scholarly journals Microbial source tracking of private well water samples across at-risk regions in southern Ontario and analysis of traditional fecal indicator bacteria assays including culture and qPCR

2016 ◽  
Vol 14 (6) ◽  
pp. 1047-1058 ◽  
Author(s):  
Julia Krolik ◽  
Allison Maier ◽  
Shawna Thompson ◽  
Anna Majury
Keyword(s):  
At Risk ◽  
Water Samples ◽  
Rural Areas ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Well Water ◽  
Prevention Strategies ◽  
E Coli ◽  
Bacteriological Testing

Many people living in rural areas rely on privately owned wells as their primary source of drinking water. These water sources are at risk for fecal contamination of human, wildlife, and livestock origin. While traditional bacteriological testing involves culture-based methods, microbial source tracking (MST) assays present an opportunity to additionally determine the source of fecal contamination. This study investigated the main host sources of contamination in private well water samples with high levels of Escherichia coli (E. coli), using MST with human and multi-species specific markers. Fecal contamination of human origin was detected in approximately 50% of samples, indicating that current contamination prevention strategies require reconsideration. The relationship between cattle density and fecal contamination of bovine origin was investigated using a Bovine Bacteroidales specific MST assay. Regional variations of microbial sources were examined, and may inform local primary prevention strategies. Additionally, in order to assess MST and E. coli quantitative real time polymerase chain reaction (qPCR) assays as indicators of fecal contamination, these were compared to E. coli culture methods. Variation in results was observed across all assay methods investigated, suggesting the most appropriate routine bacteriological testing methodology cannot be determined without comparison to a method that directly detects the presence of fecal contamination.

scholarly journals Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries

2007 ◽  
Vol 73 (15) ◽  
pp. 4857-4866 ◽  
Author(s):  
Michèle Gourmelon ◽  
Marie Paule Caprais ◽  
Raphaël Ségura ◽  
Cécile Le Mennec ◽  
Solen Lozach ◽  
...  
Keyword(s):  
Water Samples ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Rrna Gene ◽  
Specific Marker ◽  
Gene Markers ◽  
High Level ◽  
Bird Feces

ABSTRACT In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193′), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries, but in all sewage samples. Most detected F RNA bacteriophages were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird feces and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal, or mixed fecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing Escherichia coli or enterococcus concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers.

scholarly journals Microbial source tracking and spatial analysis of E. coli contaminated private well waters in southeastern Ontario

2013 ◽  
Vol 12 (2) ◽  
pp. 348-357 ◽  
Author(s):  
Julia Krolik ◽  
Gerald Evans ◽  
Paul Belanger ◽  
Allison Maier ◽  
Geoffrey Hall ◽  
...  
Keyword(s):  
Rural Communities ◽  
Water Samples ◽  
Human Health Risk ◽  
Primary Source ◽  
Developed Countries ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Future Research ◽  
Well Water ◽  
Specific Marker

Private water supplies, which are the primary source of drinking water for rural communities in developed countries, are at risk of becoming fecally contaminated. It is important to identify the source of contamination in order to better understand and address this human health risk. Microbial source tracking methods using human, bovine and general Bacteroidales markers were performed on 716 well water samples from southeastern Ontario, which had previously tested positive for Escherichia coli. The results were then geospatially analyzed in order to elucidate contamination patterns. Markers for human feces were found in nearly half (49%) of all samples tested, and a statistically significant spatial cluster was observed. A quarter of the samples tested positive for only general Bacteroidales markers (25.7%) and relatively few bovine specific marker positives (12.6%) were found. These findings are fundamental to the understanding of pathogen dynamics and risk in the context of drinking well water and will inform future research regarding host-specific pathogens in private well water samples.

scholarly journals 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

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.

scholarly journals The Use of Ribosomal RNA as a Microbial Source Tracking Target Highlights the Assay Host-Specificity Requirement in Water Quality Assessments

2021 ◽  
Vol 12 ◽  
Author(s):  
Annastiina Rytkönen ◽  
Ananda Tiwari ◽  
Anna-Maria Hokajärvi ◽  
Sari Uusheimo ◽  
Asko Vepsäläinen ◽  
...  
Keyword(s):  
Surface Water ◽  
Ribosomal Rna ◽  
Water Samples ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Municipal Sewage ◽  
Source Tracking ◽  
Fecal Samples ◽  
Dna Template ◽  
Surface Water Samples

