Use of a<i>Bacteroides thetaiotaomicron</i>-specific α-1-6, mannanase quantitative PCR to detect human faecal pollution in water

Yampara-Iquise, Helen; Zheng, Guoan; Jones, J. J.; Carson, C. A.

doi:10.1111/j.1365-2672.2008.03895.x

Cited by 64 publications

(50 citation statements)

References 34 publications

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“…Water samples from each site were collected in 5-liter (for microbial indicators and bacterial pathogens) and 10-liter (for enteric viruses) sterile containers. For microbial indicators and bacterial pathogens, the volumes of water samples analyzed were 100 ml for each of the culture-based methods, 200 ml for quantitative PCR (qPCR) detection of bacterial indicators (4,6,(11)(12)(13), and 500 ml (after adjusting the pH to 3.5 to promote better electrostatic interactions between HPyVs and filters) for human polyomavirus (5). From May to June 2012, 20 additional water samples were conducted at 12 other stations (sites 6 to 17) throughout Singapore (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…As such, human sewage contamination may pose higher risks to human health than animal wastes. Bacteroides thetaiotaomicron, human polyomaviruses (HPyVs), and Methanobrevibacter smithii are some of the potential markers that have shown high specificity for human contamination (4)(5)(6). Many studies have examined the correlation between these alternative markers and human pathogens in natural aquatic environments.…”

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confidence: 99%

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Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment

Liang

Goh

Vergara

et al. 2015

Appl Environ Microbiol

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The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F؉ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions. Indicator bacteria, such as Escherichia coli and enterococci (ENT), have been used extensively in past decades to indicate the presence of human enteric pathogens because of the great diversity of pathogens, the large volumes required, and the difficulty in concentrating the typically low concentrations of pathogens from water samples. In Singapore, microbial water quality guidelines for recreational freshwater currently target enterococci (less than 200 counts per 100 ml for 95% of the time).Despite the wide use of fecal indicator bacteria in microbial water quality monitoring, their suitability to represent a level of health risk is still being questioned. One of the reasons is the lack of data correlating the presence and concentrations of the indicators with the presence of disease-associated pathogens. With improvements in microbiological test methods and bacterial species identification, there is growing evidence that fecal indicator bacteria, including E. coli and ENT, do not necessarily correlate well with some of the enteric pathogens, particularly viruses (1). There is also evidence that E. ...

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment

Liang

Goh

Vergara

et al. 2015

Appl Environ Microbiol

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“…Based on the results, the authors concluded that the gyrB assay might serve as a complementary tool for 16S rRNA-based assays when they fail to separate closely related bacteria (Bacteroides and Prevotella) in human wastewater. Yampara-Iquise and colleagues [58] developed a qPCR assay targeting a single-copy putative α-1-6-mannanase gene based on the complete genomic sequence of Bacteroides thetaiotaomicron VP1 5482. The markers were highly prevalent (1.4ˆ10 8 cells per L) in raw sewage samples.…”

Section: Introductionmentioning

confidence: 99%

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

Ahmed

Hughes

Harwood

2016

Water

109

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Abstract:Microbial source tracking (MST) endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. This review summarizes the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or "markers" of sewage pollution, including known advantages and deficiencies of the many polymerase chain reaction (PCR)-based methods that have been published since 2000. Host specificity is a paramount criterion for confidence that detection of a marker is a true indicator of the target host. Host sensitivity, or the prevalence of the marker in feces/waste from the target host, is necessary for confidence that absence of the marker is indicative of the absence of the pollution source. Each of these parameters can vary widely depending on the type of waste assessed and the geographic location. Differential decay characteristics of bacterial targets and their associated DNA contribute to challenges in interpreting MST results in the context of human health risks. The HF183 marker, derived from the 16S rRNA gene of Bacteroides dorei and closely related taxa, has been used for almost two decades in MST studies, and is well characterized regarding host sensitivity and specificity, and in prevalence and concentration in sewage in many countries. Other markers such as HumM2 and HumM3 show promise, but require further performance testing to demonstrate their widespread utility. An important limitation of the one-marker-one-assay approach commonly used for MST is that given the complexities of microbial persistence in environmental waters, and the methodological challenges of quantitative PCR (qPCR) in such samples, the absence of a given marker does not ensure the absence of fecal pollution in the source water. Approaches under development, such as microarray and community analysis, have the potential to improve MST practices, thereby increasing our ability to protect human and ecosystem health.

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“…Researchers and managers alike recognize the advantages of animal source information to help solve long-standing ambient water quality problems. As a result, a number of fecal source identification technologies have been developed (2)(3)(4)(5)(6)(7)(8)(9). These methods have been employed to address challenges such as the identification of septic pollution (10)(11)(12), the evaluation of agricultural waste management practices (13)(14)(15), the assessment of combined sewer overflow water quality impact (16,17), and the estimation of recreational water public health risk (18).…”

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confidence: 99%

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

Shanks

Kelty

Oshiro

et al. 2016

Appl Environ Microbiol

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There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (notemplate and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria proposed in this study should help scientists, managers, reviewers, and the public evaluate the technical quality of future findings against an established benchmark. Fecal pollution remains a significant challenge for ambient water quality managers worldwide. In the United States alone, it is estimated that 39.2% of all rivers, lakes, and streams are unsafe for recreational use, with fecal pathogens as the number one cause of impairment (1). General fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, shed by nearly all warm-blooded animals, are routinely used to assess water quality. However, general FIB cannot discriminate between different animal groups, making it challenging to pinpoint the origin of fecal pollution. Researchers and managers alike recognize the advantages of animal source information to help solve long-standing ambient water quality problems. As a result, a number of fecal source identification technologies have been developed (2-9). These methods have been employed to address challenges such as the identification ...

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Use of aBacteroides thetaiotaomicron-specific α-1-6, mannanase quantitative PCR to detect human faecal pollution in water

Cited by 64 publications

References 34 publications

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment

Current Status of Marker Genes of Bacteroides and Related Taxa for Identifying Sewage Pollution in Environmental Waters

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

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