Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater

ABSTRACTQuantitative real-time PCR (qPCR) assays that target the human-associated HF183 bacterial cluster within members of the genusBacteroidesare among the most widely used methods for the characterization of human fecal pollution in ambient surface waters. In this study, we show that a current TaqMan HF183 qPCR assay (HF183/BFDrev) routinely forms nonspecific amplification products and introduce a modified TaqMan assay (HF183/BacR287) that alleviates this problem. The performance of each qPCR assay was compared in head-to-head experiments investigating limits of detection, analytical precision, predicted hybridization to 16S rRNA gene sequences from a reference database, and relative marker concentrations in fecal and sewage samples. The performance of the modified HF183/BacR287 assay is equal to or improves upon that of the original HF183/BFDrev assay. In addition, a qPCR chemistry designed to combat amplification inhibition and a multiplexed internal amplification control are included. In light of the expanding use of PCR-based methods that rely on the detection of extremely low concentrations of DNA template, such as qPCR and digital PCR, the new TaqMan HF183/BacR287 assay should provide more accurate estimations of human-derived fecal contaminants in ambient surface waters.

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Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples

Journal of Water and Health ◽

10.2166/wh.2003.0017 ◽

2003 ◽

Vol 1 (4) ◽

pp. 141-151 ◽

Cited By ~ 98

Author(s):

John F. Griffith ◽

Stephen B. Weisberg ◽

Charles D. McGee

Keyword(s):

Surface Waters ◽

Water Samples ◽

Fecal Contamination ◽

Source Material ◽

Source Tracking ◽

Fecal Material ◽

Comparative Testing ◽

Specific Pcr ◽

Phenotypic Methods ◽

Better Than

Microbiological source tracking (MST) methods are increasingly being used to identify fecal contamination sources in surface waters, but these methods have been subjected to limited comparative testing. In this study, 22 researchers employing 12 different methods were provided sets of identically prepared blind water samples. Each sample contained one to three of five possible fecal sources (human, dog, cattle, seagull or sewage). Researchers were also provided with portions of the fecal material used to inoculate the blind water samples for use as library material. No MST method that was tested predicted the source material in the blind samples perfectly. Host-specific PCR performed best at differentiating between human and non-human sources, but primers are not yet available for differentiating between all of the non-human sources. Virus and F+ coliphage methods reliably identified sewage, but were unable to identify fecal contamination from individual humans. Library-based isolate methods correctly identified the dominant source in most samples, but also had frequent false positives in which fecal sources not in the samples were incorrectly identified as being present. Among the library-based methods, genotypic methods generally performed better than phenotypic methods.

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Occurrence of antibiotic resistance inEscherichia colifrom surface waters and fecal pollution sources near Hamilton, Ontario

Canadian Journal of Microbiology ◽

10.1139/w05-028 ◽

2005 ◽

Vol 51 (6) ◽

pp. 501-505 ◽

Cited By ~ 64

Author(s):

Thomas A Edge ◽

Stephen Hill

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Surface Waters ◽

Municipal Wastewater ◽

Average Rate ◽

Fecal Pollution ◽

Pollution Sources ◽

Source Tracking ◽

E Coli ◽

Bird Feces

Antibiotic resistance was examined in 462 Escherichia coli isolates from surface waters and fecal pollution sources around Hamilton, Ontario. Escherichia coli were resistant to the highest concentrations of each of the 14 antibiotics studied, although the prevalence of high resistance was mostly low. Two of 12 E. coli isolates from sewage in a CSO tank had multiple resistance to ampicillin, ciprofloxacin, gentamicin, and tetracycline above their clinical breakpoints. Antibiotic resistance was less prevalent in E. coli from bird feces than from municipal wastewater sources. A discriminant function calculated from antibiotic resistance data provided an average rate of correct classification of 68% for discriminating E. coli from bird and wastewater fecal pollution sources. The preliminary microbial source tracking results suggest that, at times, bird feces might be a more prominent contributor of E. coli to Bayfront Park beach waters than municipal wastewater sources.Key words: antibiotic resistance, Escherichia coli, surface water, fecal pollution.

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eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters

Environmental Monitoring and Assessment ◽

10.1007/s10661-021-09668-w ◽

2022 ◽

Vol 194 (2) ◽

Author(s):

Rose Ragot ◽

Richard Villemur

Keyword(s):

Surface Waters ◽

Fecal Contamination ◽

Source Tracking

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Male-specific coliphages for source tracking fecal contamination in surface waters and prevalence of Shiga-toxigenic Escherichia coli in a major produce production region of the Central Coast of California

Environmental Science Processes & Impacts ◽

10.1039/c4em00537f ◽

2015 ◽

Vol 17 (7) ◽

pp. 1249-1256 ◽

Cited By ~ 4

Author(s):

Subbarao V. Ravva ◽

Chester Z. Sarreal ◽

Michael B. Cooley

Keyword(s):

Escherichia Coli ◽

Surface Waters ◽

Fecal Contamination ◽

Enteric Pathogens ◽

Source Tracking ◽

Central Coast ◽

Prevalence Data ◽

Production Region ◽

Male Specific

F+ RNA coliphages are invaluable for predicting the sources of fecal contamination in the environment and their prevalence data may aid in preventing the spread of enteric pathogens from likely sources.

