scholarly journals Evaluation of Bovine Feces-Associated Microbial Source Tracking Markers and Their Correlations with Fecal Indicators and Zoonotic Pathogens in a Brisbane, Australia, Reservoir

2013 ◽  
Vol 79 (8) ◽  
pp. 2682-2691 ◽  
Author(s):  
W. Ahmed ◽  
T. Sritharan ◽  
A. Palmer ◽  
J. P. S. Sidhu ◽  
S. Toze
Keyword(s):  
Host Specificity ◽  
Water Samples ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Decay Rates ◽  
Source Tracking ◽  
Content Type ◽  
Zoonotic Pathogens ◽  
Maximum Value ◽  
Bovine Feces

ABSTRACTThis study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB),Campylobacterspp.,Escherichia coliO157, andSalmonellaspp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for theCampylobacter16S rRNA andE. coliO157rfbEgenes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens.

scholarly journals Assessment of Giardia and Cryptosporidium spp. as a Microbial Source Tracking Tool for Surface Water: Application in a Mixed-Use Watershed

2014 ◽  
Vol 80 (8) ◽  
pp. 2328-2336 ◽  
Author(s):  
Natalie Prystajecky ◽  
Peter M. Huck ◽  
Hans Schreier ◽  
Judith L. Isaac-Renton
Keyword(s):  
Surface Water ◽  
Host Specificity ◽  
Water Samples ◽  
Environmental Protection Agency ◽  
Current Knowledge ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Genomic Sequencing ◽  
Content Type ◽  
Surface Water Samples

ABSTRACTKnowledge of host specificity, combined with genomic sequencing ofGiardiaandCryptosporidiumspp., has demonstrated a microbial source tracking (MST) utility for these common waterborne microbes. To explore the source attribution potential of these pathogens, water samples were collected in a mixed rural-urban watershed in the Township of Langley, in southwestern British Columbia (BC), Canada, over a 2-year period.Cryptosporidiumwas detected in 63% of surface water samples at concentrations ranging from no positive detection (NPD) to 20,600 oocysts per 100 liters.Giardiawas detected in 86% of surface water samples at concentrations ranging from NPD to 3,800 cysts per 100 liters of water. Sequencing at the 18S rRNA locus revealed that 50% ofCryptosporidiumsamples and 98% ofGiardiasamples contained species/genotypes (Cryptosporidium) or assemblages (Giardia) that are capable of infecting humans, based on current knowledge of host specificity and taxonomy.Cryptosporidiumgenotyping data were more promising for source tracking potential, due to the greater number of host-adapted (i.e., narrow-host-range) species/genotypes compared toGiardia, since 98% ofGiardiaisolates were zoonotic and the potential host could not be predicted. This report highlights the benefits of parasite genomic sequencing to complement Method 1623 (U.S. Environmental Protection Agency) and shows thatCryptosporidiumsubtyping for MST purposes is superior to the use ofGiardiasubtyping, based on better detection limits forCryptosporidium-positive samples than forGiardia-positive samples and on greater host specificity amongCryptosporidiumspecies. These additional tools could be used for risk assessment in public health and watershed management decisions.

scholarly journals Development and Evaluation of a Quantitative PCR Assay Targeting Sandhill Crane (Grus canadensis) Fecal Pollution

2012 ◽  
Vol 78 (12) ◽  
pp. 4338-4345 ◽  
Author(s):  
Hodon Ryu ◽  
Jingrang Lu ◽  
Jason Vogel ◽  
Michael Elk ◽  
Felipe Chávez-Ramírez ◽  
...  
Keyword(s):  
Host Specificity ◽  
Quantitative Pcr ◽  
Water Samples ◽  
False Negative ◽  
Environmental Water ◽  
Fecal Pollution ◽  
Source Tracking ◽  
Rrna Gene ◽  
Content Type ◽  
Sandhill Crane

