1
|
Paar J, Willis JR, Sette L, Wood SA, Bogomolni A, Dulac M, Sivaganesan M, Shanks OC. Occurrence of recreational water quality monitoring general fecal indicator bacteria and fecal source identification genetic markers in gray seal scat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173220. [PMID: 38761521 DOI: 10.1016/j.scitotenv.2024.173220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/11/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
The number of gray seals (Halichoerus grypus) observed along the United States Northwest Atlantic region has been increasing for decades. These colonial animals often haul-out on beaches seasonally in numbers ranging from a few individuals to several thousands. While these larger aggregations are an important part of gray seal behavior, there is public concern that haul-outs could lead to large amounts of fecal waste in recreational areas, potentially resulting in beach closures. Yet, data to confirm whether these animals contribute to beach closures is lacking and minimal information is available on the occurrence of key water quality monitoring genetic markers in gray seal scat. This study evaluates the concentration of E. coli (EC23S857), enterococci (Entero1a), and fecal Bacteroidetes (GenBac3) as well as six fecal source identification genetic markers (HF183/BacR287, HumM2, CPQ_056, Rum2Bac, DG3, and GFD) measured by qPCR in 48 wild gray seal scat samples collected from two haul-out areas in Cape Cod (Massachusetts, U.S.A.). Findings indicate that FIB genetic markers are shed in gray seal scat at significantly different concentrations with the Entero1a genetic marker exhibiting the lowest average concentration (-0.73 log10 estimated mean copies per nanogram of DNA). In addition, systematic testing of scat samples demonstrated that qPCR assays targeting host-associated genetic markers indicative of human, ruminant, and canine fecal pollution sources remain highly specific in waters frequented by gray seals (>97 % specificity).
Collapse
Affiliation(s)
- Jack Paar
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA 01863, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - Lisa Sette
- Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Stephanie A Wood
- University of Massachusetts, Boston, Biology Department, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Andrea Bogomolni
- Massachusetts Maritime Academy, Marine Science, Safety and Environmental Protection, 101 Academy Drive, Buzzards Bay, MA 02532, USA
| | - Monique Dulac
- U.S. Environmental Protection Agency, New England Regional Laboratory, North Chelmsford, MA 01863, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA.
| |
Collapse
|
2
|
Sivaganesan M, Willis JR, Diedrich A, Shanks OC. A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements. WATER RESEARCH 2024; 255:121482. [PMID: 38598887 DOI: 10.1016/j.watres.2024.121482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.
Collapse
Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Adam Diedrich
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
| |
Collapse
|
3
|
Armenta-Leyva B, Munguía-Ramírez B, Cheng TY, Ye F, Henao-Díaz A, Giménez-Lirola LG, Zimmerman J. Normalizing real-time PCR results in routine testing. J Vet Diagn Invest 2024; 36:78-85. [PMID: 37919959 PMCID: PMC10734596 DOI: 10.1177/10406387231206080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
Normalization, the process of controlling for normal variation in sampling and testing, can be achieved in real-time PCR assays by converting sample quantification cycles (Cqs) to "efficiency standardized Cqs" (ECqs). We calculated ECqs as E-ΔCq, where E is amplification efficiency and ΔCq is the difference between sample and reference standard Cqs. To apply this approach to a commercial porcine reproductive and respiratory syndrome virus (PRRSV) RT-qPCR assay, we created reference standards by rehydrating and then diluting (1 × 10-4) a PRRSV modified-live vaccine (PRRS MLV; Ingelvac) with serum or oral fluid (OF) to match the sample matrix to be tested. Sample ECqs were calculated using the mean E and reference standard Cq calculated from the 4 reference standards on each plate. Serum (n = 132) and OF (n = 130) samples were collected from each of 12 pigs vaccinated with a PRRSV MLV from -7 to 42 d post-vaccination, tested, and sample Cqs converted to ECqs. Mean plate Es were 1.75-2.6 for serum and 1.7-2.3 for OF. Mean plate reference standard Cqs were 29.1-31.3 for serum and 29.2-31.5 for OFs. Receiver operating characteristic analysis calculated the area under the curve for serum and OF sample ECqs as 0.999 (95% CI: 0.997, 1.000) and 0.947 (0.890, 1.000), respectively. For serum, diagnostic sensitivity and specificity of the commercial PRRSV RT-qPCR assay were estimated as 97.9% and 100% at an ECq cutoff ≥ 0.20, and for OF, 82.6% and 100%, respectively, at an ECq cutoff ≥ 0.45.
Collapse
Affiliation(s)
- Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| | - Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, the Ohio State University, Columbus, OH, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | | | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| | - Jeffrey Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| |
Collapse
|
4
|
Nagelkerke E, Hetebrij WA, Koelewijn JM, Kooij J, van der Drift AMR, van der Beek RFHJ, de Jonge EF, Lodder WJ. PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance. Front Public Health 2023; 11:1141494. [PMID: 38026384 PMCID: PMC10652756 DOI: 10.3389/fpubh.2023.1141494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral concentrations in samples based on standard curves, by including preparations of a reference material with known nucleic acid or virus concentrations in the RT-qPCR analyses. In high-throughput monitoring programs it is possible to combine data from multiple previous runs, circumventing the need for duplication and resulting in decreased costs and prolonged periods during which the reference material is obtained from the same batch. However, over time, systematic shifts in standard curves are likely to occur. This would affect the reliability and usefulness of wastewater surveillance as a whole. We aim to find an optimal combination of standard curve data to compensate for run-to-run measurement variance while ensuring enough flexibility to capture systematic longitudinal shifts. Based on more than 4000 observations obtained with the CDC N1 and N2 assays, taken as a part of the National Sewage Surveillance program at the Dutch National Institute for Public Health and the Environment, we show that seasonal and long-term shifts in RT-qPCR efficiency and sensitivity occur. We find that in our setting, using five days of standard-curve data to quantify, results in the least error prone curve or best approximation. This results in differences up to 100% in quantified viral loads when averaged out over a nationwide program of >300 treatment plants. Results show that combining standard curves from a limited set of runs can be a valid approach to quantification without obscuring the trends in the viral load of interest.
Collapse
Affiliation(s)
- Erwin Nagelkerke
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Sresung M, Paisantham P, Ruksakul P, Kongprajug A, Chyerochana N, Gallage TP, Srathongneam T, Rattanakul S, Maneein S, Surasen C, Passananon S, Mongkolsuk S, Sirikanchana K. Microbial source tracking using molecular and cultivable methods in a tropical mixed-use drinking water source to support water safety plans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162689. [PMID: 36898534 DOI: 10.1016/j.scitotenv.2023.162689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Microbial contamination deteriorates source water quality, posing a severe problem for drinking water suppliers worldwide and addressed by the Water Safety Plan framework to ensure high-quality and reliable drinking water. Microbial source tracking (MST) is used to examine different microbial pollution sources via host-specific intestinal markers for humans and different types of animals. However, the application of MST in tropical surface water catchments that provide raw water for drinking water supplies is limited. We analyzed a set of MST markers, namely, three cultivable bacteriophages and four molecular PCR and qPCR assays, together with 17 microbial and physicochemical parameters, to identify fecal pollution from general, human-, swine-, and cattle-specific sources. Seventy-two river water samples at six sampling sites were collected over 12 sampling events during wet and dry seasons. We found persistent fecal contamination via the general fecal marker GenBac3 (100 % detection; 2.10-5.42 log10 copies/100 mL), with humans (crAssphage; 74 % detection; 1.62-3.81 log10 copies/100 mL) and swine (Pig-2-Bac; 25 % detection; 1.92-2.91 log10 copies/100 mL). Higher contamination levels were observed during the wet season (p < 0.05). The conventional PCR screening used for the general and human markers showed 94.4 % and 69.8 % agreement with the respective qPCR results. Specifically, in the studied watershed, coliphage could be a screening parameter for the crAssphage marker (90.6 % and 73.7 % positive and negative predictive values; Spearman's rank correlation coefficient = 0.66; p < 0.001). The likelihood of detecting the crAssphage marker significantly increased when total and fecal coliforms exceeded 20,000 and 4000 MPN/100 mL, respectively, as Thailand Surface Water Quality Standards, with odds ratios and 95 % confidence intervals of 15.75 (4.43-55.98) and 5.65 (1.39-23.05). Our study confirms the potential benefits of incorporating MST monitoring into water safety plans, supporting the use of this approach to ensure high-quality drinking water supplies worldwide.
Collapse
Affiliation(s)
- Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Phongsawat Paisantham
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Pacharaporn Ruksakul
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Tharindu Pollwatta Gallage
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Thitima Srathongneam
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Siriwara Maneein
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Chatsinee Surasen
- Water Resources and Environment Department, Metropolitan Waterworks Authority, Bangkok 10210, Thailand
| | - Somsak Passananon
- Line of Deputy Governor (Water Production), Metropolitan Waterworks Authority, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand.
| |
Collapse
|
6
|
González-Fernández A, Symonds EM, Gallard-Gongora JF, Mull B, Lukasik JO, Rivera Navarro P, Badilla Aguilar A, Peraud J, Mora Alvarado D, Cantor A, Breitbart M, Cairns MR, Harwood VJ. Risk of Gastroenteritis from Swimming at a Wastewater-Impacted Tropical Beach Varies across Localized Scales. Appl Environ Microbiol 2023; 89:e0103322. [PMID: 36847564 PMCID: PMC10057883 DOI: 10.1128/aem.01033-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/21/2023] [Indexed: 03/01/2023] Open
Abstract
Population growth and changing climate are expected to increase human exposure to pathogens in tropical coastal waters. We examined microbiological water quality in three rivers within 2.3 km of each other that impact a Costa Rican beach and in the ocean outside their plumes during the rainy and dry seasons. We performed quantitative microbial risk assessment (QMRA) to predict the risk of gastroenteritis associated with swimming and the amount of pathogen reduction needed to achieve safe conditions. Recreational water quality criteria based on enterococci were exceeded in >90% of river samples but in only 13% of ocean samples. Multivariate analysis grouped microbial observations by subwatershed and season in river samples but only by subwatershed in the ocean. The modeled median risk from all pathogens in river samples was between 0.345 and 0.577, 10-fold above the U.S. Environmental Protection Agency (U.S. EPA) benchmark of 0.036 (36 illnesses/1,000 swimmers). Norovirus genogroup I (NoVGI) contributed most to risk, but adenoviruses raised risk above the threshold in the two most urban subwatersheds. The risk was greater in the dry compared to the rainy season, due largely to the greater frequency of NoVGI detection (100% versus 41%). Viral log10 reduction needed to ensure safe swimming conditions varied by subwatershed and season and was greatest in the dry season (3.8 to 4.1 dry; 2.7 to 3.2 rainy). QMRA that accounts for seasonal and local variability of water quality contributes to understanding the complex influences of hydrology, land use, and environment on human health risk in tropical coastal areas and can contribute to improved beach management. IMPORTANCE This holistic investigation of sanitary water quality at a Costa Rican beach assessed microbial source tracking (MST) marker genes, pathogens, and indicators of sewage. Such studies are still rare in tropical climates. Quantitative microbial risk assessment (QMRA) found that rivers impacting the beach consistently exceeded the U.S. EPA risk threshold for gastroenteritis of 36/1,000 swimmers. The study improves upon many QMRA studies by measuring specific pathogens, rather than relying on surrogates (indicator organisms or MST markers) or estimating pathogen concentrations from the literature. By analyzing microbial levels and estimating the risk of gastrointestinal illness in each river, we were able to discern differences in pathogen levels and human health risks even though all rivers were highly polluted by wastewater and were located less than 2.5 km from one another. This variability on a localized scale has not, to our knowledge, previously been demonstrated.
