Specificity of a
            <i>Bacteroides thetaiotaomicron</i>
            Marker for Human Feces

Carson, C. A.; Christiansen, Jessica M.; Yampara-Iquise, Helen; Benson, Verel W.; Baffaut, Claire; Davis, Jerri V.; Broz, Robert R.; Kurtz, William Β.; Rogers, Wendi; Fales, William H.

doi:10.1128/aem.71.8.4945-4949.2005

Cited by 77 publications

(64 citation statements)

References 27 publications

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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%

“…Therefore, cross-reactivity may occur when this region is targeted for MST marker development [56]. It has been suggested that genes directly involved in host-microbe interactions may provide more host specificity than the highly conserved 16S rRNA gene, and may, therefore, be suitable targets for marker development [57]. Several researchers developed qPCR assays targeting Bacteroides genes other than those for 16S rRNA.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Host Specificitymentioning

confidence: 92%

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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“…Thus, MST methods that do not require cultivation, such as the direct detection of bacterial 16S rRNA gene sequences using PCR, are becoming more widespread (5,9). While these assays have now been used in field applications (5,9,20), a recent study demonstrates understandable cross-reactivity when highly conserved genomic regions are targeted (7). Since ribosomal genes are not directly involved in microbe-host interactions, it is possible that other bacterial genetic markers encoding factors related to host specificity might be better candidates for MST assays.…”

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confidence: 99%

Identification of Bacterial DNA Markers for the Detection of Human Fecal Pollution in Water

Shanks

Domingo

et al. 2007

Appl Environ Microbiol

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We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human and pig fecal samples, 351 plasmid clones were sequenced and were determined to define 289 different genomic DNA regions. These putative humanspecific fecal bacterial DNA sequences were then analyzed by dot blot hybridization, which confirmed that 98% were present in the source human fecal microbial community and absent from the original pig fecal DNA extract. Comparative sequence analyses of these sequences suggested that a large number (43.5%) were predicted to encode bacterial secreted or surface-associated proteins. Deoxyoligonucleotide primers capable of annealing to a subset of 26 of the candidate sequences predicted to encode factors involved in interactions with host cells were then used in the PCR and did not amplify markers in DNA from any additional pig fecal specimens. These 26 PCR assays exhibited a range of specificity in tests with 11 other animal sources, with more than half amplifying markers only in specimens from dogs or cats. Four assays were more specific, detecting markers only in specimens from humans, including those from 18 different human populations examined. We then demonstrated the potential utility of these assays by using them to detect human fecal contamination in several impacted watersheds.

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“…Both ruminant and human-associated Bacteroidales markers (RBac and HBac) tested positive for their target host organisms, however, they also displayed cross-reactivity with brush-tail possums (as confirmed from sequencing for HBac), other marsupials, gulls and rabbits. Bacteroidales markers have been widely used overseas and have shown limited crossreactivity with other organisms*HBac markers have been detected from dog (Carson et al 2005;Kildare et al 2007;Harwood et al 2009), cat (Kildare et al 2007) and chicken faeces (Carson et al 2005;Kildare et al 2007;Gourmelon et al 2007;Harwood et al 2009), and the RBac marker has detected in faeces from chickens (Ahmed et al 2008a), horse (this study and V. Harwood, personal communication), pigs (Gourmelon et al 2007) and humans (Gourmelon et al 2007). Overall, the sensitivity (100% for faecal and wastewater samples both) and specificity (87%) of the HBac marker assay was comparable with the sensitivity and specificity reported in the studies conducted in the USA (sensitivity 50Á85% and 100% for faecal and wastewater samples, and specificity 86Á100%; Bernhard & Field 2000b;Carson et al 2005), in France (sensitivity 86Á98% and specificity 94Á99%; Gourmelon et al 2007) and in Australia (sensitivity 100% and specificity 100%; Ahmed et al 2008a, b).…”

Section: Discussionmentioning

confidence: 99%

“…Bacteroidales markers have been widely used overseas and have shown limited crossreactivity with other organisms*HBac markers have been detected from dog (Carson et al 2005;Kildare et al 2007;Harwood et al 2009), cat (Kildare et al 2007) and chicken faeces (Carson et al 2005;Kildare et al 2007;Gourmelon et al 2007;Harwood et al 2009), and the RBac marker has detected in faeces from chickens (Ahmed et al 2008a), horse (this study and V. Harwood, personal communication), pigs (Gourmelon et al 2007) and humans (Gourmelon et al 2007). Overall, the sensitivity (100% for faecal and wastewater samples both) and specificity (87%) of the HBac marker assay was comparable with the sensitivity and specificity reported in the studies conducted in the USA (sensitivity 50Á85% and 100% for faecal and wastewater samples, and specificity 86Á100%; Bernhard & Field 2000b;Carson et al 2005), in France (sensitivity 86Á98% and specificity 94Á99%; Gourmelon et al 2007) and in Australia (sensitivity 100% and specificity 100%; Ahmed et al 2008a, b). In contrast, the sensitivity of the RBac marker was 85% and specificity 65%, which is considerably lower when compared with the studies conducted in the USA (97Á100% sensitivity, 100% specificity; Bernhard & Field 2000b) and in Australia (sensitivity 100% and specificity 97%; Ahmed et al 2008a), but similar to the results reported for samples collected in France (sensitivity 100% and specificity roughly 67Á77%; Gourmelon et al 2007).…”

Section: Discussionmentioning

confidence: 99%

Source tracking faecal contamination in an urbanised and a rural waterway in the Nelson-Tasman region, New Zealand

Kirs

Harwood

Fidler

et al. 2011

New Zealand Journal of Marine and Freshwater Research

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Microbial contamination of New Zealand's rivers, lakes and coastal waters can pose a risk to human health through both recreational contact and the consumption of contaminated shellfish. Microbial source tracking (MST) methods provide a means to identify potential contaminant sources, which can lead to high faecal indicator bacteria concentrations and elevated human health risk because of associated pathogens. Eight MST markers, including general, ruminant and human-associated Bacteroidales markers, a duck-associated E2 marker, a gull-associated Catellicoccus marimammalium marker and three additional human markers [Enterococcus faecium esp gene, Methanobrevibacter smithii nifH gene, and human polyomaviruses (HPyVs)] were tested for host specificity and sensitivity using an array of animal faecal samples of known origin and wastewater samples. The cross-reactivity identified for some of the markers, although limited, signals a need to validate overseas markers further in New Zealand before employing them in field studies. Application of MST markers on water samples collected from an urbanised section of the Maitai River (Nelson, New Zealand) identified the presence of faecal contamination originating from humans, ruminants and birds. Human faecal contamination was present in the lower section of the Matai River, and in stormwater drains entering the river, in association with elevated faecal coliform concentrations. Application of the markers to the rural Little Sydney Stream (near Motueka, Tasman district, NZ) identified faecal contamination derived from ruminants, which is consistent with the agricultural (pasture) use of the catchment. This study indicates that some of the markers developed overseas can be used effectively to track sources of microbial contamination in New Zealand watersheds.

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Specificity of a Bacteroides thetaiotaomicron Marker for Human Feces

Cited by 77 publications

References 27 publications

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

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

Identification of Bacterial DNA Markers for the Detection of Human Fecal Pollution in Water

Source tracking faecal contamination in an urbanised and a rural waterway in the Nelson-Tasman region, New Zealand

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