ABSTRACTWhile the microbial water quality in the Platte River is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. Here we characterized microbial populations in crane feces using phylogenetic analysis of 16S rRNA gene fecal clone libraries. Using these sequences, a novel crane quantitative PCR (Crane1) assay was developed, and its applicability as a microbial source tracking (MST) assay was evaluated by determining its host specificity and detection ability in environmental waters. Bacteria from crane excreta were dominated by bacilli and proteobacteria, with a notable paucity of sequences homologous toBacteroidetesandClostridia. The Crane1 marker targeted a dominant clade of unclassifiedLactobacillalessequences closely related toCatellicoccus marimammalium. The host distribution of the Crane1 marker was relatively high, being positive for 69% (66/96) of the crane excreta samples tested. The assay also showed high host specificity, with 95% of the nontarget fecal samples (i.e.,n= 553; 20 different free-range hosts) being negative. Of the presumed crane-impacted water samples (n= 16), 88% were positive for the Crane1 assay, whereas none of the water samples not impacted by cranes were positive (n= 165). Bayesian statistical models of the Crane1 MST marker demonstrated high confidence in detecting true-positive signals and a low probability of false-negative signals from environmental water samples. Altogether, these data suggest that the newly developed marker could be used in environmental monitoring studies to study crane fecal pollution dynamics.

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 New Molecular Quantitative PCR Assay for Detection of Host-Specific Bifidobacteriaceae Suitable for Microbial Source Tracking

2012 ◽  
Vol 78 (16) ◽  
pp. 5788-5795 ◽  
Author(s):  
Marta Gómez-Doñate ◽  
Elisenda Ballesté ◽  
Maite Muniesa ◽  
Anicet R. Blanch
Keyword(s):  
Host Specificity ◽  
Quantitative Pcr ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Content Type ◽  
Practical Applications ◽  
Urban Sewage ◽  
Culture Independent ◽  
Low Prevalence ◽  
High Degree

ABSTRACTBifidobacteriumspp. belong to the commensal intestinal microbiota of warm-blooded animals. Some strains ofBifidobacteriumshow host specificity and have thus been proposed as host-specific targets to determine the origin of fecal pollution. Most strains have been used in microbial-source-tracking (MST) studies based on culture-dependent methods. Although some of these approaches have proved very useful, the low prevalence of culturableBifidobacteriumstrains in the environment means that molecular culture-independent procedures could provide practical applications for MST. Reported here is a set of common primers and fourBifidobacteriumsp. host-associated (human, cattle, pig, and poultry) probes for quantitative-PCR (qPCR) assessment of fecal source tracking. This set was tested using 25 water samples of diverse origin: urban sewage samples, wastewater from four abattoirs (porcine, bovine, and poultry), and water from a river with a low pollution load. The selected sequences showed a high degree of host specificity. There were no cross-reactions between the qPCR assays specific for each origin and samples from different fecal origins. On the basis of the findings, it was concluded that the host-specific qPCRs are sufficiently robust to be applied in environmental MST studies.

scholarly journals Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking

2021 ◽  
Author(s):  
Brittany Suttner ◽  
Blake G. Lindner ◽  
Minjae Kim ◽  
Roth Edward Conrad ◽  
Luis M Rodriguez ◽  
...  
Keyword(s):  
Host Specificity ◽  
Primary Source ◽  
Microbial Source Tracking ◽  
Decay Rates ◽  
Source Tracking ◽  
Waterborne Diseases ◽  
Decay Kinetics ◽  
Dialysis Bag ◽  
Kinetics Of ◽  
Respective Host

Fecal material in the environment is a primary source of pathogens that cause waterborne diseases and affect over a billion people worldwide. Microbial source tracking (MST) assays based on single genes (e.g., 16S rRNA) do not always provide the resolution needed to attribute fecal contamination sources. In this work, we used dialysis bag mesocosms simulating a freshwater habitat that were spiked separately with cow, pig, or human feces to monitor the decay of host-specific fecal signals over time with metagenomics, traditional qPCR, and culture-based methods. Sequencing of the host fecal communities used as inocula recovered 79 non-redundant metagenome-assembled genomes (MAGs) whose abundance patterns showed that the majority of the fecal community signal was not detectable in the mesocosm metagenomes after four days. Several MAGs showed high host specificity, and thus are promising candidates for biomarkers for their respective host type. Traditional qPCR methods varied in their correlation with MAG decay kinetics. Notably, the human-specific Bacteroides assay, HF183/BFDRev, consistently under-estimated fecal pollution due to not being present in all hosts and/or primer mismatches. This work provides new insights on the persistence and decay kinetics of host-specific gut microbes in the environment and identifies several MAGs as putative biomarkers for improved MST.