Collapse
Affiliation(s)
| | - Erin M. Symonds
- College of Marine Science, University of South Florida, Saint Petersburg, Florida, USA
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
| | | | - Bonnie Mull
- BCS Laboratories, Inc., Gainesville, Florida, USA
| | | | - Pablo Rivera Navarro
- Laboratorio Nacional de Aguas, Instituto Costarricense de Acueductos y Alcantarillados, Tres Ríos, Cartago, Costa Rica
| | - Andrei Badilla Aguilar
- Laboratorio Nacional de Aguas, Instituto Costarricense de Acueductos y Alcantarillados, Tres Ríos, Cartago, Costa Rica
| | - Jayme Peraud
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Darner Mora Alvarado
- Laboratorio Nacional de Aguas, Instituto Costarricense de Acueductos y Alcantarillados, Tres Ríos, Cartago, Costa Rica
| | - Allison Cantor
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, Florida, USA
| | - Maryann R. Cairns
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
7
|
Burnet JB, Cauchie HM, Walczak C, Goeders N, Ogorzaly L. Persistence of endogenous RNA biomarkers of SARS-CoV-2 and PMMoV in raw wastewater: Impact of temperature and implications for wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159401. [PMID: 36240930 PMCID: PMC9554201 DOI: 10.1016/j.scitotenv.2022.159401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/21/2022] [Accepted: 10/08/2022] [Indexed: 05/28/2023]
Abstract
Understanding the persistence of SARS-CoV-2 biomarkers in wastewater should guide wastewater-based epidemiology users in selecting best RNA biomarkers for reliable detection of the virus during current and future waves of the pandemic. In the present study, the persistence of endogenous SARS-CoV-2 were assessed during one month for six different RNA biomarkers and for the pepper mild mottle virus (PMMoV) at three different temperatures (4, 12 and 20 °C) in one wastewater sample. All SARS-CoV-2 RNA biomarkers were consistently detected during 6 days at 4° and differences in signal persistence among RNA biomarkers were mostly observed at 20 °C with N biomarkers being globally more persistent than RdRP, E and ORF1ab ones. SARS-CoV-2 signal persistence further decreased in a temperature dependent manner. At 12 and 20 °C, RNA biomarker losses of 1-log10 occurred on average after 6 and 4 days, and led to a complete signal loss after 13 and 6 days, respectively. Besides the effect of temperature, SARS-CoV-2 RNA signals were more persistent in the particulate phase compared to the aqueous one. Finally, PMMoV RNA signal was highly persistent in both phases and significantly differed from that of SARS-CoV-2 biomarkers. We further provide a detailed overview of the latest literature on SARS-CoV-2 and PMMoV decay rates in sewage matrices.
Collapse
Affiliation(s)
- Jean-Baptiste Burnet
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Henry-Michel Cauchie
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Cécile Walczak
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Nathalie Goeders
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Leslie Ogorzaly
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg.
| |
Collapse
|
8
|
Sivaganesan M, Willis JR, Karim M, Babatola A, Catoe D, Boehm AB, Wilder M, Green H, Lobos A, Harwood VJ, Hertel S, Klepikow R, Howard MF, Laksanalamai P, Roundtree A, Mattioli M, Eytcheson S, Molina M, Lane M, Rediske R, Ronan A, D'Souza N, Rose JB, Shrestha A, Hoar C, Silverman AI, Faulkner W, Wickman K, Kralj JG, Servetas SL, Hunter ME, Jackson SA, Shanks OC. Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917. WATER RESEARCH 2022; 225:119162. [PMID: 36191524 PMCID: PMC9932931 DOI: 10.1016/j.watres.2022.119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material® 2917 (NIST SRM® 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n = 1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.
Collapse
Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mohammad Karim
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - Akin Babatola
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - David Catoe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Maxwell Wilder
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Hyatt Green
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Aldo Lobos
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Stephanie Hertel
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Regina Klepikow
- U.S. Environmental Protection Agency, Region 7 Laboratory, Kansas City, KS, USA
| | | | | | - Alexis Roundtree
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie Eytcheson
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Molly Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Richard Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Amanda Ronan
- U.S. Environmental Protection Agency, Region 2 Laboratory, Edison, NJ, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | | | | | - Jason G Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
| |
Collapse
|
9
|
Medici G, Tassinari M, Galvani G, Bastianini S, Gennaccaro L, Loi M, Mottolese N, Alvente S, Berteotti C, Sagona G, Lupori L, Candini G, Baggett HR, Zoccoli G, Giustetto M, Muotri A, Pizzorusso T, Nakai H, Trazzi S, Ciani E. Expression of a Secretable, Cell-Penetrating CDKL5 Protein Enhances the Efficacy of Gene Therapy for CDKL5 Deficiency Disorder. Neurotherapeutics 2022; 19:1886-1904. [PMID: 36109452 PMCID: PMC9723029 DOI: 10.1007/s13311-022-01295-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2022] [Indexed: 12/14/2022] Open
Abstract
Although delivery of a wild-type copy of the mutated gene to cells represents the most effective approach for a monogenic disease, proof-of-concept studies highlight significant efficacy caveats for treatment of brain disorders. Herein, we develop a cross-correction-based strategy to enhance the efficiency of a gene therapy for CDKL5 deficiency disorder, a severe neurodevelopmental disorder caused by CDKL5 gene mutations. We created a gene therapy vector that produces an Igk-TATk-CDKL5 fusion protein that can be secreted via constitutive secretory pathways and, due to the cell-penetration property of the TATk peptide, internalized by cells. We found that, although AAVPHP.B_Igk-TATk-CDKL5 and AAVPHP.B_CDKL5 vectors had similar brain infection efficiency, the AAVPHP.B_Igk-TATk-CDKL5 vector led to higher CDKL5 protein replacement due to secretion and penetration of the TATk-CDKL5 protein into the neighboring cells. Importantly, Cdkl5 KO mice treated with the AAVPHP.B_Igk-TATk-CDKL5 vector showed a behavioral and neuroanatomical improvement in comparison with vehicle or AAVPHP.B_CDKL5 vector-treated Cdkl5 KO mice. In conclusion, we provide the first evidence that a gene therapy based on a cross-correction approach is more effective at compensating Cdkl5-null brain defects than gene therapy based on the expression of the native CDKL5, opening avenues for the development of this innovative approach for other monogenic diseases.
Collapse
Affiliation(s)
- Giorgio Medici
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Marianna Tassinari
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Giuseppe Galvani
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Stefano Bastianini
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Laura Gennaccaro
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Manuela Loi
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Nicola Mottolese
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Sara Alvente
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Chiara Berteotti
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Giulia Sagona
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128, Pisa, Italy
- Department of Neuroscience, Drug Research and Child Health (NEUROFARBA), University of Florence, 50139, Psychology, Italy
| | - Leonardo Lupori
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128, Pisa, Italy
- Scuola Normale Superiore, 56126, Pisa, Italy
| | - Giulia Candini
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Helen Rappe Baggett
- Departments of Molecular and Medical Genetics and Molecular Immunology and Microbiology Oregon Health & Science University, OR, 97239, Portland, USA
| | - Giovanna Zoccoli
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy
| | - Maurizio Giustetto
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, OR, 10126, Turin, Italy
| | - Alysson Muotri
- School of Medicine, Department of Pediatrics/Rady Children's Hospital, University of California San Diego, San Diego, USA
- Department of Cellular & Molecular Medicine, Kavli Institute for Brain and Mind, Archealization Center (ArchC), Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA, 92037, USA
| | - Tommaso Pizzorusso
- Scuola Normale Superiore, 56126, Pisa, Italy
- Institute of Neuroscience, National Research Council, 56126, Pisa, Italy
| | - Hiroyuki Nakai
- Departments of Molecular and Medical Genetics and Molecular Immunology and Microbiology Oregon Health & Science University, OR, 97239, Portland, USA
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Stefania Trazzi
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy.
| | - Elisabetta Ciani
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126, Bologna, Italy.
| |
Collapse
|
10
|
Willis JR, Sivaganesan M, Haugland RA, Kralj J, Servetas S, Hunter ME, Jackson SA, Shanks OC. Performance of NIST SRM® 2917 with 13 recreational water quality monitoring qPCR assays. WATER RESEARCH 2022; 212:118114. [PMID: 35091220 PMCID: PMC10786215 DOI: 10.1016/j.watres.2022.118114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Fecal pollution remains a significant challenge for recreational water quality management worldwide. In response, there is a growing interest in the use of real-time quantitative PCR (qPCR) methods to achieve same-day notification of recreational water quality and associated public health risk as well as to characterize fecal pollution sources for targeted mitigation. However, successful widespread implementation of these technologies requires the development of and access to a high-quality standard control material. Here, we report a single laboratory qPCR performance assessment of the National Institute of Standards and Technology Standard Reference Material 2917 (NIST SRM® 2917), a linearized plasmid DNA construct that functions with 13 recreational water quality qPCR assays. Performance experiments indicate the generation of standard curves with amplification efficiencies ranging from 0.95 ± 0.006 to 0.99 ± 0.008 and coefficient of determination values (R2) ≥ 0.980. Regardless of qPCR assay, variability in repeated measurements at each dilution level were very low (quantification threshold standard deviations ≤ 0.657) and exhibited a heteroscedastic trend characteristic of qPCR standard curves. The influence of a yeast carrier tRNA added to the standard control material buffer was also investigated. Findings demonstrated that NIST SRM® 2917 functions with all qPCR methods and suggests that the future use of this control material by scientists and water quality managers should help reduce variability in concentration estimates and make results more consistent between laboratories.
Collapse
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.
| |
Collapse
|
11
|
Tan F, Xiao P, Yang JR, Chen H, Jin L, Yang Y, Lin TF, Willis A, Yang J. Precision early detection of invasive and toxic cyanobacteria: A case study of Raphidiopsis raciborskii. HARMFUL ALGAE 2021; 110:102125. [PMID: 34887005 DOI: 10.1016/j.hal.2021.102125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Blooms of the toxic cyanobacterium, Raphidiopsis raciborskii (basionym Cylindrospermopsis raciborskii), are becoming a major environmental issue in freshwater ecosystems globally. Our precision prevention and early detection of R. raciborskii blooms rely upon the accuracy and speed of the monitoring method. A duplex digital PCR (dPCR) monitoring approach was developed and validated to detect the abundance and toxin-producing potential of R. raciborskii simultaneously in both laboratory spiked and environmental samples. Results of dPCR were strongly correlated with traditional real time quantitative PCR (qPCR) and microscopy for both laboratory and environmental samples. However, discrepancies between methods were observed when measuring R. raciborskii at low abundance (1 - 105 cells L - 1), with dPCR showing a higher precision compared to qPCR at low cell concentration. Furthermore, the dPCR assay had the highest detection rate for over two hundred environmental samples especially under low abundance conditions, followed by microscopy and qPCR. dPCR assay had the advantages of simple operation, time-saving, high sensitivity and excellent reproducibility. Therefore, dPCR would be a fast and precise monitoring method for the early warning of toxic bloom-forming cyanobacterial species and assessment of water quality risks, which can improve prediction and prevention of the impacts of harmful cyanobacterial bloom events in inland waters.
Collapse
Affiliation(s)
- Fengjiao Tan
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Xiao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jun R Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Engineering Research Center of Ecology and Agricultural Use of Wetland (Ministry of Education), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Jin
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yigang Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tsair-Fuh Lin
- Department of Environmental Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Hobart 7000, Tasmania, Australia
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| |
Collapse
|
12
|
Makkaew P, Kongprajug A, Chyerochana N, Sresung M, Precha N, Mongkolsuk S, Sirikanchana K. Persisting antibiotic resistance gene pollution and its association with human sewage sources in tropical marine beach waters. Int J Hyg Environ Health 2021; 238:113859. [PMID: 34655856 DOI: 10.1016/j.ijheh.2021.113859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/25/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022]
Abstract
Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are pollutants of worldwide concern that threaten human health and ecosystems. Anthropogenic activities and wastewater could be ARB and ARG pollution sources; however, research on ARG abundance and microbial source tracking (MST) of contamination in tropical marine waters is limited. This study examined spatiotemporal variations of six ARGs (blaNDM, blaTEM, blaVIM, mcr-1, sul1, and tetQ) against the widely used antibiotic groups and a class 1 integron-integrase gene (intI1) at two Thai tropical recreational beaches (n = 41). Correlations between ARGs and sewage-specific MST markers (i.e., crAssphage and human polyomaviruses [HPyVs]) and fecal indicator bacteria (i.e., total coliforms, fecal coliforms, and enterococci) were also investigated. BlaTEM, intI1, sul1, and tetQ were ubiquitous at both beaches (85.4-100% detection rate); intI1 was the most abundant (3-6 orders in log10 copies/100 mL), followed by blaTEM (2-4 orders), sul1 (2-3 orders), and tetQ (2-4 orders). BlaNDM was found in 7.3% (up to 4 orders), and no mcr-1 was detected. Interestingly, blaVIM was prevalent at one beach (2-5 orders; n = 17), but found in only one sample at the other (4 orders). Temporal, but not spatial, differences were noticed; blaTEM was at higher levels in the wet season. IntI1 correlated with sul1 and tetQ (Spearman's rho = 0.47-0.97), suggesting potential horizontal gene transfer. CrAssphage, but not HPyVs, correlated with intI1, sul1, and tetQ (Spearman's rho = 0.50-0.74). Higher numbers of ARGs tended to co-occur in samples with higher crAssphage concentrations, implying sewage contribution to the marine water, with a persisting ARG background. This study provides insight into the ARG pollution status of tropical coastal waters and suggests crAssphage as a proxy for ARG pollution, which could facilitate effective management policies to minimize ARG dissemination in marine environments.
