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 Use of Bacteroidales Microbial Source Tracking To Monitor Fecal Contamination in Fresh Produce Production

2013 ◽  
Vol 80 (2) ◽  
pp. 612-617 ◽  
Author(s):  
Kruti Ravaliya ◽  
Jennifer Gentry-Shields ◽  
Santos Garcia ◽  
Norma Heredia ◽  
Anna Fabiszewski de Aceituno ◽  
...  
Keyword(s):  
Fresh Produce ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Rrna Gene ◽  
Specific Marker ◽  
Production Environment ◽  
Content Type ◽  
Food Borne

ABSTRACTIn recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. Most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. Microbial source tracking (MST) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. This study investigated the utility of an MST method based onBacteroidales16S rRNA gene sequences as a means of identifying potential fecal contamination, and its source, in the fresh produce production environment. The method was applied to rinses of fresh produce, source and irrigation waters, and harvester hand rinses collected over the course of 1 year from nine farms (growing tomatoes, jalapeño peppers, and cantaloupe) in Northern Mexico. Of 174 samples, 39% were positive for a universalBacteroidalesmarker (AllBac), including 66% of samples from cantaloupe farms (3.6 log10genome equivalence copies [GEC]/100 ml), 31% of samples from tomato farms (1.7 log10GEC/100 ml), and 18% of samples from jalapeño farms (1.5 log10GEC/100 ml). Of 68 AllBac-positive samples, 46% were positive for one of three human-specific markers, and none were positive for a bovine-specific marker. There was no statistically significant correlation betweenBacteroidalesand genericEscherichia coliacross all samples. This study provides evidence thatBacteroidalesmarkers may serve as alternative indicators for fecal contamination in fresh produce production, allowing for determination of both general contamination and that derived from the human host.

scholarly journals Application of library-independent microbial source tracking methods for identifying the sources of faecal contamination in coastal areas

2010 ◽  
Vol 61 (6) ◽  
pp. 1401-1409 ◽  
Author(s):  
M. Gourmelon ◽  
M. P. Caprais ◽  
C. Le Mennec ◽  
S. Mieszkin ◽  
C. Ponthoreau ◽  
...  
Keyword(s):  
Water Samples ◽  
Microbial Source Tracking ◽  
Coastal Areas ◽  
Source Tracking ◽  
Rrna Gene ◽  
Multiple Sources ◽  
Gene Markers ◽  
Faecal Contamination ◽  
Water Courses ◽  
Specific Bacteriophage

Faecal contamination sources were identified in coastal areas around the Guerande-Atlantique peninsula using two microbial source tracking (MST) methods: (i) Bacteroidales host-specific 16S rRNA gene markers measured by real-time PCR and (ii) F-specific bacteriophage (FRNAPH) genotyping. Both methods were used on 63 water samples from 7 water courses. HF183 marker and bacteriophage genogroup II (FRNAPH II) were detected in all water samples and in the majority of water samples, respectively, from La Torre stream (W5), Piriac (W2), R2000 (W3) and Mazy (W7) rain water drains, and also detected, less frequently, in Le Nau drain (W4), suggesting contamination by human faecal sources at these sites. These human markers were weakly detected in Pouliguen channel (W6). Furthermore, BacR and bacteriophage genogroup I (FRNAPH I) were also detected, but at lower concentration and frequency. So, site W6 seems to be contaminated by multiple sources, though mainly human. Finally, BacR was detected twice in Pont d'Armes channel (W1), whereas HF183 was not detected. FRNAPH I and II were detected in only 3 out of 12 water samples. Site W1 seems mainly contaminated by animal sources. As a result of our findings, actions were taken to remediate water and shellfish quality.

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 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 Molecular surveillance of Cryptosporidium spp. for microbial source tracking of fecal contamination in Laguna Lake, Philippines

2021 ◽  
Author(s):  
Laurice Beatrice Raphaelle O. dela Peña ◽  
Mark Raymond A. Vejano ◽  
Windell L. Rivera
Keyword(s):  
Water Samples ◽  
Fecal Contamination ◽  
Small Subunit ◽  
Source Tracking ◽  
Rrna Gene ◽  
Molecular Surveillance ◽  
Cryptosporidium Spp ◽  
To Come ◽  
Water Quality Deterioration ◽  
Laguna Lake

Abstract Water quality deterioration in source waters poses increased health, environmental, and economic risks. Here, we genotyped Cryptosporidium spp. obtained from water samples of Laguna Lake, Philippines, and its tributaries for the purpose of source-tracking fecal contamination. A total of 104 surface water samples were collected over a 1-year period (March 2018 to April 2019). Detection of Cryptosporidium was carried out using genus-specific primers targeting a fragment of the small subunit (SSU) rRNA gene. The study revealed 8 (14%) tributary samples and 1 (2.77%) lake sample positive for contamination. The species were determined to be C. parvum (n = 4), C. muris (n = 2), C. hominis (n = 1), C. galli (n = 1), C. baileyi (n = 1), C. suis (n = 1), as well as rat genotype IV (n = 1). Two species were detected in duck (C. baileyi) and cattle (C. parvum) fecal samples. The data presented suggest that Cryptosporidium contamination is likely to come from sewage or human feces as well as various agricultural sources (i.e. cattle, swine, and poultry). This information reveals the importance of mitigating fecal pollution in the lake system and minimizing health risks due to exposure to zoonotic Cryptosporidium species.

