Bacteroidales markers for microbial source tracking in Southeast Asia

Nshimyimana, Jean Pierre; Cruz, Mercedes Cecilia; Thompson, Janelle R.; Wuertz, Stefan

doi:10.1016/j.watres.2017.04.027

Cited by 53 publications

(52 citation statements)

References 40 publications

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“…A similar result was obtained in the previous study while targeting functional genes, gyr B (Lee and Lee ) and Bacteroides thetaiotaomicron (Nshimyimana et al . ).…”

Section: Discussionmentioning

confidence: 97%

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Validation of host‐specific Bacteroidales quantitative PCR assays and their application to microbial source tracking of drinking water sources in the Kathmandu Valley, Nepal

et al. 2018

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“…A similar result was obtained in the previous study while targeting functional genes, gyr B (Lee and Lee ) and Bacteroides thetaiotaomicron (Nshimyimana et al . ).…”

Section: Discussionmentioning

confidence: 97%

“…), and a study done in Singapore (Nshimyimana et al . ). In addition, the findings of an inter‐laboratory comparison study (Boehm et al .…”

Section: Methodsmentioning

confidence: 97%

Validation of host‐specific Bacteroidales quantitative PCR assays and their application to microbial source tracking of drinking water sources in the Kathmandu Valley, Nepal

et al. 2018

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“…This communicates the crucial detail that although the hCYTB484 assay can exhibit low levels of false-positives, these false-positives can be avoided by using the aLoD or aLLoQ as the threshold, with the aLLoQ offering a very high specificity performance. Assays targeting the HF183 human-associated Bacteroides sequences have been shown to exhibit some of the weaknesses of the microbial DNA based markers as discussed in the introduction (6, 8, 10, 11). Considering these findings, researchers have proposed that it may be beneficial to utilize HF183 markers in conjunction with other markers to address its weaknesses in the so-called MST “toolbox” approach.…”

Section: Discussionmentioning

confidence: 99%

“…Within the microbial source tracking (MST) field, the development of an ideal human-specific, culture- and library-independent marker has been a goal for many research efforts for a variety of reasons—notably, its potential as a relatively rapid and broadly-applicable method not requiring the extent of local validation of the host and marker relationship that is required in library-dependent methods (1–4). However, MST marker studies have demonstrated variable specificity (true negative detection rate, calculated by the number of true negatives divided by the sum of true negatives and false positives) and sensitivity (true positive detection rate, calculated by the number of true positives divided by the sum of true positives and false negatives) performances for human-associated microbial DNA markers across varying geographies (1, 5–8), possibly influenced by variations in the human gut microbiome (9) and human-animal interactions (5, 6). Microbial DNA markers have also exhibited variable performance across different scales of fecal pollution: high sensitivity in wastewater collected from sewage networks but lower sensitivity in human fecal samples (10).…”

Section: Introductionmentioning

confidence: 99%

“…Microbial DNA markers have also exhibited variable performance across different scales of fecal pollution: high sensitivity in wastewater collected from sewage networks but lower sensitivity in human fecal samples (10). While much effort has been made in the development of human-specific, culture- and library-independent markers, the variable performance of such microbial markers across various settings necessitates their local validation in the intended setting prior to use to ensure that the fecal signal can be unambiguously attributed to a source (6, 8, 11).…”

Section: Introductionmentioning

confidence: 99%

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A Novel Droplet Digital PCR Human mtDNA Assay for Global Fecal Source Tracking