Collapse
Affiliation(s)
- Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat, 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat, 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology EHT, Ministry of Education, Bangkok, 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology EHT, Ministry of Education, Bangkok, 10400, Thailand.
| |
Collapse
|
13
|
Bivins A, Kaya D, Bibby K, Simpson SL, Bustin SA, Shanks OC, Ahmed W. Variability in RT-qPCR assay parameters indicates unreliable SARS-CoV-2 RNA quantification for wastewater surveillance. WATER RESEARCH 2021; 203:117516. [PMID: 34412018 PMCID: PMC8341816 DOI: 10.1016/j.watres.2021.117516] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
Due to the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) has been used to generate large datasets aimed at detecting and quantifying SARS-CoV-2 RNA in wastewater. Although RT-qPCR is rapid and sensitive, there is no standard method yet, there are no certified quantification standards, and experiments are conducted using different assays, reagents, instruments, and data analysis protocols. These variations can induce errors in quantitative data reports, thereby potentially misleading interpretations, and conclusions. We review the SARS-CoV-2 wastewater surveillance literature focusing on variability of RT-qPCR data as revealed by inconsistent standard curves and associated parameters. We find that variation in these parameters and deviations from best practices, as described in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines suggest a frequent lack of reproducibility and reliability in quantitative measurements of SARS-CoV-2 RNA in wastewater.
Collapse
Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Devrim Kaya
- School of Chemical, Biological, & Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Stephen A Bustin
- Medical Technology Research Center, Faculty of Health, Education and Social Care, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK
| | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH, 45268, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park 4102, QLD, Australia.
| |
Collapse
|
14
|
Holcomb DA, Knee J, Capone D, Sumner T, Adriano Z, Nalá R, Cumming O, Brown J, Stewart JR. Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11667-11679. [PMID: 34382777 PMCID: PMC8429117 DOI: 10.1021/acs.est.1c01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two nonspecific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique, participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced Escherichia coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide the implementation of effective interventions to safeguard health.
Collapse
Affiliation(s)
- David A. Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Drew Capone
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jill R. Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| |
Collapse
|
15
|
Ramezani A. CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm. J Microbiol Methods 2021; 187:106267. [PMID: 34116107 DOI: 10.1016/j.mimet.2021.106267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/05/2021] [Accepted: 06/06/2021] [Indexed: 11/25/2022]
Abstract
In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for converting the data obtained from different runs containing identical standard samples into one run with the same amplification efficiency and threshold value. For this purpose, two formulas were designed; one to convert the amplification efficiency of the each run to 100%, and the other one for converting data from different runs into one run. Utilizing these two formulas, an algorithm was developed and named CtNorm. The online version of CtNorm algorithm is available at http://ctnorm.sums.ac.ir/. We used qRT-PCR technique to validate the accuracy of the designed algorithm for the normalization of four different human internal control genes. Normalizing the Ct values obtained from separate runs with the CtNorm algorithm has eliminated the differences and the average of the Ct values has become similar to the condition in which all the samples were amplified in a single run. The CtNorm algorithm could be utilized for equalizing the Ct values of several qRT-PCR runs with the same standard samples. The algorithm has also the ability to convert the amplification efficiency to 100% which is useful in absolute and relative quantification.
Collapse
Affiliation(s)
- Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
16
|
Kongprajug A, Denpetkul T, Chyerochana N, Mongkolsuk S, Sirikanchana K. Human Fecal Pollution Monitoring and Microbial Risk Assessment for Water Reuse Potential in a Coastal Industrial-Residential Mixed-Use Watershed. Front Microbiol 2021; 12:647602. [PMID: 33959110 PMCID: PMC8093506 DOI: 10.3389/fmicb.2021.647602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Rapid economic development has caused industrial expansion into residential communities, leading to higher fecal pollution loads that could be discharged into aquatic environments. However, little is known regarding the potential microbial impact on human health. This study investigated microbial contamination from coastal industrial–residential community areas in nine sampling sites in waterways during three dry events. A general microbial source tracking (MST) marker, GenBac3, was detected in all samples from all three events, indicating continuing fecal pollution in the area, mostly from human sewage contamination. This was shown by the human-specific genetic marker crAssphage (88.9%) and human polyomavirus (HPyVs; 92.6%) detection. Enteric human adenovirus (HAdV40/41) showed three positive results only from residential sites in the first event. No spatial difference was observed for MST markers and traditional fecal indicators (total coliforms and Escherichia coli) in each event. Still, a significantly lower abundance of GenBac3, HPyVs, and total coliforms in the first sampling event was detected. Spearman’s rho analysis indicated a strong correlation among certain pairs of microbial parameters. Multivariate analysis revealed two clusters of samples separated by land use type (industrial vs. residential). According to factor analysis of mixed data, the land use parameter was more associated with physicochemical parameters (i.e., salinity, conductivity, water temperature, and dissolved oxygen). A Quantitative Microbial Risk Assessment (QMRA) was then conducted to estimate the annual infection risks of HAdV40/41 for non-potable water reuse purposes using predicted concentrations from crAssphage and HPyVs. The highest risks (95th percentiles) were ranked by food crop irrigation, aquaculture, and toilet flushing, at 10–1, 10–2, and 10–3 per person per year (pppy). Required treatment levels to achieve a 10–4 pppy annual infection risk were estimated. QMRA-based water treatment scenarios were suggested, including chlorination for toilet flushing reuse and depth filtration prior to chlorination for aquaculture and food crop irrigation. Microbial monitoring combined with a QMRA could provide better insights into fecal pollution patterns and the associated risks, facilitating effective water quality management and appropriate prior treatments for water reuse.
Collapse
Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Thammanitchpol Denpetkul
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
| |
Collapse
|
17
|
Li X, Kelty CA, Sivaganesan M, Shanks OC. Variable fecal source prioritization in recreational waters routinely monitored with viral and bacterial general indicators. WATER RESEARCH 2021; 192:116845. [PMID: 33508720 PMCID: PMC8186395 DOI: 10.1016/j.watres.2021.116845] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Somatic and F+ coliphage methods are under consideration as potential routine surface water quality monitoring tools to identify unsafe levels of fecal pollution in recreational waters. However, little is known about the cooccurrence of these virus-based fecal indicators and host-associated genetic markers used to prioritize key pollution sources for remediation. In this study, paired measurements of cultivated coliphage (somatic and F+) and bacterial (E. coli and enterococci) general fecal indicators and genetic markers indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), canine (DG3), and avian (GFD) fecal pollution sources were assessed in 365 water samples collected from six Great Lakes Basin beach and river sites over a 15-week recreational season. Water samples were organized into groups based on defined viral and bacterial fecal indicator water quality thresholds and average log10 host-associated genetic marker fecal score ratios were estimated to compare pollutant source inferences based on variable routine water quality monitoring practices. Eligible log10 fecal score ratios ranged from -0.051 (F+ coliphage, GFD) to 2.08 (enterococci, Rum2Bac). Using a fecal score ratio approach, findings suggest that general fecal indicator selection for routine water quality monitoring can influence the interpretation of host-associated genetic marker measurements, in some cases, prioritizing different pollutant sources for remediation. Variable trends were also observed between Great Lake beach and river sites suggesting disparate management practices may be useful for each water type.
Collapse
Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055
| | - Catherine A Kelty
- 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
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
| |
Collapse
|
18
|
Sangkaew W, Kongprajug A, Chyerochana N, Ahmed W, Rattanakul S, Denpetkul T, Mongkolsuk S, Sirikanchana K. Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand. WATER RESEARCH 2021; 190:116706. [PMID: 33310444 DOI: 10.1016/j.watres.2020.116706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log10 copies/100 mL), crAssphage (5.28-7.38 log10 copies/100 mL), and HPyVs (3.66-6.53 log10 copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log10 copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log10 copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log10 copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log10 copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.
Collapse
Affiliation(s)
- Watsawan Sangkaew
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Thammanitchpol Denpetkul
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, 272 Rama 6 Road, Ratchathevi, Bangkok, 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, 272 Rama 6 Road, Ratchathevi, Bangkok, 10400, Thailand.
| |
Collapse
|
19
|
Harvey AP, Fuhrmeister ER, Cantrell ME, Pitol AK, Swarthout JM, Powers JE, Nadimpalli ML, Julian TR, Pickering AJ. Longitudinal Monitoring of SARS-CoV-2 RNA on High-Touch Surfaces in a Community Setting. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:168-175. [PMID: 34192125 PMCID: PMC7927285 DOI: 10.1021/acs.estlett.0c00875] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 05/19/2023]
Abstract
Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3%) surface samples were positive for SARS-CoV-2 RNA, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000) by quantitative microbial risk assessment, suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n = 33 unique surfaces per week) best predicted variation in city-level COVID-19 cases with a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces may be a useful tool to provide early warning of COVID-19 case trends.
Collapse
Affiliation(s)
- Abigail P. Harvey
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | | | - Molly E. Cantrell
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Ana K. Pitol
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jenna M. Swarthout
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Julie E. Powers
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Maya L. Nadimpalli
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf CH-8600, Switzerland
- Swiss Tropical and Public Health Institute, Basel CH-4051, Switzerland
- University of Basel, Basel CH-4055, Switzerland
| | - Amy J. Pickering
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
- Department of Civil and Environmental Engineering, University of California, Berkeley, 94720
| |
Collapse
|
20
|
Brumfield KD, Cotruvo JA, Shanks OC, Sivaganesan M, Hey J, Hasan NA, Huq A, Colwell RR, Leddy MB. Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed. FRONTIERS IN WATER 2021; 3:626849. [PMID: 34263162 PMCID: PMC8274573 DOI: 10.3389/frwa.2021.626849] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Microbial contamination of recreation waters is a major concern globally, with pollutants originating from many sources, including human and other animal wastes often introduced during storm events. Fecal contamination is traditionally monitored by employing culture methods targeting fecal indicator bacteria (FIB), namely E. coli and enterococci, which provides only limited information of a few microbial taxa and no information on their sources. Host-associated qPCR and metagenomic DNA sequencing are complementary methods for FIB monitoring that can provide enhanced understanding of microbial communities and sources of fecal pollution. Whole metagenome sequencing (WMS), quantitative real-time PCR (qPCR), and culture-based FIB tests were performed in an urban watershed before and after a rainfall event to determine the feasibility and application of employing a multi-assay approach for examining microbial content of ambient source waters. Cultivated E. coli and enterococci enumeration confirmed presence of fecal contamination in all samples exceeding local single sample recreational water quality thresholds (E. coli, 410 MPN/100 mL; enterococci, 107 MPN/100 mL) following a rainfall. Test results obtained with qPCR showed concentrations of E. coli, enterococci, and human-associated genetic markers increased after rainfall by 1.52-, 1.26-, and 1.11-fold log10 copies per 100 mL, respectively. Taxonomic analysis of the surface water microbiome and detection of antibiotic resistance genes, general FIB, and human-associated microorganisms were also employed. Results showed that fecal contamination from multiple sources (human, avian, dog, and ruminant), as well as FIB, enteric microorganisms, and antibiotic resistance genes increased demonstrably after a storm event. In summary, the addition of qPCR and WMS to traditional surrogate techniques may provide enhanced characterization and improved understanding of microbial pollution sources in ambient waters.