For microbial source tracking (MST), the 16S ribosomal RNA genes (rDNA) of host-specific bacteria and mitochondrial DNA (mtDNA) of animal species, known to cause fecal contamination of water, have been commonly used as molecular targets. However, low levels of contamination might remain undetected by using these DNA-based qPCR assays. The high copy numbers of ribosomal RNA (rRNA) could offer a solution for such applications of MST. This study compared the performance of eight MST assays: GenBac3 (general Bacteroidales), HF183 (human), BacCan (dog), Rum-2-Bac (ruminant), Pig-2-Bac (swine), Gull4 (gull), GFD, and Av4143 (birds) between rRNA-based and rDNA-based approaches. Three mtDNA-based approaches were tested: DogND5, SheepCytB, and HorseCytB. A total of 151 animal fecal samples and eight municipal sewage samples from four regions of Finland were collected for the marker evaluation. The usability of these markers was tested by using a total of 95 surface water samples with an unknown pollution load. Overall, the performance (specificity, sensitivity, and accuracy) of mtDNA-based assays was excellent (95–100%), but these markers were very seldom detected from the tested surface water samples. The rRNA template increased the sensitivity of assays in comparison to the rDNA template. All rRNA-based assays (except Av4143) had more than 80% sensitivity. In contrast, only half (HF183, Rum-2-Bac, Pig-2-Bac, and Gull4) of rDNA-based assays reached this value. For markers targeted to bird feces, the use of the rRNA-based assay increased or at least did not change the performance. Regarding specificity, all the assays had >95% specificity with a DNA template, except the BacCan assay (71%). While using the RNA template for the assays, HF183 and BacCan exhibited only a low level of specificity (54 and 55%, respectively). Further, the HF183 assay amplified from multiple non-targeted animal fecal samples with the RNA template and the marker showed cross-amplification with the DNA template as well. This study recommends using the rRNA-based approach for MST assays targeting bird fecal contamination. In the case of mammal-specific MST assays, the use of the rRNA template increases the sensitivity but may reduce the specificity and accuracy of the assay. The finding of increased sensitivity calls for a further need to develop better rRNA-based approaches to reach the required assay performance.

scholarly journals Comparative microbial source tracking methods for identification of fecal contamination sources at Sunnyside Beach in the Toronto region area of concern

2016 ◽  
Vol 14 (5) ◽  
pp. 839-850 ◽  
Author(s):  
Zachery R. Staley ◽  
Thomas A. Edge
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Fecal Contamination ◽  
Bird Species ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Pcr Marker ◽  
E Coli ◽  
Remediation Strategies ◽  
Humber River ◽  
Area Of Concern

Several beaches within the Toronto region area of concern have persistent issues with fecal contamination, causing a beach beneficial use impairment (BUI). In this study, Escherichia coli, including ampicillin-resistant strains, were enumerated via culturable and quantitative polymerase chain reaction (qPCR) methods. Microbial source tracking (MST) markers (for general Bacteroidales, human, ruminant/cow, gull, and dog) were detected and enumerated via PCR and qPCR to identify sources of fecal contamination at Sunnyside Beach and in the Humber River. Human, cow, and dog markers had good host-specificity, while gull markers sometimes amplified a few other bird species. The ruminant endpoint PCR marker amplified a variety of other animal species rendering it less useful. Both human and gull fecal contamination were prevalent in the Humber River, while Sunnyside Beach was predominantly impacted by gull fecal contamination. Human sewage impacts were more prevalent in the lower Humber River, particularly in Black Creek. However, to reduce Sunnyside beach postings, reducing bird fecal contamination in the river and at the beach would be necessary. When there are high levels of E. coli throughout a beachshed, an MST toolbox approach can add value to discriminate source(s) of E. coli contamination and guide decisions relating to public health risk and remediation strategies.

scholarly journals Phenotypic library-based microbial source tracking methods: Efficacy in the California collaborative study

2003 ◽  
Vol 1 (4) ◽  
pp. 153-166 ◽  
Author(s):  
Valerie J. Harwood ◽  
Bruce Wiggins ◽  
Charles Hagedorn ◽  
R. D. Ellender ◽  
Jan Gooch ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Water Samples ◽  
False Positive ◽  
Collaborative Study ◽  
Microbial Source Tracking ◽  
Fecal Coliforms ◽  
Source Tracking ◽  
E Coli ◽  
Fecal Streptococci ◽  
Positive Rate

