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

Evaluating acute gastroenteritis-causing pathogen reduction in wastewater and the applicability of river water for wastewater-based epidemiology in the Kathmandu Valley, Nepal

Rapid urbanization and population growth without the implementation of proper waste management are capable of contaminating water sources, which can lead to acute gastroenteritis. This study examined the detection and reduction of five gastroenteritis-causing enteropathogens, Salmonella, Campylobacter coli, Campylobacter jejuni, Clostridium perfringens, and genogroup IV norovirus, and one respiratory pathogen, influenza A virus, in two municipal wastewater treatment plants (WWTP) using an oxidation ditch system (WWTP A; n = 20) and a stabilization pond system (WWTP B; n = 18) in the Kathmandu Valley, Nepal, collected between August 2017 and August 2019. All enteropathogens were detected in wastewater via quantitative PCR. The concentrations of the pathogens ranged from 5.7 to 7.9 log10 copies/L in WWTP A and from 4.9 to 8.1 log10 copies/L in WWTP B. The log10 reduction values of the pathogens ranged from 0.3 to 1.0 in WWTP A and from -0.1 to 0.2 in WWTP B. The association between the pathogen concentrations and the number of clinical cases in the corresponding week could not be evaluated; however, the consistent detection of pathogens in the wastewater despite low number of case reports suggested the use of wastewater-based epidemiology (WBE) for early warning of acute gastroenteritis (AGE) in the Kathmandu Valley. The pathogens were also detected in river water at approximately 7.0 log10 copies/L and exhibited no significant difference in concentration compared to wastewater, suggesting the applicability of river water for WBE of AGE. Insufficient treatment of all pathogens in the wastewater was observed, suggesting the need for full rehabilitation of the treatment plants. However, the influent may be utilized for early detection of AGE-causing pathogens in the city, whereas the river water may serve as an alternative in areas without connection to the WWTPs.

Bacteroidales as a fecal contamination indicator in fresh produce industry: A baseline measurement

Foodborne outbreaks caused by fecal contamination of fresh produce represent a serious concern to public health and the economy. As the consumption of fresh produce increases, public health officials and organizations have pushed for improvements in food safety procedures and environmental assessments to reduce the risk of contamination. Visual inspections and the establishment of "buffer zones" between animal feeding operations and producing fields are the current best practices for environmental assessments. However, a generalized distance guideline and visual inspections may not be enough to account for all environmental risk variables. Here, we report a baseline measurement surveying the background Bacteroidales concentration, as a quantitative fecal contamination indicator, in California's Salinas Valley. We collected a total of 1632 samples from two romaine lettuce commercial fields at the time of harvesting through two seasons in a year. The quantification of Bacteroidales concentration was performed using qPCR, revealing a notably low concentration (0-2.00 copies/cm2) in the commercial fields. To further enhance the applicability of our findings, we developed a user-friendly method for real-world fecal contamination risk assessment that seamlessly integrates with industry practices. Through the generation of heatmaps that visually illustrate varying risk levels across fields, this approach can identify site-specific risks and offer fresh produce stakeholders a more comprehensive understanding of their land. We anticipate this work can encourage the use of Bacteroidales in the fresh produce industry to monitor fecal contamination and prevent future foodborne outbreaks.

Assessing the Occurrence of Host-Specific Faecal Indicator Markers in Water Systems as a Function of Water, Sanitation and Hygiene Practices: A Case Study in Rural Communities of Vhembe District Municipality, South Africa

In settings where humans and animals closely coexist, the introduction of faecal material into unprotected water sources significantly increases the risk of contracting diarrhoeal and zoonotic waterborne diseases. The data were gathered from a survey conducted through interviews at randomly sampled villages; additionally, water samples were collected in randomly selected households and their associated feeder catchments. Molecular techniques were used, specifically qPCR, to run host-specific Bacteroides microbial source tracking (MST) assays for human, cattle, pig, chicken and dog faecal contamination. Unexpectedly, the qPCR assays revealed dogs to be the most prevalent (40.65%) depositor of faecal matter in unprotected surface water, followed by humans (40.63%); this finding was contradictory to survey findings indicating cattle as the leading source. At the household level, dogs (16.67%) and chickens (15.28%) played prominent roles, as was expected. Reflecting on some of the basic daily practices in households, nearly 89.00% of the population was found to store water due to erratic supply, in contrast to 93.23% using an improved water source. Additionally, a significant association was found between water, sanitation and hygiene (WASH) variables and the occurrence of MST markers after performing a bivariate linear regression. However, the inconsistency between the MST results and household surveys suggests pervasive sanitation issues, even in households without domesticated animals.

