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

2022 ◽  
Vol 194 (2) ◽  
Author(s):  
Rose Ragot ◽  
Richard Villemur
Keyword(s):  
Surface Waters ◽  
Fecal Contamination ◽  
Source Tracking

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

2003 ◽  
Vol 1 (4) ◽  
pp. 141-151 ◽  
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.

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

2015 ◽  
Vol 17 (7) ◽  
pp. 1249-1256 ◽  
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.

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

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.

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.

The use of antibiotic resistance profiling as a means of tracing sources of fecal contamination in source waters

2010 ◽  
Vol 10 (2) ◽  
pp. 209-215
Author(s):  
M. S. Mthembu ◽  
P. T. Biyela ◽  
T. G. Djarova ◽  
A. K. Basson
Keyword(s):  
Antibiotic Resistance ◽  
Municipal Wastewater ◽  
Fecal Contamination ◽  
Source Tracking ◽  
Human Consumption ◽  
Biochemical Tests ◽  
Isolation And Identification ◽  
E Coli ◽  
Intestinal Pathogens ◽  
Source Waters

Fecal contamination of source waters and its associated intestinal pathogens continues to pose risks to public health although the extent and effect of microbial contamination of source waters gets very little attention in designing treatment plants in most developing countries. Coliform counts give an indication of the overall bacterial contamination of water and thus its safety for human consumption. However, their presence fails to provide information about the source of fecal contamination which is vital to managing fecal contamination problems in surface waters. This study explored the use of multiple antibiotic resistance (MAR) indexing as means of differentiating E. coli isolates from different sources. A total of 322 E. coli isolates were obtained from municipal wastewater and from fecal samples from domestic and wild animals. Conventional culture methods and standard chemical and biochemical tests were used for isolation and identification of E. coli. Isolates were assayed against 10 antibiotics using the micro-dilution technique. The results obtained generated antibiotic resistance profiles which were used to statistically group the isolates into different subsets. Correct source classification was obtained for 60% of human-derived and 95% non-human-derived E. coli respectively. These results indicate the validity of the usefulness of MAR indexing as a method of bacterial source tracking.

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.

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