scholarly journals Microbial Source Tracking of Fecal Indicating Bacteria in Coral Reef Waters, Recreational Waters, and Groundwater of Saipan by Real-Time Quantitative PCR

2021 ◽  
Vol 11 ◽  
Author(s):  
Christopher Sinigalliano ◽  
Kiho Kim ◽  
Maribeth Gidley ◽  
Kathy Yuknavage ◽  
Karen Knee ◽  
...  
Keyword(s):  
Surface Waters ◽  
Coastal Waters ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Gene Marker ◽  
Primary Input ◽  
Gene Markers ◽  
Nitrogen Inputs ◽  
Microbial Contaminants

The Commonwealth of the Northern Mariana Islands (CNMI) recently identified the need to improve its capacity for detecting and tracking land-based sources of pollution (LBSP) in coastal waters, particularly microbial contaminants like fecal indicator bacteria (FIB). Reported here is a baseline study of a suite of host-specific FIB microbial source tracking (MST) markers in the coastal shoreline and reef waters around the island of Saipan. Three sampling campaigns were conducted in September 2017, March 2018, and August 2018. Samples were collected from the nearshore surface waters of Saipan, the reef waters of Saipan Lagoon, and groundwater from beaches along the Saipan Lagoon shoreline. Measurements of submarine groundwater discharge (SGD) into nearshore waters and isotopic source tracking of nitrogen inputs were conducted concurrently with MST. Environmental DNA was extracted from the samples and analyzed by quantitative polymerase chain reaction (qPCR) for MST gene markers of fecal Bacteroidales specifically associated with humans, dogs, cows, and pigs, and for an MST gene marker of Catellicoccus associated with seabirds. MST assessments were combined with local knowledge, assessments of sanitary infrastructure, and routine watershed surveys. This study identified hotspots of human FIB along the western Saipan Lagoon shoreline in both surface waters and groundwater, plus another hotspot of human FIB at a popular tourist bathing area known as the Grotto. FIB hotspots on the Lagoon shoreline coincided with areas of high SGD and nitrogen isotopic data indicating sewage-derived N inputs. It appears that faulty sanitary infrastructure may be contributing to inputs to Saipan Lagoon, while bather shedding is likely a primary input for the Grotto area. Moderate levels of dog fecal contamination were common and widespread across the island. High levels of seabird fecal contamination were more random, both spatially and temporally, and mostly concentrated along the less developed northeast region of Saipan. No significant levels of cow or pig fecal marker were detected in coastal water samples. This study provides demonstration and establishment of analytical capacity to resource management in CNMI for MST technology to aid in trouble-shooting water quality issues involving land-based sources of microbial contaminants to CNMI coastal waters.

scholarly journals Relative Decay of Bacteroidales Microbial Source Tracking Markers and Cultivated Escherichia coli in Freshwater Microcosms

2010 ◽  
Vol 76 (10) ◽  
pp. 3255-3262 ◽  
Author(s):  
Linda K. Dick ◽  
Erin A. Stelzer ◽  
Erin E. Bertke ◽  
Denise L. Fong ◽  
Donald M. Stoeckel
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Microbial Source Tracking ◽  
Decay Rates ◽  
Source Tracking ◽  
Rrna Gene ◽  
Fecal Indicator ◽  
Gene Markers ◽  
E Coli ◽  
Log Reduction

ABSTRACT Fecal indicator bacteria (FIB), commonly used to regulate sanitary water quality, cannot discriminate among sources of contamination. The use of alternative quantitative PCR (qPCR) methods for monitoring fecal contamination or microbial source tracking requires an understanding of relationships with cultivated FIB, as contamination ages under various conditions in the environment. In this study, the decay rates of three Bacteroidales 16S rRNA gene markers (AllBac for general contamination and qHF183 and BacHum for human-associated contamination) were compared with the decay rate of cultivated Escherichia coli in river water microcosms spiked with human wastewater. The following five sets of microcosms were monitored over 11 days: control, artificial sunlight, sediment exposure, reduced temperature, and no autochthonous predation. Decay was characterized by estimation of the time needed to produce a 2-log reduction (t 99). No treatment-associated differences in the decay of the 4 targets were evident except with reduced predation, where E. coli, qHF183, and BacHum markers had lower levels of decay by day 3. However, there were substantial target-associated differences. Decay curves for the AllBac marker indicated a larger persistent population than those of the other targets. Exposure to sunlight, sediment, and reduced predation resulted in more rapid decay of the human-associated markers relative to cultivable E. coli, but there were no differences in t 99 values among the 4 targets under control conditions or at reduced temperatures. Further evaluation of epidemiological relationships will be needed in order to relate the markers directly to health risk. These findings suggest that the tested human-associated markers can complement E. coli as indicators of the human impact on sanitary water quality under the constrained conditions described in this paper.

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.

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