Collapse
Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | | | - Orin C. Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincin nati, OH, United States
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincin nati, OH, United States
| | - Jessica Hey
- U.S. Environmental Protection Agency, Office of Research and Development, Cincin nati, OH, United States
| | - Nur A. Hasan
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
- CosmosID Inc., Rockville, MD, United States
- Correspondence: Rita R. Colwell , Menu B. Leddy
| | - Menu B. Leddy
- Essential Environmental and Engineering Systems, Huntington Beach, CA, United States
- Correspondence: Rita R. Colwell , Menu B. Leddy
| |
Collapse
|
21
|
Oliver JP, Hurst JJ, Gooch CA, Stappenbeck A, Sassoubre L, Aga DS. On-farm screw press and rotary drum treatment of dairy manure-associated antibiotic residues and resistance. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:134-143. [PMID: 33438205 DOI: 10.1002/jeq2.20161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 08/22/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
An on-farm solid-liquid separator (SLS) and rotary drum composter (RD) manure treatment system was monitored for its impact on antibiotic residues and antibiotic resistance genes (ARGs). Administered antibiotics were tracked, and treatment system mass flows were quantified. Total amounts of antibiotic residues and ARGs were calculated from measured concentrations and mass flows. Only oxytetracycline (OTC) and sulfadimethoxine (SDM) were detected in the manure treatment system influent. No β-lactams were measured despite comprising ∼25% of the antibiotics administered. Nearly 80% of OTC and >90% of SDM partitioned into SLS liquid effluent (SL). The RD reduced the mass of OTC remaining in the SLS solid effluent (SS) significantly by 50%, whereas the mass of SDM appeared to increase after RD treatment. All four ARGs tested were detected in influent, with >70% of the sul1, blaOXA-1 , and intI1 genes (normalized by the 16S ribosomal RNA gene) partitioning into the SL. In contrast, about eight times more normalized tetO gene copies partitioned into the SS than in the SL. All ARGs remaining in the SS were significantly reduced by the RD treatment, with a noteworthy 98% reduction in normalized tetO gene copies. This study provides insight into on-farm levels of antibiotic residues and ARGs in dairy manure, their partitioning during SLS treatment, and their fate after a high-temperature RD treatment reaching 72.2 ± 0.18 °C near the outlet. It also notes the importance of mass-flow standardization of data, and the need to work towards standardization of manure system sampling protocols for antibiotic residues and ARGs.
Collapse
Affiliation(s)
- Jason P Oliver
- Animal Science, PRO-DAIRY Dairy Environmental Systems Program, Cornell Univ., Ithaca, NY, 14853, USA
- Agricultural Sciences, Groton Central School District, Groton, NY, 13073, USA
| | - Jerod J Hurst
- Chemistry, Univ. at Buffalo, The State Univ. of New York, Buffalo, NY, 14260, USA
| | - Curt A Gooch
- Animal Science, PRO-DAIRY Dairy Environmental Systems Program, Cornell Univ., Ithaca, NY, 14853, USA
| | - Ashley Stappenbeck
- Animal Science, PRO-DAIRY Dairy Environmental Systems Program, Cornell Univ., Ithaca, NY, 14853, USA
| | - Lauren Sassoubre
- Civil, Structural & Environmental Engineering, Univ. of Buffalo, The State Univ. of New York, Buffalo, NY, 14260, USA
- Dep. of Engineering, Univ. of San Francisco, San Francisco, CA, 94117, USA
| | - Diana S Aga
- Chemistry, Univ. at Buffalo, The State Univ. of New York, Buffalo, NY, 14260, USA
| |
Collapse
|
22
|
Jennings WC, Gálvez-Arango E, Prieto AL, Boehm AB. CrAssphage for fecal source tracking in Chile: Covariation with norovirus, HF183, and bacterial indicators. WATER RESEARCH X 2020; 9:100071. [PMID: 33083778 PMCID: PMC7552103 DOI: 10.1016/j.wroa.2020.100071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/20/2020] [Accepted: 09/26/2020] [Indexed: 05/12/2023]
Abstract
Anthropogenic fecal pollution in urban waterbodies can promote the spread of waterborne disease. The objective of this study was to test crAssphage, a novel viral human fecal marker not previously applied for fecal source tracking in Latin America, as a fecal pollution marker in an urban river in Chile. Human fecal markers crAssphage CPQ_064 and Bacteroides HF183, the human pathogen norovirus GII, and culturable fecal indicator bacteria (FIB) were quantified at six locations spanning reaches of the Mapocho River from upstream to downstream of Santiago, as well as in repeated sub-daily frequency samples at two urban locations. Norovirus showed positive correlation trends with crAssphage (τ = 0.57, p = 0.06) and HF183 (τ = 0.64, p = 0.03) in river water, but not with E. coli or enterococci. CrAssphage and HF183 concentrations were strongly linearly related (slope = 0.97, p < 0.001). Chlorinated wastewater effluent was an important source of norovirus GII genes to the Mapocho. Precipitation showed non-significant positive relationships with human and general fecal indicators. Concentrations of crAssphage and HF183 in untreated sewage were 8.35 and 8.07 log10 copy/100 ml, respectively. Preliminary specificity testing did not detect crAssphage or HF183 in bird or dog feces, which are predominant non-human fecal sources in the urban Mapocho watershed. This study is the first to test crAssphage for microbial source tracking in Latin America, provides insight into fecal pollution dynamics in a highly engineered natural system, and indicates river reaches where exposure to human fecal pollution may pose a public health risk.
Collapse
Affiliation(s)
- Wiley C. Jennings
- 473 Via Ortega, Room 189, Department of Civil & Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Ana L. Prieto
- Departamento de Ingeniería Civil, Universidad de Chile, Av. Blanco Encalada 2002, 3er Piso, Santiago, Chile
| | - Alexandria B. Boehm
- 473 Via Ortega, Room 189, Department of Civil & Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
- Corresponding author.
| |
Collapse
|
23
|
Harvey AP, Fuhrmeister ER, Cantrell M, Pitol AK, Swarthout JM, Powers JE, Nadimpalli ML, Julian TR, Pickering AJ. Longitudinal monitoring of SARS-CoV-2 RNA on high-touch surfaces in a community setting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.10.27.20220905. [PMID: 33140065 PMCID: PMC7605577 DOI: 10.1101/2020.10.27.20220905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3 %) surface samples were positive for SARS-CoV-2, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000), suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n=33 unique surfaces per week) best predicted variation in city-level COVID-19 cases using a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces could be a useful tool to provide early warning of COVID-19 case trends.
Collapse
Affiliation(s)
- Abigail P. Harvey
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | | | - Molly Cantrell
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Ana K. Pitol
- Department of Civil and Environmental Engineering, Imperial College London, United Kingdom
| | - Jenna M. Swarthout
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Julie E. Powers
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Maya L. Nadimpalli
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf CH-8600, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Amy J. Pickering
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02155
- Department of Civil and Environmental Engineering, University of California, Berkeley
| |
Collapse
|
24
|
Mattioli MC, Benedict KM, Murphy J, Kahler A, Kline KE, Longenberger A, Mitchell PK, Watkins S, Berger P, Shanks OC, Barrett CE, Barclay L, Hall AJ, Hill V, Weltman A. Identifying septic pollution exposure routes during a waterborne norovirus outbreak - A new application for human-associated microbial source tracking qPCR. J Microbiol Methods 2020; 180:106091. [PMID: 33137355 DOI: 10.1016/j.mimet.2020.106091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 11/18/2022]
Abstract
In June 2017, the Pennsylvania Department of Health (PADOH) was notified of multiple norovirus outbreaks associated with 179 ill individuals who attended separate events held at an outdoor venue and campground over a month period. Epidemiologic investigations were unable to identify a single exposure route and therefore unable to determine whether there was a persistent contamination source to target for exposure mitigation. Norovirus was detected in a fresh recreational water designated swimming area and a drinking water well. A hydrogeological site evaluation suggested a nearby septic leach field as a potential contamination source via ground water infiltration. Geological characterization revealed a steep dip of the bedrock beneath the septic leach field toward the well, providing a viral transport pathway in a geologic medium not previously documented as high risk for viral ground water contamination. The human-associated microbial source tracking (MST) genetic marker, HF183, was used as a microbial tracer to demonstrate the hydrogeological connection between the malfunctioning septic system, drinking water well, and recreational water area. Based on environmental investigation findings, venue management and local public health officials implemented a series of outbreak prevention strategies including discontinuing the use of the contaminated well, issuing a permit for a new drinking water well, increasing portable toilet and handwashing station availability, and promoting proper hand hygiene. Despite the outbreaks at the venue and evidence of ground water contamination impacting nearby recreational water and the drinking water well, no new norovirus cases were reported during a large event one week after implementing prevention practices. This investigation highlights a new application for human-associated MST methods to trace hydrological connections between multiple fecal pollutant exposure routes in an outbreak scenario. In turn, pollutant source information can be used to develop effective intervention practices to mitigate exposure and prevent future outbreaks associated with human fecal contaminated waters.
Collapse
Affiliation(s)
- Mia C Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA.
| | - Katharine M Benedict
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Jennifer Murphy
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Amy Kahler
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Kelly E Kline
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| | - Allison Longenberger
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| | - Patrick K Mitchell
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA; Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sharon Watkins
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| | - Philip Berger
- U.S. Environmental Protection Agency, Office of Ground Water and Drinking Water, Washington, DC, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Catherine E Barrett
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Leslie Barclay
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, USA
| | - Aron J Hall
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, USA
| | - Vincent Hill
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, USA
| | - Andre Weltman
- Pennsylvania Department of Health, Division of Infectious Disease Epidemiology, USA
| |
Collapse
|
25
|
Kongprajug A, Chyerochana N, Mongkolsuk S, Sirikanchana K. Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8232-8244. [PMID: 32484662 DOI: 10.1021/acs.est.0c01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log10 copies/g and 0.41 log10 copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log10 copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.
Collapse
Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| |
Collapse
|
26
|
Shrestha A, Dorevitch S. Slow adoption of rapid testing: Beach monitoring and notification using qPCR. J Microbiol Methods 2020; 174:105947. [DOI: 10.1016/j.mimet.2020.105947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 01/03/2023]
|
27
|
Brown MS, Evans BS, Afonso LOB. Discordance for genotypic sex in phenotypic female Atlantic salmon (Salmo salar) is related to a reduced sdY copy number. Sci Rep 2020; 10:9651. [PMID: 32541863 PMCID: PMC7296011 DOI: 10.1038/s41598-020-66406-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/18/2020] [Indexed: 11/10/2022] Open
Abstract
The master sex determinant in rainbow trout (Oncorhynchus mykiss), sexually dimorphic on the Y chromosome (sdY), is strongly but not perfectly associated with male phenotype in several other species from the family Salmonidae. Currently, the cause and implications of discordance for sdY-predicted genotypic sex and phenotypic sex in these species is unclear. Using an established multiplex PCR test for exons 2 and 3 of sdY, we demonstrated that sdY-predicted genotypic sex was discordant with histologically evidenced phenotypic sex in 4% of 176 Tasmanian Atlantic salmon. All discordant individuals were phenotypic females presenting a male genotype. Using real-time qPCR assays that we developed and validated for exons 2, 3 and 4 of sdY, all genotype-phenotype discordant females were confirmed to possess sdY, albeit at a reduced number of copies when compared to phenotypic males. The real-time qPCR assays also demonstrated reduced levels of sdY in 30% of phenotypic females that the established multiplex PCR-based test indicated to be devoid of sdY. These findings suggest sdY may be reduced in copy number or mosaicked in the genomic DNA of sdY-positive phenotypic female Atlantic salmon and highlight the importance of understanding the effects of reduced sdY copies on the development of phenotypic sex.