scholarly journals Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii

2016 ◽  
Vol 82 (22) ◽  
pp. 6757-6767 ◽  
Author(s):  
Marek Kirs ◽  
Roberto A. Caffaro-Filho ◽  
Mayee Wong ◽  
Valerie J. Harwood ◽  
Philip Moravcik ◽  
...  
Keyword(s):  
Water Quality ◽  
Epidemiological Studies ◽  
Microbial Source Tracking ◽  
Decay Rates ◽  
Indicator Bacteria ◽  
Source Tracking ◽  
Recreational Water ◽  
Fecal Samples ◽  
Content Type ◽  
Sewage Contamination

ABSTRACTIdentification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associatedBacteroidesspp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n= 11], 30% of mongoose [n= 10], and 10% of feline [n= 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii.IMPORTANCEThis study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci andEscherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers.

scholarly journals Tracking the Primary Sources of Fecal Pollution in a Tropical Watershed in a One-Year Study

2013 ◽  
Vol 79 (5) ◽  
pp. 1689-1696 ◽  
Author(s):  
Carlos Toledo-Hernandez ◽  
Hodon Ryu ◽  
Joel Gonzalez-Nieves ◽  
Evelyn Huertas ◽  
Gary A. Toranzos ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Water Samples ◽  
Wastewater Treatment Plants ◽  
Fecal Pollution ◽  
Primary Sources ◽  
Source Tracking ◽  
Detection Rates ◽  
Content Type ◽  
One Year ◽  
Tropical Watershed

ABSTRACTA study was conducted to determine the primary sources of fecal pollution in a subtropical watershed using host-specific assays developed in temperate regions. Water samples (n= 534) from 10 different sites along the Rio Grande de Arecibo (RGA) watershed were collected mostly on a weekly basis (54 sampling events) during 13 months. DNA extracts from water samples were used in PCR assays to determine the occurrence of fecal bacteria (Bacteroidales,Clostridium coccoides, and enterococci) and human-, cattle-, swine-, and chicken-specific fecal sources. Feces from 12 different animals (n= 340) and wastewater treatment samples (n= 16) were analyzed to determine the specificity and distribution of host-specific assays. The human-specific assay (HF183) was found to be highly specific, as it did not cross-react with nontarget samples. The cattle marker (CF128) cross-reacted to some extent with swine, chicken, and turkeys and was present in 64% of the cattle samples tested. The swine assays showed poor host specificity, while the three chicken assays showed poor host distribution. Differences in the detection of host-specific markers were noted per site. While human and cattle assays showed moderate average detection rates throughout the watershed, areas impacted by wastewater treatment plants and cattle exhibited the highest prevalence of these markers. When conditional probability for positive signals was determined for each of the markers, the results indicated higher confidence levels for the human assay and lower levels for all the other assays. Overall, the results from this study suggest that additional assays are needed, particularly to track cattle, chicken, and swine fecal pollution sources in the RGA watershed. The results also suggest that the geographic stability of genetic markers needs to be determined prior to conducting applied source tracking studies in tropical settings.

scholarly journals Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems

2016 ◽  
Vol 82 (5) ◽  
pp. 1625-1635 ◽  
Author(s):  
Xiang Li ◽  
Valerie J. Harwood ◽  
Bina Nayak ◽  
Jennifer L. Weidhaas
Keyword(s):  
Legionella Pneumophila ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Marine Water ◽  
Treated Wastewater ◽  
Human Polyomavirus ◽  
Source Tracking ◽  
Marker Genes ◽  
Content Type ◽  
Gene Copies

ABSTRACTPathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% forEscherichia coliand human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such asLegionella pneumophila,Shigella flexneri, andCampylobacter fetuswere detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment.

scholarly journals Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats

2013 ◽  
Vol 80 (1) ◽  
pp. 110-118 ◽  
Author(s):  
Adelumola Oladeinde ◽  
Thomas Bohrmann ◽  
Kelvin Wong ◽  
S. T. Purucker ◽  
Ken Bradshaw ◽  
...  
Keyword(s):  
Decay Rate ◽  
Fecal Indicator Bacteria ◽  
Decay Rates ◽  
Indicator Bacteria ◽  
Source Tracking ◽  
Fecal Indicator ◽  
Bacterial Populations ◽  
Content Type ◽  
E Coli ◽  
Decay Dynamic

ABSTRACTUnderstanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (Escherichia coliand enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of theE. colipopulation (P< 0.0001), with a rate of −0.176 day−1for the shaded treatment and −0.297 day−1for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (P> 0.05). In addition,E. colipopulations showed a significant growth rate (0.881 day−1) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate ofE. colipopulations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers thanE. coliconcentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic ofE. colipopulations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands.

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