Molecular Indicators Used in the Development of Predictive Models for Microbial Source Tracking

Ballesté, Elisenda; Bonjoch, Xavier; Belanche, Lluís; Blanch, Anicet R.

doi:10.1128/aem.02350-09

Cited by 69 publications

(50 citation statements)

References 61 publications

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“…Laboratory validation of the HPyV and HF183 markers in this study showed the HPyV target to be 100% specific against dog, cattle, and bird fecal samples while the HF183 marker cross-reacted with dog and bird fecal samples and was 81.25% specific to human fecal contamination. Previous studies have reported similar results for both markers (4,18,33). Higher concentrations of HF183 compared to HPyVs in sewage, however, resulted in an M LOD approximately 100-fold lower (more sensitive) for HF183 than for HPyVs in sterile buffered water.…”

Section: Discussionsupporting

confidence: 65%

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

Staley

Gordon

Schoen

et al. 2012

Appl Environ Microbiol

141

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Before new, rapid quantitative PCR (qPCR) methods for assessment of recreational water quality and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant source has been diluted in environmental waters is needed. This study determined the limits of detection and quantification of the human-associated Bacteroides sp. (HF183) and human polyomavirus (HPyV) qPCR methods for sewage diluted in buffer and in five ambient, Florida water types (estuarine, marine, tannic, lake, and river). HF183 was quantifiable in sewage diluted up to 10 ؊6 in 500-ml ambient-water samples, but HPyVs were not quantifiable in dilutions of >10 ؊4 . Specificity, which was assessed using fecal composites from dogs, birds, and cattle, was 100% for HPyVs and 81% for HF183. Quantitative microbial risk assessment (QMRA) estimated the possible norovirus levels in sewage and the human health risk at various sewage dilutions. When juxtaposed with the MST marker detection limits, the QMRA analysis revealed that HF183 was detectable when the modeled risk of gastrointestinal (GI) illness was at or below the benchmark of 10 illnesses per 1,000 exposures, but the HPyV method was generally not sensitive enough to detect potential health risks at the 0.01 threshold for frequency of illness. The tradeoff between sensitivity and specificity in the MST methods indicates that HF183 data should be interpreted judiciously, preferably in conjunction with a more host-specific marker, and that better methods of concentrating HPyVs from environmental waters are needed if this method is to be useful in a watershed management or monitoring context. Fecal indicator bacteria (FIB), including fecal coliforms, Escherichia coli, and enterococci, have been approved indicators of sewage contamination in recreational waters for decades (49, 51). Swimmers exposed to waters contaminated with sewage are at a greater risk of infection by human pathogens, and subsequent gastrointestinal or other illnesses, than those exposed to unimpacted waters (57). The use of FIB to detect sewage contamination, however, relies on the assumptions that elevated FIB concentrations are representative of pathogen presence and that the fate of these bacteria mimics that of pathogens. Unfortunately, previous studies have shown that concentrations of FIB do not necessarily correlate well with bacterial, protozoan, and viral pathogens (2,20).To address the limitations of FIB, microbial source tracking (MST) methods have been developed to identify human fecal contamination (e.g., sewage) in recreational waters (7, 32). These methods are culture independent and are therefore more rapid than FIB methodologies that require a culture step. The potential for same-day results provides the possibility of advisories that reflect current conditions, rather than day-old ones, which allows more-immediate action to protect against public health risks posed by recreational water use (12, 56). The selecti...

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Section: Discussionsupporting

confidence: 65%

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

Staley

Gordon

Schoen

et al. 2012

Appl Environ Microbiol

141

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“…It has also been suggested that exposure to sunlight is more detrimental to live cells (as assessed by propidium monoazide treatment) than it is to DNA, implying that the disagreement in the reported literature may be due to the physiological state rather than to a direct effect of sunlight (33). Considerably less is known about the impact of biotic interactions (e.g., predation, competition, and viral lysis); existing laboratory-scale and mesocosm studies suggest that these interactions can play an important role (23,24,26,28), but this assertion has not been confirmed in field studies.…”

mentioning

confidence: 81%

“…Most decay studies to date either have been conducted in the laboratory under simulated environmental conditions or have used closed-microcosm systems (e.g., glass beakers or aquarium tanks) ex situ to mimic ambient conditions (23)(24)(25)(26)(27). Nonetheless, the decay of various Bacteroides host-associated genetic markers has been reported to increase with higher temperatures representative of summer conditions (23,26,28,29), and it appears to be more rapid in freshwater compared to marine waters (25,26,30). The effect of ambient sunlight, however, remains ambiguous.…”

mentioning

confidence: 99%

Biotic Interactions and Sunlight Affect Persistence of Fecal Indicator Bacteria and Microbial Source Tracking Genetic Markers in the Upper Mississippi River

Korajkic

McMinn

Shanks

et al. 2014

Appl Environ Microbiol

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The sanitary quality of recreational waters that may be impacted by sewage is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); these organisms are found in the gastrointestinal tracts of humans and many other animals, and hence their presence provides no information about the pollution source. Microbial source tracking (MST) methods can discriminate between different pollution sources, providing critical information to water quality managers, but relatively little is known about factors influencing the decay of FIB and MST genetic markers following release into aquatic environments. An in situ mesocosm was deployed at a temperate recreational beach in the Mississippi River to evaluate the effects of ambient sunlight and biotic interactions (predation, competition, and viral lysis) on the decay of culture-based FIB, as well as molecularly based FIB (Entero1a and GenBac3) and human-associated MST genetic markers (HF183 and HumM2) measured by quantitative real-time PCR (qPCR). In general, culturable FIB decayed the fastest, while molecularly based FIB and human-associated genetic markers decayed more slowly. There was a strong correlation between the decay of molecularly based FIB and that of humanassociated genetic markers (r 2 , 0.96 to 0.98; P < 0.0001) but not between culturable FIB and any qPCR measurement. Overall, exposure to ambient sunlight may be an important factor in the early-stage decay dynamics but generally was not after continued exposure (i.e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence.

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“…Several studies have reported 100% host specificity of the HF183 marker for non-human fecal samples [51,[66][67][68][69][70]. In contrast, the occasional presence of the HF183 markers in non-human fecal samples has also been reported [52,57,61,71,72], particularly in dog, deer, and chicken feces.…”

Section: Host Specificitymentioning

confidence: 92%

“…Many studies have reported the cross-reactivity of Bacteroides 16S rRNA assays by testing non-human fecal samples [49,[51][52][53][54][55]. The 16S rRNA region is highly conserved between different species of Bacteria and Archaea.…”

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

114

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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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Molecular Indicators Used in the Development of Predictive Models for Microbial Source Tracking

Cited by 69 publications

References 61 publications

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

Biotic Interactions and Sunlight Affect Persistence of Fecal Indicator Bacteria and Microbial Source Tracking Genetic Markers in the Upper Mississippi River

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

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