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

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

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.

Integrated analyses of fecal indicator bacteria, microbial source tracking markers, and pathogens for Southeast Asian beach water quality assessment

The degradation of coastal water quality from fecal pollution poses a health risk to visitors at recreational beaches. Fecal indicator bacteria (FIB) are a proxy for fecal pollution; however the accuracy of their representation of fecal pollution health risks at recreational beaches impacted by non-point sources is disputed due to non-human derivation. This study aimed to investigate the relationship between FIB and a range of culturable and molecular-based microbial source tracking (MST) markers and pathogenic bacteria, and physicochemical parameters and rainfall. Forty-two marine water samples were collected from seven sampling stations during six events at two tourist beaches in Thailand. Both beaches were contaminated with fecal pollution as evident from the GenBac3 marker at 88%-100% detection and up to 8.71 log₁₀ copies/100 mL. The human-specific MST marker human polyomaviruses JC and BK (HPyVs) at up to 4.33 log₁₀ copies/100 mL with 92%-94% positive detection indicated that human sewage was likely the main contamination source. CrAssphage showed lower frequencies and concentrations; its correlations with the FIB group (i.e., total coliforms, fecal coliforms, and enterococci) and GenBac3 diminished its use as a human-specific MST marker for coastal water. Human-specific culturable AIM06 and SR14 bacteriophages and general fecal indicator coliphages also showed less sensitivity than the human-specific molecular assays. The applicability of the GenBac3 endpoint PCR assay as a lower-cost prescreening step prior to the GenBac3 qPCR assay was supported by its 100% positive predictive value, but its limited negative predictive values required subsequent qPCR confirmation. Human enteric adenovirus and Vibrio cholerae were not found in any of the samples. The HPyVs related to Vibrio parahaemolyticus, Vibrio vulnificus, and 5-d rainfall records, all of which were more prevalent and concentrated during the wet season. More monitoring is therefore recommended during wet periods. Temporal differences but no spatial differences were observed, suggesting the need for a sentinel site at each beach for routine monitoring. The exceedance of FIB water quality standards did not indicate increased prevalence or concentrations of the HPyVs or Vibrio spp. pathogen group, so the utility of FIB as an indicator of health risks at tropical beaches maybe challenged. Accurate assessment of fecal pollution by incorporating MST markers could lead to developing a more effective water quality monitoring plan to better protect human health risks in tropical recreational beaches.

Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand

Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log₁₀ copies/100 mL), crAssphage (5.28-7.38 log₁₀ copies/100 mL), and HPyVs (3.66-6.53 log₁₀ copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log₁₀ copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log₁₀ copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log₁₀ copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log₁₀ copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer

The Edwards Aquifer serves as a primary source of drinking water to more than 2 million people in south-central Texas, and as a karst aquifer, is vulnerable to human and animal fecal contamination which poses a serious risk to human and environmental health. A one-year study (Jan 2018 - Feb 2019) was conducted to determine the primary sources of fecal pollution along the Balcones and Leon Creek within the Edwards Aquifer recharge and contributing zones using general (E. coli, enterococci, and universal Bacteriodales) and host-associated (human-, dog-, cow- and chicken/duck-associated Bacteriodales) microbial source tracking (MST) assays. Additionally, sites were classified based on surrounding land use as a potential source predictor and marker levels were correlated with rain events and water quality parameters. Levels for the three general indicators were highest and exhibited similar trends across the sampling sites, suggesting that the sole use of these markers is not sufficient for specific fecal source identification. Among the host-associated markers, highest concentrations were observed for the dog marker (BacCan) in the Leon Creek area and the cow marker (BacCow) in the Balcones Creek area. Additionally, Chicken/Duck-Bac, BacCan and BacCow all exhibited higher concentrations during the spring season and the end of fall/early winter. Relatively lower concentrations were observed for the human-associated markers (HF183 and BacHum), however, levels were higher in the Leon Creek area and highest following rainfall events. Additionally, relatively higher levels in HF183 and BacHum were observed at sites having greater human population and septic tank density and may be attributed to leaks or breaks in these infrastructures. This study is the first to examine and compare fecal contamination at rural and urban areas in the recharge and contributing zones of the Edwards Aquifer using a molecular MST approach targeting Bacteroidales 16S rRNA gene-based assays. The Bacteroidales marker assays, when combined with land use and weather information, can allow for a better understanding of the sources and fluxes of fecal contamination, which can help devise effective mitigation measures to protect water quality.

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

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 log₁₀ copies/g and 0.41 log₁₀ 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 log₁₀ 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.

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

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.

Human and animal microbial source tracking in a tropical river with multiple land use activities

The enhancement and restoration of the water quality of deteriorating surface water resources can be challenging, particularly for rivers with multiple usages, such as agriculture, animal husbandry, human residence, and industries. Recently, the performance of DNA-based microbial source tracking (MST) indicators detected by end-point and quantitative PCR assays for identifying sources of fecal pollution from human sewage, swine, and cattle and non-host-specific (universal) fecal pollution in the Tha Chin River basin, Thailand, was evaluated. The present study monitored these validated MST markers and various physicochemical and microbial water quality parameters in samples collected from twelve stations along the Tha Chin River during four sampling events in the wet and dry seasons. No significant difference in precipitation was observed between the wet and dry samplings. Universal markers (both PCR and qPCR) were detected in all 48 samples, indicating persistent and continuing fecal contamination. The sewage- and swine-specific qPCR marker concentrations did not vary among the sampling events, whereas cattle-specific qPCR markers were detected only in the wet season. Animal-specific markers were detected in the lower Tha Chin River section, which is characterized by intensive animal farming. Sewage-specific markers were also found in the lower section and near an upstream residential area. The high agreement (87.5-100%) between the PCR and qPCR results suggested that PCR could serve as a lower-cost MST screening test that requires less technical expertise. A multivariate analysis conducted using the survival analysis procedure to include censored data also emphasized the high pollution in the lower section of the river at all sampling events. Universal and swine-specific markers showed moderate correlations with microbial indicators, including total coliforms, fecal coliforms, E. coli, and enterococci. None of the MST markers or microbial parameters were associated with the measured physicochemical parameters. This study provides the first evaluation of MST markers for monitoring surface freshwater in Thailand, and the findings might aid the pollution surveillance of impaired water bodies and the development of strategies for improving their water quality.

Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds

Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixteen endpoint and quantitative PCR (qPCR) assays targeting universal and human-, swine-, and cattle-specific Bacteroidales gene markers were modified for endpoint PCR, evaluated for their performance with sewage and fecal samples from the Tha Chin watershed and subsequently validated with samples from the Chao Phraya watershed, Thailand. Sample sizes of 81 composite samples (from over 1620 individual samples) of farm animals of each type as well as 19 human sewage samples from the Tha Chin watershed were calculated using a stratified random sampling design to achieve a 90% confidence interval and an expected prevalence (i.e., desired assay's sensitivity) of 0.80. The best universal and human-, swine-, and cattle-specific fecal markers were BacUni EP, HF183/BFDrev EP, Pig-2-Bac EP, and Bac3 assays, respectively. The detection limits for these assays ranged from 30 to 3000 plasmid copies per PCR. The positive predictive values were high in universal and swine- and cattle-specific markers (85-100%), while the positive predictive value of the human-specific assay was 52.2%. The negative predictive values in all assays were relatively high (90.8-100%). A suite of PCR assays in Thailand was established for potential MST use in environmental waters, which supports the worldwide applicability of Bacteroidales gene markers. This study also emphasizes the importance of using a proper sample size in assessing the performance of MST markers in a new geographic region.