As part of a larger microbial source tracking (MST) study, several laboratories used library-based, phenotypic subtyping techniques to analyse fecal samples from known sources (human, sewage, cattle, dogs and gulls) and blinded water samples that were contaminated with the fecal sources. The methods used included antibiotic resistance analysis (ARA) of fecal streptococci, enterococci, fecal coliforms and E. coli; multiple antibiotic resistance (MAR) and Kirby-Bauer antibiotic susceptibility testing of E. coli; and carbon source utilization for fecal streptococci and E. coli. Libraries comprising phenotypic patterns of indicator bacteria isolated from known fecal sources were used to predict the sources of isolates from water samples that had been seeded with fecal material from the same sources as those used to create the libraries. The accuracy of fecal source identification in the water samples was assessed both with and without a cut-off termed the minimum detectable percentage (MDP). The libraries (∼300 isolates) were not large enough to avoid the artefact of source-independent grouping, but some important conclusions could still be drawn. Use of a MDP decreased the percentage of false-positive source identifications, and had little effect on the high percentage of true-positives in the most accurate libraries. In general, the methods were more prone to false-positive than to false-negative errors. The most accurate method, with a true-positive rate of 100% and a false-positive rate of 39% when analysed with a MDP, was ARA of fecal streptococci. The internal accuracy of the libraries did not correlate with the accuracy of source prediction in water samples, showing that one should not rely solely on parameters such as the average rate of correct classification of a library to indicate its predictive capabilities.

scholarly journals Drivers of microbiological quality of household drinking water – a case study in rural Ethiopia

2017 ◽  
Vol 16 (2) ◽  
pp. 275-288 ◽  
Author(s):  
Muhammed A. Usman ◽  
Nicolas Gerber ◽  
Evita H. Pangaribowo
Keyword(s):  
Drinking Water ◽  
Water Samples ◽  
Rural Areas ◽  
Fecal Contamination ◽  
Microbiological Quality ◽  
Water Sources ◽  
Multiple Use ◽  
Water Safety ◽  
E Coli

Abstract This study aims at assessing the determinants of microbiological contamination of household drinking water under multiple-use water systems in rural areas of Ethiopia. For this analysis, a random sample of 454 households was surveyed between February and March 2014, and water samples from community sources and household storage containers were collected and tested for fecal contamination. The number of Escherichia coli (E. coli) colony-forming units per 100 mL water was used as an indicator of fecal contamination. The microbiological tests demonstrated that 58% of household stored water samples and 38% of protected community water sources were contaminated with E. coli. Moreover, most improved water sources often considered to provide safe water showed the presence of E. coli. The result shows that households' stored water collected from unprotected wells/springs had higher levels of E. coli than stored water from alternative sources. Distance to water sources and water collection containers are also strongly associated with stored water quality. To ensure the quality of stored water, the study suggests that there is a need to promote water safety from the point-of-source to point-of-use, with due considerations for the linkages between water and agriculture to advance the Sustainable Development Goal 6 of ensuring access to clean water for everyone.

scholarly journals Relevance of Bacteroidales and F-Specific RNA Bacteriophages for Efficient Fecal Contamination Tracking at the Level of a Catchment in France

2012 ◽  
Vol 78 (15) ◽  
pp. 5143-5152 ◽  
Author(s):  
Aourell Mauffret ◽  
Marie-Paule Caprais ◽  
Michèle Gourmelon
Keyword(s):  
Water Samples ◽  
Fecal Contamination ◽  
Source Tracking ◽  
Pig Manure ◽  
Contamination Level ◽  
Strongly Correlated ◽  
Content Type ◽  
Exact Test ◽  
E Coli ◽  
Sample Classification

ABSTRACTThe relevance of three host-associatedBacteroidalesmarkers (HF183, Rum2Bac, and Pig2Bac) and four F-specific RNA bacteriophage genogroups (FRNAPH I to IV) as microbial source tracking markers was assessed at the level of a catchment (Daoulas, France). They were monitored together with fecal indicators (Escherichia coliand enterococci) and chemophysical parameters (rainfall, temperature, salinity, pH, and turbidity) by monthly sampling over 2 years (n= 240 water samples) and one specific sampling following an accidental pig manure spillage (n= 5 samples). During the 2-year regular monitoring, levels ofE. coli, enterococci, total F-specific RNA bacteriophages, and the generalBacteroidalesmarker AllBac were strongly correlated with one another and with Rum2Bac (r= 0.37 to 0.50,P< 0.0001). Their correlations with HF183 and FRNAPH I and II were lower (r= 0.21 to 0.29,P< 0.001 toP< 0.0001), and HF183 and enterococci were associated rather than correlated (Fisher's exact test,P< 0.01). Rum2Bac and HF183 enabled 73% of water samples that had ≥2.7 log10most probably number (MPN) ofE. coli/100 ml to be classified. FRNAPH I and II enabled 33% of samples at this contamination level to be classified. FRNAPH I and II complemented the water sample classification obtained with the twoBacteroidalesmarkers by an additional 8%. Pig2Bac and FRNAPH III and IV were observed in a small number of samples (n= 0 to 4 of 245). The present study validates Rum2Bac and HF183 as relevant tools to trace fecal contamination originating from ruminant or human waste, respectively, at the level of a whole catchment.

