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 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 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 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.

Luminescence and decay properties of the 1D2 level of Pr3+-doped YPO4

2011 ◽  
Vol 89 (3) ◽  
pp. 415-422 ◽  
Author(s):  
J. Collins ◽  
M. Bettinelli ◽  
B. Di Bartolo
Keyword(s):  
Low Temperature ◽  
Temperature Dependence ◽  
Radiative Decay ◽  
Spectroscopic Properties ◽  
Decay Rates ◽  
Decay Kinetics ◽  
Population Redistribution ◽  
Individual Crystal ◽  
Decay Properties ◽  
Kinetics Of

This investigation reports on the spectroscopic properties of trivalent Pr in YPO4. In particular, we show how the luminescence from the 1D2 level depends on the polarization of the emission and on the temperature of the sample. We also report on the decay kinetics of the 1D2 level, which show the lifetime decreasing as temperature is increased. Our observed lifetime of 440 µs is at low temperature and is significantly longer than that reported by other workers. We explain the temperature dependence of the 1D2 emission by considering the population redistribution in the 1D2 level, without invoking the existence of multiphonon relaxation. Finally, we estimate the radiative decay rates of individual crystal field levels within the 1D2 manifold.

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 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 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.

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