Collapse
Affiliation(s)
- Morgan S Brown
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University Warrnambool Campus, Warrnambool, Victoria, 3280, Australia
| | - Brad S Evans
- Breeding & Research, Tassal Operations, Hobart, Tasmania, 7000, Australia
| | - Luis O B Afonso
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University Warrnambool Campus, Warrnambool, Victoria, 3280, Australia.
| |
Collapse
|
28
|
Holcomb DA, Knee J, Sumner T, Adriano Z, de Bruijn E, Nalá R, Cumming O, Brown J, Stewart JR. Human fecal contamination of water, soil, and surfaces in households sharing poor-quality sanitation facilities in Maputo, Mozambique. Int J Hyg Environ Health 2020; 226:113496. [PMID: 32135507 PMCID: PMC7174141 DOI: 10.1016/j.ijheh.2020.113496] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/09/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Identifying the origin of fecal contamination can support more effective interventions to interrupt enteric pathogen transmission. Microbial source tracking (MST) assays may help to identify environmental routes of pathogen transmission although these assays have performed poorly in highly contaminated domestic settings, highlighting the importance of both diagnostic validation and understanding the context-specific ecological, physical, and sociodemographic factors driving the spread of fecal contamination. We assessed fecal contamination of compounds (clusters of 2-10 households that share sanitation facilities) in low-income neighborhoods of urban Maputo, Mozambique, using a set of MST assays that were validated with animal stool and latrine sludge from study compounds. We sampled five environmental compartments involved in fecal microbe transmission and exposure: compound water source, household stored water and food preparation surfaces, and soil from the entrance to the compound latrine and the entrances to each household. Each sample was analyzed by culture for the general fecal indicator Escherichia coli (cEC) and by real-time PCR for the E. coli molecular marker EC23S857, human-associated markers HF183/BacR287 and Mnif, and GFD, an avian-associated marker. We collected 366 samples from 94 households in 58 compounds. At least one microbial target (indicator organism or marker gene) was detected in 96% of samples (353/366), with both E. coli targets present in the majority of samples (78%). Human targets were frequently detected in soils (59%) and occasionally in stored water (17%) but seldom in source water or on food surfaces. The avian target GFD was rarely detected in any sample type but was most common in soils (4%). To identify risk factors of fecal contamination, we estimated associations with sociodemographic, meteorological, and physical sample characteristics for each microbial target and sample type combination using Bayesian censored regression for target concentration responses and Bayesian logistic regression for target detection status. Associations with risk factors were generally weak and often differed in direction between different targets and sample types, though relationships were somewhat more consistent for physical sample characteristics. Wet soils were associated with elevated concentrations of cEC and EC23S857 and odds of detecting HF183. Water storage container characteristics that expose the contents to potential contact with hands and other objects were weakly associated with human target detection. Our results describe a setting impacted by pervasive domestic fecal contamination, including from human sources, that was largely disconnected from the observed variation in socioeconomic and sanitary conditions. This pattern suggests that in such highly contaminated settings, transformational changes to the community environment may be required before meaningful impacts on fecal contamination can be realized.
Collapse
Affiliation(s)
- David A Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Zaida Adriano
- We Consult, Maputo, Mozambique; Departamento de Geografia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
| |
Collapse
|
29
|
Chyerochana N, Kongprajug A, Somnark P, Leelapanang Kamphaengthong P, Mongkolsuk S, Sirikanchana K. Distributions of enterococci and human-specific bacteriophages of enterococci in a tropical watershed. Int J Hyg Environ Health 2020; 226:113482. [DOI: 10.1016/j.ijheh.2020.113482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/17/2020] [Accepted: 02/04/2020] [Indexed: 01/10/2023]
|
30
|
Fuhrmeister E, Ercumen A, Pickering AJ, Jeanis KM, Crider Y, Ahmed M, Brown S, Alam M, Sen D, Islam S, Kabir MH, Islam M, Rahman M, Kwong LH, Arnold BF, Luby SP, Colford JM, Nelson KL. Effect of Sanitation Improvements on Pathogens and Microbial Source Tracking Markers in the Rural Bangladeshi Household Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4316-4326. [PMID: 32167305 PMCID: PMC7144219 DOI: 10.1021/acs.est.9b04835] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 05/19/2023]
Abstract
Diarrheal illnesses from enteric pathogens are a leading cause of death in children under five in low- and middle-income countries (LMICs). Sanitation is one way to reduce the spread of enteric pathogens in the environment; however, few studies have investigated the effectiveness of sanitation in rural LMICs in reducing pathogens in the environment. In this study, we measured the impact of a sanitation intervention (dual-pit latrines, sani-scoops, child potties delivered as part of a randomized control trial, WASH Benefits) in rural Bangladeshi household compounds by assessing prevalence ratios, differences, and changes in the concentration of pathogen genes and host-specific fecal markers. We found no difference in the prevalence of pathogenic Escherichia coli, norovirus, or Giardia genes in the domestic environment in the sanitation and control arms. The prevalence of the human fecal marker was lower on child hands and the concentration of animal fecal marker was lower on mother hands in the sanitation arm in adjusted models, but these associations were not significant after correcting for multiple comparisons. In the subset of households with ≥10 individuals per compound, the prevalence of enterotoxigenic E. coli genes on child hands was lower in the sanitation arm. Incomplete removal of child and animal feces or the compound (versus community-wide) scale of intervention could explain the limited impacts of improved sanitation.
Collapse
Affiliation(s)
- Erica
R. Fuhrmeister
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Ayse Ercumen
- School
of Public Health, University of California, Berkeley, California 94720, United States
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Amy J. Pickering
- Civil
and Environmental Engineering, Tufts University, Medford, Massachusetts 02153, United States
| | - Kaitlyn M. Jeanis
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Yoshika Crider
- Energy
and Resources Group, University of California, Berkeley, California 94720, United States
| | - Mahaa Ahmed
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Sara Brown
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Mahfuja Alam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Debashis Sen
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Sharmin Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Mir Himayet Kabir
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Mahfuza Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Mahbubur Rahman
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Laura H. Kwong
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Benjamin F. Arnold
- School
of Public Health, University of California, Berkeley, California 94720, United States
| | - Stephen P. Luby
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
| | - John M. Colford
- School
of Public Health, University of California, Berkeley, California 94720, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
31
|
Viral and Bacterial Fecal Indicators in Untreated Wastewater across the Contiguous United States Exhibit Geospatial Trends. Appl Environ Microbiol 2020; 86:AEM.02967-19. [PMID: 32060019 DOI: 10.1128/aem.02967-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cultivated fecal indicator bacteria such as Escherichia coli and enterococci are typically used to assess the sanitary quality of recreational waters. However, these indicators suffer from several limitations, such as the length of time needed to obtain results and the fact that they are commensal inhabitants of the gastrointestinal tract of many animals and have fate and transport characteristics dissimilar to pathogenic viruses. Numerous emerging technologies that offer same-day water quality results or pollution source information or that more closely mimic persistence patterns of disease-causing pathogens that may improve water quality management are now available, but data detailing geospatial trends in wastewater across the United States are sparse. We report geospatial trends of cultivated bacteriophage (somatic, F+, and total coliphages and GB-124 phage), as well as genetic markers targeting polyomavirus, enterococci, E. coli, Bacteroidetes, and human-associated Bacteroides spp. (HF183/BacR287 and HumM2) in 49 primary influent sewage samples collected from facilities across the contiguous United States. Samples were selected from rural and urban facilities spanning broad latitude, longitude, elevation, and air temperature gradients by using a geographic information system stratified random site selection procedure. Most indicators in sewage demonstrated a remarkable similarity in concentration regardless of location. However, some exhibited predictable shifts in concentration based on either facility elevation or local air temperature. Geospatial patterns identified in this study, or the absence of such patterns, may have several impacts on the direction of future water quality management research, as well as the selection of alternative metrics to estimate sewage pollution on a national scale.IMPORTANCE This study provides multiple insights to consider for the application of bacterial and viral indicators in sewage to surface water quality monitoring across the contiguous United States, ranging from method selection considerations to future research directions. Systematic testing of a large collection of sewage samples confirmed that crAssphage genetic markers occur at a higher average concentration than key human-associated Bacteroides spp. on a national scale. Geospatial testing also suggested that some methods may be more suitable than others for widespread implementation. Nationwide characterization of indicator geospatial trends in untreated sewage represents an important step toward the validation of these newer methods for future water quality monitoring applications. In addition, the large paired-measurement data set reported here affords the opportunity to conduct a range of secondary analyses, such as the generation of new or updated quantitative microbial risk assessment models used to estimate public health risk.
Collapse
|
32
|
Lane MJ, McNair JN, Rediske RR, Briggs S, Sivaganesan M, Haugland R. Simplified Analysis of Measurement Data from A Rapid E. coli qPCR Method (EPA Draft Method C) Using A Standardized Excel Workbook. WATER 2020; 12:1-775. [PMID: 32461809 PMCID: PMC7252523 DOI: 10.3390/w12030775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Draft method C is a standardized method for quantifying E. coli densities in recreational waters using quantitative polymerase chain reaction (qPCR). The method includes a Microsoft Excel workbook that automatically screens for poor-quality data using a set of previously proposed acceptance criteria, generates weighted linear regression (WLR) composite standard curves, and calculates E. coli target gene copies in test samples. We compared standard curve parameter values and test sample results calculated with the WLR model to those from a Bayesian master standard curve (MSC) model using data from a previous multi-lab study. The two models' mean intercept and slope estimates from twenty labs' standard curves were within each other's 95% credible or confidence intervals for all labs. E. coli gene copy estimates of six water samples analyzed by eight labs were highly overlapping among labs when quantified with the WLR and MSC models. Finally, we compared multiple labs' 2016-2018 composite curves, comprised of data from individual curves where acceptance criteria were not used, to their corresponding composite curves with passing acceptance criteria. Composite curves developed from passing individual curves had intercept and slope 95% confidence intervals that were often narrower than without screening and an analysis of covariance test was passed more often. The Excel workbook WLR calculation and acceptance criteria will help laboratories implement draft method C for recreational water analysis in an efficient, cost-effective, and reliable manner.
Collapse
Affiliation(s)
- Molly J. Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
| | - James N. McNair
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
| | - Richard R. Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49401, USA
- Correspondence:
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes, and Energy (EGLE), 525 W. Allegan St., Lansing, MI 48909, USA
| | - Mano Sivaganesan
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. EPA, Cincinnati, OH 45268, USA
| | - Richard Haugland
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. EPA, Cincinnati, OH 45268, USA
| |
Collapse
|
33
|
Chen L, Zhang X, Zhi X, Dai Y, Zhang P, Xiao Y, Shen Z. Tracking faecal microorganisms using the qPCR method in a typical urban catchment in China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:158. [PMID: 32016573 DOI: 10.1007/s10661-020-8130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Faecal microorganisms represent a key threat to human health. Potential origins of faecal microbial contamination in a typical urban-representative micro-scale were evaluated. The quantitative polymerase chain reaction (qPCR) method was used in this study. The Bacteroidetes is selected as the indicative microorganism in runoff samples that are collected during four representative stormwater events in north China. The principal component analysis (PCA) method indicated the distribution feature of the environmental factors. The largest contributor is dog, followed by bird and human to the faecal pollution in stormwater runoff. The output of human and dog faecal pollutants in response to the first flush effect of nonpoint source pollution while the transmit time of bird faecal pollutant is relatively longer. In addition, the number of antecedent drying days represents the key factor for dog faecal pollution, while human faecal pollution is impacted by more factors. The results of this study will provide sound evidence for the tracking and management of nonpoint source faecal pollution in urban catchment areas.
