scholarly journals Comparative Persistence of Subgroups of F-Specific RNA Phages in River Water

2013 ◽  
Vol 79 (15) ◽  
pp. 4564-4567 ◽  
Author(s):  
Yongheng Yang ◽  
Mansel W. Griffiths
Keyword(s):  
Surface Water ◽  
River Water ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Organic Substances ◽  
Misleading Information ◽  
Factors Affecting ◽  
Major Factors ◽  
Rna Phage

ABSTRACTF-specific (F+) RNA phages are widely used as indicators for the presence of fecal contamination and/or enteric viruses in water, and identifying subgroups of F+ RNA phages provides an approach for microbial source tracking. Different survival characteristics of the F+ RNA phage subgroups result in a misinterpretation of their original proportion in water, thus giving misleading information when they are used for microbial source tracking. This study investigated the comparative persistence of subgroups of F+ RNA phages in river water under different conditions. Results suggested that temperature and pH are the major factors affecting the persistence of F+ RNA phages in river water, and organic substances promote phage survival. The comparative persistence patterns of subgroups of F+ RNA phages varied and may bias extrapolation of their initial proportions in surface water. Thus, the characteristics of water should be taken into consideration and the results should be carefully interpreted when F+ RNA phages are used for microbial source tracking.

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 Assessment of source tracking methods for application in spring water

2014 ◽  
Vol 13 (2) ◽  
pp. 473-488 ◽  
Author(s):  
Melanie Wicki ◽  
Adrian Auckenthaler ◽  
Richard Felleisen ◽  
Fatma Karabulut ◽  
Isabel Niederhauser ◽  
...  
Keyword(s):  
Surface Water ◽  
Scientific Literature ◽  
Microbial Source Tracking ◽  
Spring Water ◽  
Source Tracking ◽  
Animal Waste ◽  
Faecal Contamination ◽  
Potential Source ◽  
Host Strains

For discriminating between human and animal faecal contamination in water, microbial source tracking (MST) approaches using different indicators have been employed. In the current study, a range of 10 such MST indicators described in the scientific literature were comparatively assessed. Bacteriophages infecting host strains of Bacteroides (GA-17, GB-124 and ARABA 84) as well as sorbitol-fermenting bifidobacteria proved useful for indicating human faecal contamination while Rhodococcus coprophilus was associated with animal-derived faecal contamination. These potential source indicators were present in samples of faecal origin, i.e. either in human wastewater or animal waste, from many different regions in Switzerland and therefore showed a geographic stability. In addition, the MST indicators were abundant in surface water and were even sensitive enough to detect faecal contamination in spring water from two study areas in Switzerland. This is the first study that has compared and successfully applied MST methods in spring water.

scholarly journals Identification of Human and Animal Adenoviruses and Polyomaviruses for Determination of Sources of Fecal Contamination in the Environment

2006 ◽  
Vol 72 (12) ◽  
pp. 7886-7893 ◽  
Author(s):  
Ayalkibet Hundesa ◽  
Carlos Maluquer de Motes ◽  
Silvia Bofill-Mas ◽  
Nestor Albinana-Gimenez ◽  
Rosina Girones
Keyword(s):  
River Water ◽  
Water Samples ◽  
Environmental Samples ◽  
Fecal Contamination ◽  
Source Tracking ◽  
Animal Origin ◽  
Urban Sewage ◽  
River Water Samples ◽  
Negative Results ◽  
Wastewater Samples

ABSTRACT The Adenoviridae and Polyomaviridae families comprise a wide diversity of viruses which may be excreted for long periods in feces or urine. In this study, a preliminary analysis of the prevalence in the environment and the potential usefulness as source-tracking tools of human and animal adenoviruses and polyomaviruses has been developed. Molecular assays based on PCR specifically targeting human adenoviruses (HAdV), porcine adenoviruses (PAdV), bovine adenoviruses (BAdV), and bovine polyomaviruses (BPyV) were applied to environmental samples including urban sewage, slaughterhouse, and river water samples. PAdV and BPyV were detected in a very high percentage of samples potentially affected by either porcine or bovine fecal contamination, respectively. However, BAdV were detected in only one sample, showing a lower prevalence than BPyV in the wastewater samples analyzed. The 22 slaughterhouse samples with fecal contamination of animal origin showed negative results for the presence of HAdV. The river water samples analyzed were positive for the presence of both human and animal adenoviruses and polyomaviruses, indicating the existence of diverse sources of contamination. The identities of the viruses detected were confirmed by analyses of the amplified sequences. All BPyV isolates showed a 97% similarity in nucleotide sequences. This is the first time that PAdV5, BAdV6, and BPyV have been reported to occur in environmental samples. Human and porcine adenoviruses and human and bovine polyomaviruses are proposed as tools for evaluating the presence of viral contamination and for tracking the origin of fecal/urine contamination in environmental samples.

Multi-Year Microbial Source Tracking Study Characterizing Fecal Contamination in an Urban Watershed

2017 ◽  
Vol 89 (2) ◽  
pp. 127-143 ◽  
Author(s):  
Rebecca N. Bushon ◽  
Amie M.G. Brady ◽  
Eric D. Christensen ◽  
Erin A. Stelzer
Keyword(s):  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Urban Watershed

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 Reveals Origins of Fecal Contamination in a Recovering Watershed

Water ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2162 ◽  
Author(s):  
Hyatt Green ◽  
Daniel Weller ◽  
Stephanie Johnson ◽  
Edward Michalenko
Keyword(s):  
Urban Areas ◽  
Bacterial Contamination ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Mitigation Strategies ◽  
Source Tracking ◽  
Chemical Parameters ◽  
Fecal Indicator ◽  
Combined Sewer ◽  
Rain Events

Fecal contamination of waterbodies due to poorly managed human and animal waste is a pervasive problem that can be particularly costly to address, especially if mitigation strategies are ineffective at sufficiently reducing the level of contamination. Identifying the most worrisome sources of contamination is particularly difficult in periurban streams with multiple land uses and requires the distinction of municipal, agricultural, domestic pet, and natural (i.e., wildlife) wastes. Microbial source-tracking (MST) methods that target host-specific members of the bacterial order Bacteroidales and others have been used worldwide to identify the origins of fecal contamination. We conducted a dry-weather study of Onondaga Creek, NY, where reducing fecal contamination has been approached mainly by mitigating combined sewer overflow events (CSOs). Over three sampling dates, we measured in-stream concentrations of fecal indicator bacteria; MST markers targeting human, ruminant, and canine sources; and various physical–chemical parameters to identify contaminants not attributable to CSOs or stormwater runoff. We observed that despite significant ruminant inputs upstream, these contaminants eventually decayed and/or were diluted out and that high levels of urban bacterial contamination are most likely due to failing infrastructure and/or illicit discharges independent of rain events. Similar dynamics may control other streams that transition from agricultural to urban areas with failing infrastructure.

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.

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