PCR data and comparative performance of Bacteroidales microbial source tracking genetic markers

Somnark, Pornjira; Chyerochana, Natcha; Kongprajug, Akechai; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

doi:10.1016/j.dib.2018.04.129

Cited by 14 publications

(20 citation statements)

References 27 publications

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“…Selected universal and human-, swine-, and cattlespecific Bacteroidetes gene markers, including GenBac3, 62 HF183/BFDrev, 56 Pig-2-Bac, 20 and Bac3 63 as well as the human-specific crAssphage marker CPQ_056, 19 were used in this study because they have been previously studied in the central Thailand region. 3,23,37,38,64 For the conventional, standard-curve-dependent qPCR analysis, assigning DNQ as positive or negative would affect the calculation of the performance measures. For the LinRegPCR analysis, only…”

Section: ■ Introductionmentioning

confidence: 99%

“…In many cases, more than one source will have contributed to the pollution, and the qPCR technique can rank the different contributions and identify significant sources. Many qPCR assays have been designed and validated for tracking fecal contamination from humans and animals such as cattle, swine, chicken, and so on. − However, the diversity in the abundance and distribution of the gut microbial community in different geographical regions implies that the performance of MST assays needs to be evaluated before introducing the procedure in a new area. − In general, five performance measures represent the intrinsic properties of each MST gene marker when testing fecal materials from a target source, which is expected to contain a marker of the target species, and from nontarget sources. Sensitivity represents the prevalence of the target marker within a target population, whereas specificity reflects the marker’s presence exclusively within the target population.…”

Section: Introductionmentioning

confidence: 99%

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Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution

Kongprajug

Chyerochana

Mongkolsuk

et al. 2020

Environ. Sci. Technol.

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The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log 10 copies/g and 0.41 log 10 copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log 10 copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.

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Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution

Kongprajug

Chyerochana

Mongkolsuk

et al. 2020

Environ. Sci. Technol.

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“…However, the cow marker gene (one of the possible ruminants) was not detected. It is possible that the primers used in this study for the ruminant marker gene may have cross-reactivity with horses or other animals [19,40,[57][58][59]. Keeping this in mind, the team looked for the possible cultural events that had taken place near the beach at that time and discovered that throughout the summer, a horse-drawn carriage for sightseeing had been parked for some time near sites 8 and 9.…”

Section: Discussionmentioning

confidence: 99%

Microbial Source Tracking as a Method of Determination of Beach Sand Contamination

Valério

Santos

Teixeira

et al. 2022

IJERPH

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Beach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring.

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“…Next, spiked and unspiked reactors were pH adjusted to 3.50 prior to vacuum filtration with a 0.45‐μm‐pore‐size HAWP membrane (Merck Millipore; Kongprajug, Chyerochana, et al, ). Filtered membranes were cut, and DNA extracted using a Quick‐DNA Fecal Soil Microbe Miniprep kit (Zymo Research, Irvine, CA, USA; Somnark, Chyerochana, Kongprajug, Mongkolsuk, & Sirikanchana, ; Somnark, Chyerochana, Mongkolsuk, & Sirikanchana, ). DNA concentrations were measured with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

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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PCR data and comparative performance of Bacteroidales microbial source tracking genetic markers

Cited by 14 publications

References 27 publications

Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution

Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution

Microbial Source Tracking as a Method of Determination of Beach Sand Contamination

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

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