Collapse
Affiliation(s)
- Lei Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiaoyue Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiaosha Zhi
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
- Satellite Environment Centre, Ministry of Environmental Protection, Beijing, 100094, People's Republic of China
| | - Ying Dai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Pu Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Yuechen Xiao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
| |
Collapse
|
34
|
Petcharat T, Kongprajug A, Chyerochana N, Sangkaew W, Mongkolsuk S, Sirikanchana K. Assessing human-specific CrAssphage recovery after acidification-filtration concentrating method in environmental water. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:35-41. [PMID: 31433097 DOI: 10.1002/wer.1209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Pinpointing water pollution sources using host-specific gastrointestinal microbes, known as microbial source tracking (MST), have significant benefits for countries with water quality management issues related to pollution. A recently discovered bacteriophage, crAssphage, shows promise as a human-specific MST marker. However, loss of genetic materials during the recovery and the detection processes could alter the ability to measure virus quantities in a water sample. This study determined the crAssphage recovery efficiencies in water sources, including seawater, freshwater, and influent and effluent from a wastewater treatment plant, by spiking natural crAssphage concentrates prior to DNA extraction and quantitative PCR analysis. The results showed that river and seawater with no or low crAssphage background experienced no recovery loss. Evaluating recovery efficiencies in samples with high crAssphage backgrounds posed a challenge due to the inability to prepare high crAssphage titers. This study highlights the importance of intra-laboratory assessment of recovery efficiency in environmental samples for retrieving absolute crAssphage quantification with correction of bias among water samples and increase in data accuracy. PRACTITIONER POINTS: In laboratory assessment of recovery efficiency is crucial for bias correction and data accuracy for absolute crAssphage quantification in water samples. No loss in crAssphage recovery was observed in river and seawater that contained no or low crAssphage backgrounds. Inability to prepare high crAssphage spike concentrations remains the major limitation for evaluating recovery in samples with high crAssphage backgrounds. The results underline the importance of evaluating method recovery in real environmental samples that reflect actual matrix effect. Absolute crAssphage quantification, as human-specific pollution marker, could be used for prioritizing water quality restoration and area-based management plan.
Collapse
Affiliation(s)
- Thitirat Petcharat
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Watsawan Sangkaew
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| |
Collapse
|
35
|
Fuhrmeister E, Ercumen A, Pickering AJ, Jeanis KM, Ahmed M, Brown S, Arnold BF, Hubbard AE, Alam M, Sen D, Islam S, Kabir MH, Kwong LH, Islam M, Unicomb L, Rahman M, Boehm AB, Luby SP, Colford JM, Nelson KL. Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10023-10033. [PMID: 31356066 PMCID: PMC6727619 DOI: 10.1021/acs.est.8b07192] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 05/19/2023]
Abstract
Fecal indicator organisms are measured to indicate the presence of fecal pollution, yet the association between indicators and pathogens varies by context. The goal of this study was to empirically evaluate the relationships between indicator Escherichia coli, microbial source tracking markers, select enteric pathogen genes, and potential sources of enteric pathogens in 600 rural Bangladeshi households. We measured indicators and pathogen genes in stored drinking water, soil, and on mother and child hands. Additionally, survey and observational data on sanitation and domestic hygiene practices were collected. Log10 concentrations of indicator E. coli were positively associated with the prevalence of pathogenic E. coli genes in all sample types. Given the current need to rely on indicators to assess fecal contamination in the field, it is significant that in this study context indicator E. coli concentrations, measured by IDEXX Colilert-18, provided quantitative information on the presence of pathogenic E. coli in different sample types. There were no significant associations between the human fecal marker (HumM2) and human-specific pathogens in any environmental sample type. There was an increase in the prevalence of Giardia lamblia genes, any E. coli virulence gene, and the specific E. coli virulence genes stx1/2 with every log10 increase in the concentration of the animal fecal marker (BacCow) on mothers' hands. Thus, domestic animals were important contributors to enteric pathogens in these households.
Collapse
Affiliation(s)
- Erica
R. Fuhrmeister
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Ayse Ercumen
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Amy J. Pickering
- Civil
and Environmental Engineering, Tufts University, Medford, Massachusetts 02153, United States
| | - Kaitlyn M. Jeanis
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Mahaa Ahmed
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Sara Brown
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Benjamin F. Arnold
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Alan E. Hubbard
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Mahfuja Alam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Debashis Sen
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Sharmin Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Mir Himayet Kabir
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Laura H. Kwong
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Mahfuza Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Leanne Unicomb
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Mahbubur Rahman
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Alexandria B. Boehm
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Stephen P. Luby
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
| | - John M. Colford
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
36
|
Aw TG, Sivaganesan M, Briggs S, Dreelin E, Aslan A, Dorevitch S, Shrestha A, Isaacs N, Kinzelman J, Kleinheinz G, Noble R, Rediske R, Scull B, Rosenberg S, Weberman B, Sivy T, Southwell B, Siefring S, Oshima K, Haugland R. Evaluation of multiple laboratory performance and variability in analysis of recreational freshwaters by a rapid Escherichia coli qPCR method (Draft Method C). WATER RESEARCH 2019; 156:465-474. [PMID: 30953844 PMCID: PMC9994418 DOI: 10.1016/j.watres.2019.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 06/01/2023]
Abstract
There is interest in the application of rapid quantitative polymerase chain reaction (qPCR) methods for recreational freshwater quality monitoring of the fecal indicator bacteria Escherichia coli (E. coli). In this study we determined the performance of 21 laboratories in meeting proposed, standardized data quality acceptance (QA) criteria and the variability of target gene copy estimates from these laboratories in analyses of 18 shared surface water samples by a draft qPCR method developed by the U.S. Environmental Protection Agency (EPA) for E. coli. The participating laboratories ranged from academic and government laboratories with more extensive qPCR experience to "new" water quality and public health laboratories with relatively little previous experience in most cases. Failures to meet QA criteria for the method were observed in 24% of the total 376 test sample analyses. Of these failures, 39% came from two of the "new" laboratories. Likely factors contributing to QA failures included deviations in recommended procedures for the storage and preparation of reference and control materials. A master standard curve calibration model was also found to give lower overall variability in log10 target gene copy estimates than the delta-delta Ct (ΔΔCt) calibration model used in previous EPA qPCR methods. However, differences between the mean estimates from the two models were not significant and variability between laboratories was the greatest contributor to overall method variability in either case. Study findings demonstrate the technical feasibility of multiple laboratories implementing this or other qPCR water quality monitoring methods with similar data quality acceptance criteria but suggest that additional practice and/or assistance may be valuable, even for some more generally experienced qPCR laboratories. Special attention should be placed on providing and following explicit guidance on the preparation, storage and handling of reference and control materials.
Collapse
Affiliation(s)
- Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Shannon Briggs
- Water Resources Division, Michigan Department of Environmental Quality, P. O. Box 30458, 525 West Allegan Street, Lansing, MI, 48909, USA
| | - Erin Dreelin
- Center for Water Sciences, Michigan State University, 1405 South Harrison Road, East Lansing, MI, 48823, USA
| | - Asli Aslan
- Georgia Southern University, Department of Environmental Health Sciences, 501 Forest Drive, Statesboro, GA, 30458, USA
| | - Samuel Dorevitch
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Abhilasha Shrestha
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Natasha Isaacs
- U.S. Geological Survey, Upper Midwest Water Science Center, 6520 Mercantile Way, Ste 5, Lansing, MI, 48911, USA
| | - Julie Kinzelman
- City of Racine Public Health Department, 730 Washington Ave, Racine, WI, 53403, USA
| | - Greg Kleinheinz
- University of Wisconsin-Oshkosh, Environmental Research Laboratory, 800 Algoma Boulevard, Oshkosh, WI, 54901, USA
| | - Rachel Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC, 28557, USA
| | - Rick Rediske
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Brian Scull
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Susan Rosenberg
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Barbara Weberman
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI, 48710, USA
| | - Ben Southwell
- Lake Superior State University, Environmental Analysis Laboratory, 650 W. Easterday Ave, Sault Ste Marie, MI, 49783, USA
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA.
| |
Collapse
|
37
|
Sivaganesan M, Aw TG, Briggs S, Dreelin E, Aslan A, Dorevitch S, Shrestha A, Isaacs N, Kinzelman J, Kleinheinz G, Noble R, Rediske R, Scull B, Rosenberg S, Weberman B, Sivy T, Southwell B, Siefring S, Oshima K, Haugland R. Standardized data quality acceptance criteria for a rapid Escherichia coli qPCR method (Draft Method C) for water quality monitoring at recreational beaches. WATER RESEARCH 2019; 156:456-464. [PMID: 30952079 PMCID: PMC9943056 DOI: 10.1016/j.watres.2019.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 05/31/2023]
Abstract
There is growing interest in the application of rapid quantitative polymerase chain reaction (qPCR) and other PCR-based methods for recreational water quality monitoring and management programs. This interest has strengthened given the publication of U.S. Environmental Protection Agency (EPA)-validated qPCR methods for enterococci fecal indicator bacteria (FIB) and has extended to similar methods for Escherichia coli (E. coli) FIB. Implementation of qPCR-based methods in monitoring programs can be facilitated by confidence in the quality of the data produced by these methods. Data quality can be determined through the establishment of a series of specifications that should reflect good laboratory practice. Ideally, these specifications will also account for the typical variability of data coming from multiple users of the method. This study developed proposed standardized data quality acceptance criteria that were established for important calibration model parameters and/or controls from a new qPCR method for E. coli (EPA Draft Method C) based upon data that was generated by 21 laboratories. Each laboratory followed a standardized protocol utilizing the same prescribed reagents and reference and control materials. After removal of outliers, statistical modeling based on a hierarchical Bayesian method was used to establish metrics for assay standard curve slope, intercept and lower limit of quantification that included between-laboratory, replicate testing within laboratory, and random error variability. A nested analysis of variance (ANOVA) was used to establish metrics for calibrator/positive control, negative control, and replicate sample analysis data. These data acceptance criteria should help those who may evaluate the technical quality of future findings from the method, as well as those who might use the method in the future. Furthermore, these benchmarks and the approaches described for determining them may be helpful to method users seeking to establish comparable laboratory-specific criteria if changes in the reference and/or control materials must be made.
Collapse
Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, National Risk Management Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Shannon Briggs
- Water Resources Division, Michigan Department of Environmental Quality, P. O. Box 30458, 525 West Allegan Street, Lansing, MI, 48909, USA
| | - Erin Dreelin
- Center for Water Sciences, Michigan State University, 1405 South Harrison Road, East Lansing, MI, 48823, USA
| | - Asli Aslan
- Georgia Southern University, Department of Environmental Health Sciences, 501 Forest Drive, Statesboro, GA, 30458, USA
| | - Samuel Dorevitch
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Abhilasha Shrestha
- University of Illinois at Chicago, School of Public Health, 2121 W. Taylor Street, Chicago, IL, 60612, USA
| | - Natasha Isaacs
- U.S. Geological Survey, Upper Midwest Water Science Center, 6520 Mercantile Way, Ste 5, Lansing, MI, 48911, USA
| | - Julie Kinzelman
- City of Racine Public Health Department, 730 Washington Ave, Racine, WI, 53403, USA
| | - Greg Kleinheinz
- University of Wisconsin-Oshkosh, Environmental Research Laboratory, 800 Algoma Boulevard, Oshkosh, WI, 54901, USA
| | - Rachel Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC, 28557, USA
| | - Rick Rediske
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Brian Scull
- Annis Water Resources Institute, Lake Michigan Center, 740 W. Shoreline Dr, Muskegon, MI, 49441, USA
| | - Susan Rosenberg
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Barbara Weberman
- Oakland County Health Division Laboratory, 1200 N. Telegraph, Pontiac, MI, 48341, USA
| | - Tami Sivy
- Saginaw Valley State University, Department of Chemistry, 7400 Bay Road, University Center, MI, 48710, USA
| | - Ben Southwell
- Lake Superior State University, Environmental Analysis Laboratory, 650 W. Easterday Ave, Sault Ste Marie, MI, 49783, USA
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Kevin Oshima
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr, Cincinnati, OH, 45268, USA.
| |
Collapse
|
38
|
Shrestha A, Dorevitch S. Evaluation of rapid qPCR method for quantification of E. coli at non-point source impacted Lake Michigan beaches. WATER RESEARCH 2019; 156:395-403. [PMID: 30933697 DOI: 10.1016/j.watres.2019.03.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/06/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Most Great Lakes communities rely on culture-based E. coli methods for monitoring fecal indicator bacteria (FIB) at recreational beaches. These cultivation methods require 18 or more hours to generate results. As a consequence, public notifications about beach action value (BAV) exceedance are based on prior-day water quality. Rapid qPCR monitoring of bacteria in beach water solves the 24-h delay problem, though the USEPA-approved qPCR method targets enterococci bacteria, while Great Lakes communities are familiar with E. coli monitoring. For an E. coli qPCR method to be useful for water quality management, it is important to systematically characterize method performance, and establish BAVs for public notification purposes. In this study, we 1) evaluated a draft USEPA E. coli qPCR method, 2) compared E. coli qPCR measurements with two established FIB (E. coli culture and enterococci qPCR) results, and explored potential strategies to establish E. coli qPCR BAV criteria in the absence of an epidemiological study. Based on analyses of 288 water samples collected from eight of Chicago's Lake Michigan beaches, the E. coli qPCR method demonstrates acceptable performance characteristics. The method is prone to low level DNA contamination, possibly originating from assay reagents derived from E. coli bacteria. Both E. coli and enterococci BAVs were exceeded in approximately 18% of the samples. E. coli qPCR values were correlated with both E. coli culture (r = 0.83; p < 0.0001) and enterococci qPCR (r = 0.67; p < 0.0001) values. The approach recommended by the USEPA in its Technical Support Material (TSM) was used to generate candidate E. coli qPCR BAVs, as was receiver operating characteristic (ROC) analysis. Potential BAV thresholds differed substantially, ranging from 200.9 calibrator cell equivalents (CCE)/100 mL (ROC analysis, enterococci qPCR BAV as the reference) to 1000 CCE/100 mL (TSM analysis, enterococci qPCR BAV as the reference). Because we found that different approaches to establishing potential BAVs generate quite different values, guidance from USEPA about approaches to defining comparable BAVs would be useful.