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Application of enteric viruses for fecal pollution source tracking in environmental waters

Environment International ◽

10.1016/j.envint.2012.02.009 ◽

2012 ◽

Vol 45 ◽

pp. 151-164 ◽

Cited By ~ 73

Author(s):

Kelvin Wong ◽

Theng-Theng Fong ◽

Kyle Bibby ◽

Marirosa Molina

Keyword(s):

Enteric Viruses ◽

Pollution Source ◽

Fecal Pollution ◽

Source Tracking ◽

Environmental Waters

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Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Frontiers in Microbiology ◽

10.3389/fmicb.2021.660368 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hongxia Liang ◽

Zhisheng Yu ◽

Bobo Wang ◽

Fabrice Ndayisenga ◽

Ruyin Liu ◽

...

Keyword(s):

Molecular Markers ◽

Water Samples ◽

Fecal Contamination ◽

Microbial Source Tracking ◽

Fecal Pollution ◽

Small Sample ◽

16S Rrna Genes ◽

Rrna Genes ◽

Source Tracking ◽

Community Based

It is important to track fecal sources from humans and animals that negatively influence the water quality of rural rivers and human health. In this study, microbial source tracking (MST) methods using molecular markers and the community-based FEAST (fast expectation–maximization microbial source tracking) program were synergistically applied to distinguish the fecal contributions of multiple sources in a rural river located in Beijing, China. The performance of eight markers were evaluated using 133 fecal samples based on real-time quantitative (qPCR) technique. Among them, six markers, including universal (BacUni), human-associated (HF183-1 and BacH), swine-associated (Pig-2-Bac), ruminant-associated (Rum-2-Bac), and avian-associated (AV4143) markers, performed well in the study. A total of 96 water samples from the river and outfalls showed a coordinated composition of fecal pollution, which revealed that outfall water might be a potential input of the Fsq River. In the FEAST program, bacterial 16S rRNA genes of 58 fecal and 12 water samples were sequenced to build the “source” library and “sink,” respectively. The relative contribution (<4.01% of sequence reads) of each source (i.e., human, swine, bovine, or sheep) was calculated based on simultaneous screening of the operational taxonomic units (OTUs) of sources and sinks, which indicated that community-based MST methods could be promising tools for identifying fecal sources from a more comprehensive perspective. Results of the qPCR assays indicated that fecal contamination from human was dominant during dry weather and that fecal sources from swine and ruminant were more prevalent in samples during the wet season than in those during the dry season, which were consistent with the findings predicted by the FEAST program using a very small sample size. Information from the study could be valuable for the development of improved regulation policies to reduce the levels of fecal contamination in rural rivers.

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Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR

Journal of Water and Health ◽

10.2166/wh.2021.119 ◽

2021 ◽

Author(s):

Laurice Beatrice Raphaelle O. dela Peña ◽

Kevin L. Labrador ◽

Mae Ashley G. Nacario ◽

Nicole R. Bolo ◽

Windell L. Rivera

Keyword(s):

Surface Waters ◽

Fecal Contamination ◽

Microbial Source Tracking ◽

The Philippines ◽

Source Tracking ◽

Source Attribution ◽

Monitoring Methods ◽

K Nearest Neighbors ◽

Fecal Indicator ◽

Laguna Lake

Abstract Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we predicted sources of Escherichia coli in lake stations and tributaries by establishing a fecal source library composed of rep-PCR DNA fingerprints of human, cattle, swine, poultry, and sewage samples (n = 1,408). We also evaluated three statistical methods for predicting fecal contamination sources in surface waters. Random forest (RF) outperformed k-nearest neighbors and discriminant analysis of principal components in terms of average rates of correct classification in two- (84.85%), three- (82.45%), and five-way (74.77%) categorical splits. Overall, RF exhibited the most balanced prediction, which is crucial for disproportionate libraries. Source tracking of environmental isolates (n = 332) revealed the dominance of sewage (47.59%) followed by human sources (29.22%), poultry (12.65%), swine (7.23%), and cattle (3.31%) using RF. This study demonstrates the promising utility of a library-dependent method in augmenting current monitoring systems for source attribution of fecal contamination in Laguna Lake. This is also the first known report of microbial source tracking using rep-PCR conducted in surface waters of the Laguna Lake watershed.

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Fecal pollution source tracking in waters intended for human supply based on archaeal and bacterial genetic markers

Journal of Water and Health ◽

10.2166/wh.2015.292 ◽

2015 ◽

Vol 13 (4) ◽

pp. 985-995 ◽

Cited By ~ 2

Author(s):

Kayo Bianco ◽

Camila Barreto ◽

Samara Sant'Anna Oliveira ◽

Leonardo Henriques Pinto ◽

Rodolpho Mattos Albano ◽

...

Keyword(s):

High Sensitivity ◽

Pollution Source ◽

Fecal Pollution ◽

Source Tracking ◽

The Novel ◽

Tropical Water ◽

Novel Host ◽

Bacterial Genetic

The determination of fecal pollution sources in aquatic ecosystems is essential to estimate associated health risks. In this study, we evaluate eight microbial source tracking (MST) markers including host-specific Bacteroidales and Methanobrevibacter spp. for discrimination between human, bovine, equine, and swine fecal contamination in waters intended for human supply. Overall, the novel host-specific archaeal and bacterial primers proposed in this study demonstrated high sensitivity and specificity. Markers for the Archaea domain were more prevalent in the fecal and water samples studied. We conclude that the investigations regarding the sources of fecal pollution in public water supplies can contribute to improve the quality of human health. To our knowledge, this is the first analysis using both archaeal and bacterial fecal MST markers on tropical water bodies of Rio de Janeiro city, Brazil.

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