Zhu

Suttner

Konstantinidis

et al. 2019

Preprint

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229 / 250 words max.) 6 Human mitochondrial DNA (mtDNA) provides a promising target for microbial source tracking 7 because it is unique to humans and universal across human individuals. We developed a droplet 8 digital PCR (ddPCR) assay, hCYTB484, targeting the cytochrome b gene of the human mtDNA 9 and compared the performance of the hCYTB484 assay with a widely used assay targeting 10 human-associated Bacteroides, the HF183/BacR287 assay. We also defined and validated the 11 analytical limit of detection and analytical lower limit of quantification; these analytical limits 12 determine the concentration levels above which samples are declared to be positive and 13 quantifiable for the target, respectively. We found both assays to be highly specific (95%) 14 against cow and pig feces; however, the hCYTB484 was more sensitive when tested against 15 individual human feces from US, Bangladesh, and Mozambique (100% versus a mean of 51% 16 across the 3 countries). To further compare the performance of the two assays, we utilized a 17 receiver operating characteristic curve, showing that the hCYTB484 marker was widely 18 distributed across human feces from the 3 different geographical regions tested and in higher 19 quantities than the HF183/BacR287 marker. The higher performance of the hCYTB484 marker 20 in individual feces is a desirable characteristic in the detection of fecal pollution from sources to 21 which fewer individuals contribute, such as non-sewered types of sanitation that serve most of 22 Earth's population and carry the highest risk of exposure to fecal-oral pathogens. 23 Importance (142/150 words) 24 The usefulness of an ideal human-specific, culture-and library-independent marker to the 25 microbial source tracking field is reflected by the numerous efforts to develop such markers; 26 however, thus far, microbial-based markers of this type have exhibited variable source-27 specificity across geographies and variable sensitivity across scales of fecal waste. Most of the 28 3 world's population is served by non-sewered forms of sanitation that also carry the highest risk 29 of exposure to fecal-oral pathogens. This reality underscores the need for markers of human fecal 30 contamination that have high sensitivity in fecal pollution sources to which fewer individuals 31 contribute to, such as fecal sludges found in pit latrines. We show that human mtDNA-based 32 methods can be highly source-specific and highly sensitive in smaller scales of fecal pollution, 33 providing a useful addition to the microbial source tracking toolbox by complementing the 34 variable performance of microbial-based markers. 35 4 Word Count 3854/6000 (should not exceed approximately 6,000 words, exclusive of methods, 36 references, figure legends, tables, and supplemental material) 37 Introduction 38Within the microbial source tracking (MST) field, the development of an ideal human-specific, 39 culture-and library-independent marker has been a goal for many research efforts for a variety of 40 reasons-nota...

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Assessing human‐specific CrAssphage recovery after acidification‐filtration concentrating method in environmental water

Kongprajug

Chyerochana

Sangkaew

et al. 2019

Water Environment Research

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Pinpointing water pollution sources using host-specific gastrointestinal microbes, known as microbial source tracking (MST), have significant benefits for countries with water quality management issues related to pollution. A recently discovered bacteriophage, crAssphage, shows promise as a human-specific MST marker. However, loss of genetic materials during the recovery and the detection processes could alter the ability to measure virus quantities in a water sample. This study determined the crAssphage recovery efficiencies in water sources, including seawater, freshwater, and influent and effluent from a wastewater treatment plant, by spiking natural crAssphage concentrates prior to DNA extraction and quantitative PCR analysis. The results showed that river and seawater with no or low crAssphage background experienced no recovery loss. Evaluating recovery efficiencies in samples with high crAssphage backgrounds posed a challenge due to the inability to prepare high crAssphage titers. This study highlights the importance of intra-laboratory assessment of recovery efficiency in environmental samples for retrieving absolute crAssphage quantification with correction of bias among water samples and increase in data accuracy. • Practitioner points• In laboratory assessment of recovery efficiency is crucial for bias correction and data accuracy for absolute crAssphage quantification in water samples. • No loss in crAssphage recovery was observed in river and seawater that contained no or low crAssphage backgrounds. • Inability to prepare high crAssphage spike concentrations remains the major limitation for evaluating recovery in samples with high crAssphage backgrounds. • The results underline the importance of evaluating method recovery in real environmental samples that reflect actual matrix effect. • Absolute crAssphage quantification, as human-specific pollution marker, could be used for prioritizing water quality restoration and area-based management plan.

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Bacteroidales markers for microbial source tracking in Southeast Asia

Cited by 53 publications

References 40 publications

Validation of host‐specific Bacteroidales quantitative PCR assays and their application to microbial source tracking of drinking water sources in the Kathmandu Valley, Nepal

Validation of host‐specific Bacteroidales quantitative PCR assays and their application to microbial source tracking of drinking water sources in the Kathmandu Valley, Nepal

A Novel Droplet Digital PCR Human mtDNA Assay for Global Fecal Source Tracking

Assessing human‐specific CrAssphage recovery after acidification‐filtration concentrating method in environmental water

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