Collapse
Affiliation(s)
- Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, USA.
| | - Samuel Dorevitch
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, USA
| |
Collapse
|
39
|
Burnet JB, Dinh QT, Imbeault S, Servais P, Dorner S, Prévost M. Autonomous online measurement of β-D-glucuronidase activity in surface water: is it suitable for rapid E. coli monitoring? WATER RESEARCH 2019; 152:241-250. [PMID: 30677635 DOI: 10.1016/j.watres.2018.12.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/21/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Microbiological water quality is traditionally assessed using culture-based enumeration of faecal indicator bacteria such as Escherichia coli. Despite their relative ease of use, these methods require a minimal 18-24 h-incubation step before the results are obtained. This study aimed to assess the suitability of an autonomous online fluorescence-based technology measuring β-glucuronidase (GLUC) activity for rapid near-real time monitoring of E. coli in water. The analytical precision was determined and compared to an automated microbial detection system, two culture-based assays and quantitative real-time PCR (qPCR). Using replicate measurements of grab samples containing E. coli concentrations between 50 and 2330 CFU.100 mL-1, the autonomous GLUC activity measurement technology displayed an average coefficient of variation (CV) of less than 5% that was 4-8-fold lower than other methods tested. Comparable precision was observed during online in situ monitoring of GLUC activity at a drinking water intake using three independent instruments. GLUC activity measurements were not affected by sewage or sediments at concentrations likely to be encountered during long-term monitoring. Furthermore, significant (p < 0.05) correlations were obtained between GLUC activity and the other assays including defined substrate technology (r = 0.77), membrane filtration (r = 0.73), qPCR (r = 0.55) and the automated microbial detection system (r = 0.50). This study is the first to thoroughly compare the analytical performance of rapid automated detection technologies to established culture and molecular-based methods. Results show that further research is required to correlate GLUC activity to the presence of viable E. coli as measured in terms of CFU.100 mL-1. This would allow the use of autonomous online GLUC activity measurements for rapid E. coli monitoring in water supplies used for drinking water production and recreation.
Collapse
Affiliation(s)
- Jean-Baptiste Burnet
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological, and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, H3C 3A7, Canada; Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, H3C 3A7, Canada.
| | - Quoc Tuc Dinh
- Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, H3C 3A7, Canada
| | - Sandra Imbeault
- Service de l'Environnement, Ville de Laval, QC, H7L 2R3, Canada
| | - Pierre Servais
- Écologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Sarah Dorner
- Canada Research Chair in Source Water Protection, Department of Civil, Geological, and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, H3C 3A7, Canada
| | - Michèle Prévost
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological, and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, H3C 3A7, Canada
| |
Collapse
|
40
|
Hurst JJ, Oliver JP, Schueler J, Gooch C, Lansing S, Crossette E, Wigginton K, Raskin L, Aga DS, Sassoubre LM. Trends in Antimicrobial Resistance Genes in Manure Blend Pits and Long-Term Storage Across Dairy Farms with Comparisons to Antimicrobial Usage and Residual Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2405-2415. [PMID: 30707579 DOI: 10.1021/acs.est.8b05702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The use of antimicrobials by the livestock industry can lead to the release of unmetabolized antimicrobials and antimicrobial resistance genes (ARG) into the environment. However, the relationship between antimicrobial use, residual antimicrobials, and ARG prevalence within manure is not well understood, specifically across temporal and location-based scales. The current study determined ARG abundance in untreated manure blend pits and long-term storage systems from 11 conventional and one antimicrobial-free dairy farms in the Northeastern U.S. at six times over one-year. Thirteen ARGs corresponding to resistance mechanisms for tetracyclines, macrolides-lincosamides, sulfonamides, aminoglycosides, and β-lactams were quantified using a Custom qPCR Array or targeted qPCR. ARG abundance differed between locations, suggesting farm specific microbial resistomes. ARG abundance also varied temporally. Manure collected during the winter contained lower ARG abundances. Overall, normalized ARG concentrations did not correlate to average antimicrobial usage or tetracycline concentrations across farms and collection dates. Of the 13 ARGs analyzed, only four genes showed a higher abundance in samples from conventional farms and eight ARGs exhibited similar normalized concentrations in the conventional and antimicrobial-free farm samples. No clear trends were observed in ARG abundance between dairy manure obtained from blend pits and long-term storage collected during two drawdown periods (fall and spring), although higher ARG abundances were generally observed in spring compared to fall. This comprehensive study informs future studies needed to determine the contributions of ARGs from dairy manure to the environment.
Collapse
Affiliation(s)
- Jerod J Hurst
- Department of Chemistry , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| | - Jason P Oliver
- Department of Animal Sciences , Cornell University , Ithaca , New York 14850 , United States
| | - Jenna Schueler
- Department of Environmental Science & Technology , University of Maryland , College Park , Maryland 20742 , United States
| | - Curt Gooch
- Department of Animal Sciences , Cornell University , Ithaca , New York 14850 , United States
| | - Stephanie Lansing
- Department of Environmental Science & Technology , University of Maryland , College Park , Maryland 20742 , United States
| | - Emily Crossette
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Diana S Aga
- Department of Chemistry , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| | - Lauren M Sassoubre
- Department of Civil, Structural, and Environmental Engineering , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| |
Collapse
|
41
|
Kongprajug A, Chyerochana N, Somnark P, Leelapanang Kampaengthong P, Mongkolsuk S, Sirikanchana K. Human and animal microbial source tracking in a tropical river with multiple land use activities. Int J Hyg Environ Health 2019; 222:645-654. [PMID: 30686524 DOI: 10.1016/j.ijheh.2019.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/26/2018] [Accepted: 01/17/2019] [Indexed: 12/27/2022]
Abstract
The enhancement and restoration of the water quality of deteriorating surface water resources can be challenging, particularly for rivers with multiple usages, such as agriculture, animal husbandry, human residence, and industries. Recently, the performance of DNA-based microbial source tracking (MST) indicators detected by end-point and quantitative PCR assays for identifying sources of fecal pollution from human sewage, swine, and cattle and non-host-specific (universal) fecal pollution in the Tha Chin River basin, Thailand, was evaluated. The present study monitored these validated MST markers and various physicochemical and microbial water quality parameters in samples collected from twelve stations along the Tha Chin River during four sampling events in the wet and dry seasons. No significant difference in precipitation was observed between the wet and dry samplings. Universal markers (both PCR and qPCR) were detected in all 48 samples, indicating persistent and continuing fecal contamination. The sewage- and swine-specific qPCR marker concentrations did not vary among the sampling events, whereas cattle-specific qPCR markers were detected only in the wet season. Animal-specific markers were detected in the lower Tha Chin River section, which is characterized by intensive animal farming. Sewage-specific markers were also found in the lower section and near an upstream residential area. The high agreement (87.5-100%) between the PCR and qPCR results suggested that PCR could serve as a lower-cost MST screening test that requires less technical expertise. A multivariate analysis conducted using the survival analysis procedure to include censored data also emphasized the high pollution in the lower section of the river at all sampling events. Universal and swine-specific markers showed moderate correlations with microbial indicators, including total coliforms, fecal coliforms, E. coli, and enterococci. None of the MST markers or microbial parameters were associated with the measured physicochemical parameters. This study provides the first evaluation of MST markers for monitoring surface freshwater in Thailand, and the findings might aid the pollution surveillance of impaired water bodies and the development of strategies for improving their water quality.
Collapse
Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Pornjira Somnark
- Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Pinida Leelapanang Kampaengthong
- Water Quality Management Bureau, Pollution Control Department, Ministry of Natural Resources and Environment, Bangkok, 10400, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.
| |
Collapse
|
42
|
Mullen RA, Hurst JJ, Naas KM, Sassoubre LM, Aga DS. Assessing uptake of antimicrobials by Zea mays L. and prevalence of antimicrobial resistance genes in manure-fertilized soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:409-415. [PMID: 30056230 DOI: 10.1016/j.scitotenv.2018.07.199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/15/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
Manure-borne antimicrobials and antimicrobial resistance genes (ARGs) are of environmental concern due to their potential to be transferred into the food-web via plant-uptake. In this study, Zea mays L. seeds were grown in three different soil conditions: soil without dairy manure, dairy manure-amended soil, and antimicrobial spiked dairy manure-amended soil, to investigate the potential uptake of antimicrobials and ARGs present in manure. The antimicrobial spiked manure consisted of dairy manure fortified with 1 mg/Kg of each individual antimicrobial compounds belonging to the sulfonamide and tetracycline classes. Samples of the Zea mays L. plants were harvested over the course of three weeks to determine potential uptake of antimicrobials from soil to plant shoots, and to compare prevalence of ARGs in manure amended soils and plant tissue. Antimicrobial analysis was performed using liquid chromatography with tandem mass spectrometry (LC-MS/MS), and ARGs (sul1, tetO, and OXA-1) were analyzed using quantitative polymerase chain reaction (qPCR). The study found that both tetracycline and sulfamerazine antimicrobials bioaccumulated in the Zea mays L., reaching concentrations of nearly 3000 ng/g and 1260 ng/g, respectively. Tetracycline residues predominated in the soil, while sulfonamides had mainly bioaccumulated in Zea mays L. tissue. The greatest average uptake factor within the Zea mays L. tissue was 8 for tetracyclines and 110 for sulfonamides indicating larger bioaccumulation of sulfonamides. Additionally, three ARGs (sul1, tetO, and OXA-1) were detected in the soil, only after manure application. However, ARGs were not detected in any of the plant samples.
Collapse
Affiliation(s)
- Rachel A Mullen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
| | - Jerod J Hurst
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
| | - Kayla M Naas
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
| | - Lauren M Sassoubre
- Department of Civil, Structural, and Environmental Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States of America.
| |
Collapse
|
43
|
Sivaganesan M, Varma M, Siefring S, Haugland R. Quantification of plasmid DNA standards for U.S. EPA fecal indicator bacteria qPCR methods by droplet digital PCR analysis. J Microbiol Methods 2018; 152:135-142. [PMID: 30017849 DOI: 10.1016/j.mimet.2018.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
Abstract
An obstacle to establishing widely useful data acceptance criteria for U.S. Environmental Protection Agency (EPA) qPCR methods has been the unavailability of standardized reference materials. Earlier versions of EPA Methods 1609 and 1611 for enterococci used cellular reference materials for quantifying enterococci in unknown test samples, however, EPA updates to these fundamentally DNA-based analysis methods have shifted toward the use of DNA standards. This report describes the application of droplet digital PCR (ddPCR) analysis for the quantification of a set of synthetic plasmid DNA standards that have been made available for updated EPA Methods 1609.1 and 1611.1 as well as for EPA Draft Method C for Escherichia coli. To obtain the most accurate concentration estimates possible, part of this effort was to develop a data analysis model for determining the fluorescence thresholds that distinguish positive from negative droplets produced by the ddPCR reactions. Versions of this model are described for applications with individual reactions, multiple reactions within a ddPCR system run, and multiple reactions within and across different system runs. The latter version was applied toward determinations of error in the concentration estimates of the standards from replicate analyses of each standard in multiple ddPCR system runs. Mean concentration estimates for the five standards from the ddPCR analyses were 4.356, 3.381, 2.371, 1.641 and 1.071 log10 copies/5 μL with associated standard deviations of 0.074, 0.082, 0.108, 0.131 and 0.188, respectively. These estimates contrasted with expected log10 concentrations of 4.6, 3.6, 2.6, 1.9 and 1.3 copies/5 μL, respectively, based on the yield of the plasmid reported by the vendor and spectrophotometric analysis of the initial stock solution of this material. These results illustrate how the analyses of original stocks may lead to potential bias(es) in the concentration estimates of final DNA standards and subsequently in the estimates of unknown test samples determined from these standards in qPCR analyses.
