Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed

Fecal pollution management remains one of the biggest challenges for water quality authorities worldwide. Advanced fecal pollution source identification technologies are now available that can provide quantitative information from many animal groups. As public interest in these methodologies grows, it is vital to use standardized procedures with clearly defined data acceptance metrics and conduct field studies demonstrating the use of these techniques to help resolve real-world water quality challenges. Here we apply recently standardized human-associated qPCR methods with custom data acceptance metrics (HF183/BacR287 and HumM2), along with established procedures for ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution sources to (i) demonstrate the feasibility of implementing standardized qPCR procedures in a large-scale field study, and (ii) characterize trends in fecal pollution sources in the research area. A total of 602 water samples were collected over a one-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries in the Tillamook Bay Watershed (OR, USA). Host-associated qPCR results were combined with high-resolution geographic information system (GIS) land use and general indicator bacteria (E. coli) measurements to elucidate water quality fecal pollution trends. Results demonstrate the feasibility of implementing standardized fecal source identification qPCR methods with established data acceptance metrics in a large-scale field study leading to new investigative leads suggesting that elevated E. coli levels may be linked to specific pollution sources and land use activities in the Tillamook Bay Watershed.

[1]  C. Jokinen,et al.  Sources of generic Escherichia coli and factors impacting guideline exceedances for food safety in an irrigation reservoir outlet and two canals. , 2019, Water research.

[2]  S. Sauvé,et al.  Fecal contamination of storm sewers: Evaluating wastewater micropollutants, human-specific Bacteroides 16S rRNA, and mitochondrial DNA genetic markers as alternative indicators of sewer cross connections. , 2019, The Science of the total environment.

[3]  R. Haugland,et al.  A Constructed Wetland for Treatment of an Impacted Waterway and the Influence of Native Waterfowl on its Perceived Effectiveness. , 2019, Ecological engineering.

[4]  V. Harwood,et al.  Relationships between Microbial Indicators and Pathogens in Recreational Water Settings , 2018, International journal of environmental research and public health.

[5]  J. Fernández-Niño,et al.  Association between air pollution and suicide: a time series analysis in four Colombian cities , 2018, Environmental Health.

[6]  Coady Wing,et al.  Estimate of incidence and cost of recreational waterborne illness on United States surface waters , 2018, Environmental Health.

[7]  T. James-Todd,et al.  Hair product use, age at menarche and mammographic breast density in multiethnic urban women , 2018, Environmental Health.

[8]  Orin C. Shanks,et al.  Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement. , 2017, Environmental science & technology.

[9]  S. Corsi,et al.  Quantification of human-associated fecal indicators reveal sewage from urban watersheds as a source of pollution to Lake Michigan. , 2016, Water research.

[10]  T. Edge,et al.  Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls , 2016, Applied and Environmental Microbiology.

[11]  Mano Sivaganesan,et al.  Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods , 2016, Applied and Environmental Microbiology.

[12]  Laura E. Jackson,et al.  EnviroAtlas: A new geospatial tool to foster ecosystem services science and resource management , 2015 .

[13]  Orin C. Shanks,et al.  Development of rapid canine fecal source identification PCR-based assays. , 2014, Environmental science & technology.

[14]  P. Holden,et al.  Microbial source tracking in a coastal California watershed reveals canines as controllable sources of fecal contamination. , 2014, Environmental science & technology.

[15]  Mano Sivaganesan,et al.  Improved HF183 Quantitative Real-Time PCR Assay for Characterization of Human Fecal Pollution in Ambient Surface Water Samples , 2014, Applied and Environmental Microbiology.

[16]  Orin C. Shanks,et al.  Age-Related Shifts in the Density and Distribution of Genetic Marker Water Quality Indicators in Cow and Calf Feces , 2013, Applied and Environmental Microbiology.

[17]  Dan Wang,et al.  Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods. , 2013, Water research.

[18]  Stefan Wuertz,et al.  Adenovirus-associated health risks for recreational activities in a multi-use coastal watershed based on site-specific quantitative microbial risk assessment. , 2013, Water research.

[19]  T. M. Chui,et al.  Modeling sewage leakage to surrounding groundwater and stormwater drains. , 2012, Water science and technology : a journal of the International Association on Water Pollution Research.

[20]  Linda K. Dick,et al.  Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water , 2011, Applied and Environmental Microbiology.

[21]  H. Johnson,et al.  Surface-Water Nutrient Conditions and Sources in the United States Pacific Northwest , 2011, Journal of the American Water Resources Association.

