiol 2000; 66:2678-81. [PMID: 10831457 PMCID: PMC110600 DOI: 10.1128/aem.66.6.2678-2681.2000] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A strain of Stachybotrys chartarum was recently isolated from the lung of a pulmonary hemorrhage and hemosiderosis (PH) patient in Texas (designated the Houston strain). This is the first time that S. chartarum has been isolated from the lung of a PH patient. In this study, the Houston strain and 10 strains of S. chartarum isolated from case (n = 5) or control (n = 5) homes in Cleveland were analyzed for hemolytic activity, siderophore production, and relatedness as measured by random amplified polymorphic DNA analysis.
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Affiliation(s)
- S J Vesper
- National Environmental Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268, USA.
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Vesper S, Dearborn DG, Yike I, Allan T, Sobolewski J, Hinkley SF, Jarvis BB, Haugland RA. Evaluation of Stachybotrys chartarum in the house of an infant with pulmonary hemorrhage: quantitative assessment before, during, and after remediation. J Urban Health 2000; 77:68-85. [PMID: 10741843 PMCID: PMC3456606 DOI: 10.1007/bf02350963] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Stachybotrys chartarum is an indoor mold that has been associated with pulmonary hemorrhage cases in the Cleveland, Ohio, area. This study applied two new quantitative measurements to air samples from a home in which an infant developed PH. Quantitative polymerase chain reaction and a protein synthesis inhibition assay were used to determine the level of S. chartarum spores and their toxicity in air samples taken before, during, and after a remediation program was implemented to remove the fungus. Initial spore concentrations were between 0.1 and 9.3 spores/m3 of air, and the toxicity of air particulates was correspondingly low. However, the dust in the house contained between 0.4 and 2.1 x 10(3) spores/mg (as determined by hemocytometer counts). The remediation program removed all contaminated wallboard, paneling, and carpeting in the water-damaged areas of the home. In addition, a sodium hypochlorite solution was used to spray all surfaces during remediation. Although spore counts and toxicity were high during remediation, air samples taken postremediation showed no detectable levels of S. chartarum or related toxicity. Nine isolates of S. chartarum obtained from the home were analyzed for spore toxicity, hemolytic activity, and random amplified polymorphic DNA banding patterns. None of the isolates produced highly toxic spores (>90 microg T2 toxin equivalents per gram wet weight spores) after growth for 10 and 30 days on wet wallboard, but three isolates were hemolytic consistently. DNA banding patterns suggested that at least one of these isolates was related to isolates from homes of infants with previously investigated cases.
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Affiliation(s)
- S Vesper
- US Environmental Protection Agency, National Exposure Research Laboratory, Cincinnati, OH 45268, USA.
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