Collapse
Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 W. M.L. King Dr., Cincinnati, OH, United States
| | - Manju Varma
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr., Cincinnati, OH, United States
| | - Shawn Siefring
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr., Cincinnati, OH, United States
| | - Richard Haugland
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 26 W. M.L. King Dr., Cincinnati, OH, United States.
| |
Collapse
|
44
|
Jennings WC, Chern EC, O'Donohue D, Kellogg MG, Boehm AB. Frequent detection of a human fecal indicator in the urban ocean: environmental drivers and covariation with enterococci. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:480-492. [PMID: 29404550 PMCID: PMC6686843 DOI: 10.1039/c7em00594f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fecal pollution of surface waters presents a global human health threat. New molecular indicators of fecal pollution have been developed to address shortcomings of traditional culturable fecal indicators. However, there is still little information on their fate and transport in the environment. The present study uses spatially and temporally extensive data on traditional (culturable enterococci, cENT) and molecular (qPCR-enterococci, qENT and human-associated marker, HF183/BacR287) indicator concentrations in marine water surrounding highly-urbanized San Francisco, California, USA to investigate environmental and anthropogenic processes that impact fecal pollution. We constructed multivariable regression models for fecal indicator bacteria at 14 sampling stations. The human marker was detected more frequently in our study than in many other published studies, with detection frequency at some stations as high as 97%. The odds of cENT, qENT, and HF183/BacR287 exceeding health-relevant thresholds were statistically elevated immediately following discharges of partially treated combined sewage, and cENT levels dissipated after approximately 1 day. However, combined sewer discharges were not important predictors of indicator levels typically measured in weekly monitoring samples. Instead, precipitation and solar insolation were important predictors of cENT in weekly samples, while precipitation and water temperature were important predictors of HF183/BacR287 and qENT. The importance of precipitation highlights the significance of untreated storm water as a source of fecal pollution to the urban ocean, even for a city served by a combined sewage system. Sunlight and water temperature likely control persistence of the indicators via photoinactivation and dark decay processes, respectively.
Collapse
Affiliation(s)
- Wiley C Jennings
- Department of Civil and Environmental Engineering, Environmental Engineering and Science, Stanford University, 94305-4020, USA.
| | - Eunice C Chern
- San Francisco Public Utilities Commission, Water Quality Laboratory, 1000 El Camino Real, Millbrae, CA 94030, USA and EPA Region 10 Laboratory, 7411 Beach Dr E, Port Orchard, WA 98366, USA
| | - Diane O'Donohue
- San Francisco Public Utilities Commission, Oceanside Biology Laboratory, 3500 Great Highway, San Francisco, CA 94132, USA
| | - Michael G Kellogg
- San Francisco Public Utilities Commission, Oceanside Biology Laboratory, 3500 Great Highway, San Francisco, CA 94132, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Environmental Engineering and Science, Stanford University, 94305-4020, USA.
| |
Collapse
|
45
|
Sansom BJ, Sassoubre LM. Environmental DNA (eDNA) Shedding and Decay Rates to Model Freshwater Mussel eDNA Transport in a River. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:14244-14253. [PMID: 29131600 DOI: 10.1021/acs.est.7b05199] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Freshwater mussels are vital components of stream ecosystems, yet remain threatened. Thus, timely and accurate species counts are critical for proper conservation and management. Mussels live in stream sediments and can be challenging to survey given constraints related to water depth, flow, and time of year. The use of environmental DNA (eDNA) to monitor mussel distributions and diversity is a promising tool. Before it can be used as a monitoring tool, however, we need to know how much eDNA mussels shed into their environment and how long the eDNA persists. Here, we present a novel application of eDNA to estimate both the presence/absence and abundance of a freshwater mussel species, Lampsilis siliquoidea. The eDNA shedding and decay rates reported within are the first for freshwater mussels. We determined that eDNA shedding was statistically similar across mussel densities, but that first-order decay constants varied between experimental treatments. Finally, we effectively modeled downstream transport of eDNA and present a model that can be used as a complementary tool to estimate mussel density. Our results suggest that eDNA has the potential to be a complementary tool to survey mussels and enhance current efforts to monitor and protect freshwater mussel biodiversity.
Collapse
Affiliation(s)
- Brandon J Sansom
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo , Buffalo, New York 14260
| | - Lauren M Sassoubre
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo , Buffalo, New York 14260
| |
Collapse
|
46
|
Synthetic peptide TEKKRRETVEREKE derived from ezrin induces differentiation of NIH/3T3 fibroblasts. Eur J Pharmacol 2017; 811:249-259. [DOI: 10.1016/j.ejphar.2017.06.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 01/02/2023]
|
47
|
Stachler E, Kelty C, Sivaganesan M, Li X, Bibby K, Shanks OC. Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9146-9154. [PMID: 28700235 PMCID: PMC7350147 DOI: 10.1021/acs.est.7b02703] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal-indicator bacteria are used; however, they cannot distinguish human fecal waste from other animal pollution sources. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based on initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against an animal fecal reference library, and crAssphage genetic markers were highly abundant in raw sewage and sewage-impacted water samples. In addition, CPQ_056 and CPQ_064 performance was compared to HF183/BacR287 and HumM2 assays in paired experiments. Findings confirm that viral crAssphage qPCR assays perform at a similar level to well-established bacterial human-associated fecal-source-identification approaches. These new viral-based assays could become important water quality management and research tools.
Collapse
Affiliation(s)
| | - Catherine Kelty
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio 45268 United States
| | - Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio 45268 United States
| | - Xiang Li
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio 45268 United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 United States
- .,
| | - Orin C. Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio 45268 United States
- .,
| |
Collapse
|
48
|
Dorevitch S, Shrestha A, DeFlorio-Barker S, Breitenbach C, Heimler I. Monitoring urban beaches with qPCR vs. culture measures of fecal indicator bacteria: Implications for public notification. Environ Health 2017; 16:45. [PMID: 28499453 PMCID: PMC5429575 DOI: 10.1186/s12940-017-0256-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/08/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND The United States Environmental Protection Agency has established methods for testing beach water using the rapid quantitative polymerase chain reaction (qPCR) method, as well as "beach action values" so that the results of such testing can be used to make same-day beach management decisions. Despite its numerous advantages over culture-based monitoring approaches, qPCR monitoring has yet to become widely used in the US or elsewhere. Considering qPCR results obtained on a given day as the best available measure of that day's water quality, we evaluated the frequency of correct vs. incorrect beach management decisions that are driven by culture testing. METHODS Beaches in Chicago, USA, were monitored using E. coli culture and enterococci qPCR methods over 894 beach-days in the summers of 2015 and 2016. Agreement in beach management using the two methods, after taking into account agreement due to chance, was summarized using Cohen's kappa statistic. RESULTS No meaningful agreement (beyond that expected by chance) was observed between beach management actions driven by the two pieces of information available to beach managers on a given day: enterococci qPCR results ofsamples collected that morning and E. coli culture results of samples collected the previous day. The E. coli culture beach action value was exceeded 3.4 times more frequently than the enterococci qPCR beach action value (22.6 vs. 6.6% of beach-days). CONCLUSIONS The largest evaluation of qPCR-based beach monitoring to date provides little scientific rationale for continued E. coli culture testing of beach water in our setting. The observation that the E. coli culture beach action value was exceeded three times as frequently as the enterococci qPCR beach action value suggests that, although the beach action values for bacteria using different measurement methods are thought to provide comparable information about health risk, this does not appear to be the case in all settings.
Collapse
Affiliation(s)
- Samuel Dorevitch
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, 2121 W. Taylor St., M/C 922, Chicago, IL 60091 USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, 2121 W. Taylor St., M/C 922, Chicago, IL 60091 USA
| | - Stephanie DeFlorio-Barker
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, 2121 W. Taylor St., M/C 922, Chicago, IL 60091 USA
| | | | - Ira Heimler
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, 2121 W. Taylor St., M/C 922, Chicago, IL 60091 USA
| |
Collapse
|
49
|
Bosilevac JM, Wang R, Luedtke BE, Hinkley S, Wheeler TL, Koohmaraie M. Characterization of Enterohemorrhagic Escherichia coli on Veal Hides and Carcasses. J Food Prot 2017; 80:136-145. [PMID: 28221873 DOI: 10.4315/0362-028x.jfp-16-247] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) are Shiga toxin-producing E. coli associated with the most severe forms of foodborne illnesses. The U.S. Department of Agriculture, Food Safety and Inspection Service has identified a higher percentage of non-O157 EHEC compared with E. coli O157:H7-positive samples collected from veal trimmings than from products produced from other cattle slaughter classes. Therefore samples were collected from hides and preevisceration carcasses at five veal processors to assess E. coli O157:H7 and non-O157 EHEC contamination during bob veal and formula-fed veal dressing procedures. E. coli O157:H7 prevalence was measured by culture isolation and found to be on 20.3% of hides and 6.7% of carcasses. In contrast, a non-O157 EHEC molecular screening assay identified 90.3% of hides and 68.2% of carcasses as positive. Only carcass samples were taken forward to culture confirmation and 38.7% yielded one or more non-O157 EHEC isolates. The recovery of an EHEC varied by plant and sample collection date; values ranged from 2.1 to 87.8% among plants and from 4.2 to 64.2% within the same plant. Three plants were resampled after changes were made to sanitary dressing procedures. Between the two collection times at the three plants, hide-to-carcass transfer of E. coli O157:H7 and non-O157 EHEC was significantly reduced. All adulterant EHEC serogroups (O26, O45, O103, O111, O121, and O145) were isolated from veal carcasses as well as four other potentially pathogenic serogroups (O5, O84, O118, and O177). Bob veal was found to have a greater culture prevalence of E. coli O157:H7 and greater positive molecular screens for non-O157 EHEC than formula-fed veal (P < 0.05), but the percentage of culture-confirmed non-O157 EHEC was not different (P > 0.05) between the two types of calves. EHEC-O26, -O111, and -O121 were found more often in bob veal (P < 0.05), whereas EHEC-O103 was found more often in formula-fed veal (P < 0.05).
Collapse
Affiliation(s)
- Joseph M Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933
| | - Rong Wang
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933
| | - Brandon E Luedtke
- University of Nebraska-Kearney, 2401 11th Avenue, Kearney, Nebraska 68849
| | - Susanne Hinkley
- NeoSEEK Laboratory, Neogen Corp., 4131 North 48th Street, Lincoln, Nebraska 68504
| | - Tommy L Wheeler
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933
| | - Mohammad Koohmaraie
- IEH Laboratories and Consulting Group, 15300 Bothell Way N.E., Lake Forest Park, Washington 98155, USA
| |
Collapse
|
50
|
Symonds E, Sinigalliano C, Gidley M, Ahmed W, McQuaig-Ulrich S, Breitbart M. Faecal pollution along the southeastern coast of Florida and insight into the use of pepper mild mottle virus as an indicator. J Appl Microbiol 2016; 121:1469-1481. [DOI: 10.1111/jam.13252] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 11/29/2022]
Affiliation(s)
- E.M. Symonds
- College of Marine Science; University of South Florida; St. Petersburg FL USA
| | - C. Sinigalliano
- U.S. National Oceanographic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory; Miami FL USA
| | - M. Gidley
- U.S. National Oceanographic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory; Miami FL USA
| | - W. Ahmed
- Commonwealth Scientific and Industrial Research Organisation; Brisbane QLD Australia
| | | | - M. Breitbart
- College of Marine Science; University of South Florida; St. Petersburg FL USA
| |
Collapse
|