[22]  Orin C. Shanks,et al.  Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution. , 2011, Environmental science & technology.

[23]  Orin C. Shanks,et al.  Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations , 2011, Applied and Environmental Microbiology.

[24]  V. Harwood,et al.  Correlation of Quantitative PCR for a Poultry-Specific Brevibacterium Marker Gene with Bacterial and Chemical Indicators of Water Pollution in a Watershed Impacted by Land Application of Poultry Litter , 2011, Applied and Environmental Microbiology.

[25]  L. Backer,et al.  Evaluation of conventional and alternative monitoring methods for a recreational marine beach with nonpoint source of fecal contamination. , 2010, Environmental science & technology.

[26]  Orin C. Shanks,et al.  Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR. , 2010, Systematic and applied microbiology.

[27]  Timothy Bartrand,et al.  Estimated human health risks from exposure to recreational waters impacted by human and non-human sources of faecal contamination. , 2010, Water research.

[28]  Jiyoung Lee,et al.  Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination. , 2010, Journal of microbiological methods.

[29]  Mano Sivaganesan,et al.  Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples. , 2010, Environmental science & technology.

[30]  M. Gourmelon,et al.  Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real‐time PCR , 2010, Journal of applied microbiology.

[31]  Mano Sivaganesan,et al.  Performance Assessment PCR-Based Assays Targeting Bacteroidales Genetic Markers of Bovine Fecal Pollution , 2010, Applied and Environmental Microbiology.

[32]  Mano Sivaganesan,et al.  Quantitative PCR for Genetic Markers of Human Fecal Pollution , 2009, Applied and Environmental Microbiology.

[33]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[34]  C Andrew Carson,et al.  Use of a Bacteroides thetaiotaomicron‐specific α‐1‐6, mannanase quantitative PCR to detect human faecal pollution in water , 2008, Journal of applied microbiology.

[35]  T. Edge,et al.  Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces , 2008, Applied and Environmental Microbiology.

[36]  Orin C. Shanks,et al.  A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards , 2008, BMC Bioinformatics.

[37]  Orin C. Shanks,et al.  Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution , 2007, Applied and Environmental Microbiology.

[38]  S. Wuertz,et al.  16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. , 2007, Water research.

[39]  A. Farnleitner,et al.  A quantitative real‐time PCR assay for the highly sensitive and specific detection of human faecal influence in spring water from a large alpine catchment area , 2007, Letters in applied microbiology.

[40]  Orin C. Shanks,et al.  Basin-Wide Analysis of the Dynamics of Fecal Contamination and Fecal Source Identification in Tillamook Bay, Oregon , 2006, Applied and Environmental Microbiology.

[41]  A. Farnleitner,et al.  Quantitative PCR Method for Sensitive Detection of Ruminant Fecal Pollution in Freshwater and Evaluation of This Method in Alpine Karstic Regions , 2006, Applied and Environmental Microbiology.

[42]  P. Scholes,et al.  The occurrence of Campylobacter subtypes in environmental reservoirs and potential transmission routes , 2005, Journal of applied microbiology.

[43]  R. Wack,et al.  Survey of Parasites and Bacterial Pathogens from Free-Living Waterfowl in Zoological Settings , 2004, Avian diseases.

[44]  Dennis R. Helsel,et al.  Nondetects and data analysis : statistics for censored environmental data , 2004 .

[45]  D. Levy,et al.  Surveillance for waterborne-disease outbreaks--United States, 1999-2000. , 2002, Morbidity and mortality weekly report. Surveillance summaries.

[46]  N. Cox,et al.  Surveillance for influenza--United States, 1997-98, 1998-99, and 1999-00 seasons. , 2002, Morbidity and mortality weekly report. Surveillance summaries.

[47]  K. Steingart,et al.  Laboratory investigation of an E. coli O157:H7 outbreak associated with swimming in Battle Ground Lake, Vancouver, Washington. , 2002, Journal of environmental health.

[48]  Katharine G. Field,et al.  A PCR Assay To Discriminate Human and Ruminant Feces on the Basis of Host Differences in Bacteroides-Prevotella Genes Encoding 16S rRNA , 2000, Applied and Environmental Microbiology.

[49]  Orin C. Shanks,et al.  A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method. , 2018, Water research.

[50]  R. Wack,et al.  Fecal shedding and antimicrobial susceptibility of selected bacterial pathogens and a survey of intestinal parasites in free-living waterfowl. , 2001, Avian diseases.