scholarly journals Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches

2016 ◽  
Vol 82 (14) ◽  
pp. 4379-4386 ◽  
Author(s):  
W. Ahmed ◽  
K. A. Hamilton ◽  
P. Gyawali ◽  
S. Toze ◽  
C. N. Haas
Keyword(s):  
Water Quality ◽  
Water Samples ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Fecal Dna ◽  
Potential Health ◽  
Gene Copies ◽  
Tank Water ◽  
Rainwater Tanks

ABSTRACTAvian and possum fecal droppings may negatively impact roof-harvested rainwater (RHRW) water quality due to the presence of zoonotic pathogens. This study was aimed at evaluating the performance characteristics of a possum feces-associated (PSM) marker by screening 210 fecal and wastewater samples from possums (n= 20) and a range of nonpossum hosts (n= 190) in Southeast Queensland, Australia. The host sensitivity and specificity of the PSM marker were 0.90 and 0.95 (maximum value, 1.00), respectively. The mean concentrations of the GFD marker in possum fecal DNA samples (8.8 × 107gene copies per g of feces) were two orders of magnitude higher than those in the nonpossum fecal DNA samples (5.0 × 105gene copies per g of feces). The host sensitivity, specificity, and concentrations of the avian feces-associated GFD marker were reported in our recent study (W. Ahmed, V. J. Harwood, K. Nguyen, S. Young, K. Hamilton, and S. Toze, Water Res 88:613–622, 2016,http://dx.doi.org/10.1016/j.watres.2015.10.050). The utility of the GFD and PSM markers was evaluated by testing a large number of tank water samples (n= 134) from the Brisbane and Currumbin areas. GFD and PSM markers were detected in 39 of 134 (29%) and 11 of 134 (8%) tank water samples, respectively. The GFD marker concentrations in PCR-positive samples ranged from 3.7 × 102to 8.5 × 105gene copies per liter, whereas the concentrations of the PSM marker ranged from 2.0 × 103to 6.8 × 103gene copies per liter of water. The results of this study suggest the presence of fecal contamination in tank water samples from avian and possum hosts. This study has established an association between the degradation of microbial tank water quality and avian and possum feces. Based on the results, we recommend disinfection of tank water, especially for tanks designated for potable use.IMPORTANCEThe use of roof-harvested rainwater (RHRW) for domestic purposes is a globally accepted practice. The presence of pathogens in rainwater tanks has been reported by several studies, supporting the necessity for the management of potential health risks. The sources of fecal pollution in rainwater tanks are unknown. However, the application of microbial source tracking (MST) markers has the potential to identify the sources of fecal contamination in a rainwater tank. In this study, we provide evidence of avian and possum fecal contamination in tank water samples using molecular markers. This study established a potential link between the degradation of the microbial quality of tank water and avian and possum feces.

scholarly journals Exploring links between water quality and E. coli O157:H7 survival potential in well waters from a rural area of southern Changchun City, China

2017 ◽  
Vol 16 (2) ◽  
pp. 300-310 ◽  
Author(s):  
Meiyue Ding ◽  
Jiahang Li ◽  
Xiaodan Liu ◽  
Huiru Li ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Public Health ◽  
Rural Area ◽  
Water Samples ◽  
Rural Areas ◽  
Public Health Issue ◽  
Well Water ◽  
E Coli ◽  
Average Survival ◽  
Changchun City ◽  
Survival Potential

Abstract Waterborne infectious disease outbreak associated with well water contamination is a worldwide public health issue, especially for rural areas in developing countries. In the current study, we characterized 20 well water samples collected from a rural area of southern Changchun city, China, and investigated the survival potential of Escherichia coli O157:H7 in those water samples. The results showed that nitrate and ammonia concentrations in some well water samples exceed the corresponding China drinking water standards, indicating potential contamination by local agricultural farms. Our results also revealed that the average survival time (ttd) of E. coli O157:H7 in all well water samples was 30.09 days, with shortest and longest ttd being 17.95 and 58.10 days, respectively. The ttds were significantly correlated with pH and the ratio of total nitrogen to total phosphorus. In addition, it was found that the shape parameter (p) and first decimal reduction parameter (δ) were negatively (P &lt; 0.05) and positively (P &lt; 0.05) correlated to ttd, respectively. Our study showed that E. coli O157:H7 could survive up to two months in well water, suggesting that this pathogen could constitute a great public health risk.

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