Identification of fecal contamination sources of groundwater in rural areas of Vhembe District Municipality, Limpopo Province, South Africa

Groundwater is a valuable source of drinking water worldwide, recognized as an improved drinking water source. However, on-site sanitation systems may put groundwater at risk of fecal contamination. In the present study, two approaches were used to ascertain the sources of fecal contamination in groundwater used by communities of the Vhembe District Municipality. Overall, 87.5% of boreholes (n = 70) in the wet and 72.5% in the dry season were contaminated with Escherichia coli, and septic tank (n = 18) wastewaters displayed up to 104  cfu/mL E. coli. Host-specific Bacteroidales quantitative polymerase chain reaction (qPCR) assays established the presence of human (BacHum and HF183) and animal (Cytb, BacCan, and Pig-2Bac) genetic markers in groundwater from 15.7% of boreholes (wet) and 10% of boreholes (dry). No strong associations were founded between culturable E. coli counts and the presence/absence of marker genes for all the markers except for Cytb marker, which showed a weak significant correlation (r = 0.217; p = <0.01) between E. coli and the Cytb marker under dry seasonal conditions. Human markers and Cytb were present in the household septic tank wastewater samples. Significant differences in marker genes distribution in wastewater were observed using the Chi-squared test: HF183 (p = <0.001) and BacHum (p = <0.001). Overall, no association was recorded between markers in groundwater and in wastewater for 18 households' septic tanks. A combined culturable E. coli and host-specific Bacteroidales qPCR assays remain an appropriate approach for the identification of fecal contamination of groundwater. PRACTITIONER POINTS: Households primarily used private boreholes for drinking water, as a primary source. Most households used on-site sanitation systems, including ventilated improved pit latrines and flush toilets connected to septic tanks. Escherichia coli was detected in groundwater, and the sources of fecal contamination were humans and animals (pigs, dogs, and chickens). The presence of human and animal markers in groundwater suggests that humans and animals are liable for fecal contamination. Fecal contamination in drinking water sources poses a significant concern due to pathogenic microorganisms posing potential human health risks.

Assessment of multiple fecal contamination sources in surface waters using environmental mitochondrial DNA metabarcoding

Waterborne diseases are transmitted to humans through the fecal contamination of water, where homeothermic species are the main reservoir. Fecal indicator bacteria (FIB) are often used to determine the occurrence of fecal contamination. However, FIB cannot provide the source of fecal contamination. Furthermore, as fecal inputs and contamination could originate from multiple sources (e.g., human, livestock, wildlife), multiple source tracking markers are required to identify fecal sources. From a previous study, we developed a mitochondrial DNA (mtDNA) metabarcoding approach to assess the presence of multiple homeotherms in four surface waters. Here, we have broadened our approach by sampling 86 surface water samples from the L'Assomption River and Ville-Marie watersheds (Province of Quebec, Canada). Fecal coliform levels were higher than the expected sanitary recommendations for recreational water (> 200 CFU/100 mL) in 73 % samples. The occurrence of mtDNA from human, livestock, domestic animals, wild mammals and wild birds was found in 40-88 % of the samples. Multivariate analyses showed significant covariations between homeothermic taxa and fecal coliforms, enterococci, β-D-glucuronidase, conductivity, the human-specific Bacteroidales Hf183 genetic marker, and the human population, in the watersheds of L'Assomption River (p = 0.001) and Ville-Marie (p = 0.015) (Province of Quebec, Canada). Through the application of Bayes Theorem, it was determined that fecal coliforms co-occurred with the detection of bovine, beaver, robin and chicken mtDNA in 100 % of cases in the L'Assomption River watershed, and human mtDNA co-occurred with fecal coliforms in 93 % and 76 % of cases in L'Assomption River watershed and Ville-Marie sub-catchment, respectively. This study suggests that fecal contamination could be the result of multiple species, among which some wild animals may contribute to fecal inputs in surface waters, resulting in potential risk to human health. This reinforces the necessity of using the mtDNA metabarcoding method to monitor multi-animal species.

Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study

With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.

Applicability of F-specific bacteriophage subgroups, PMMoV and crAssphage as indicators of source specific fecal contamination and viral inactivation in rivers in Japan

To date, several microbes have been proposed as potential source-specific indicators of fecal pollution. 16S ribosomal RNA gene markers of the Bacteroidales species are the most widely applied due to their predominance in the water environment and source specificity. F-specific bacteriophage (FPH) subgroups, especially FRNA phage genogroups, are also known as potential source-specific viral indicators. Since they can be quantified by both culture-based and molecular assays, they may also be useful as indicators for estimating viral inactivation in the environment. Pepper mild mottle virus (PMMoV) and crAssphage, which are frequently present in human feces, are also potentially useful as human-specific indicators of viral pollution. This study aimed to evaluate the applicability of FPH subgroups, PMMoV, and crAssphage as indicators of source-specific fecal contamination and viral inactivation using 108 surface water samples collected at five sites affected by municipal and pig farm wastewater. The host specificity of the FPH subgroups, PMMoV, and crAssphage was evaluated by principal component analysis (PCA) along with other microbial indicators, such as 16S ribosomal RNA gene markers of the Bacteroidales species. The viabilities (infectivity indices) of FRNA phage genogroups were estimated by comparing their numbers determined by infectivity-based and molecular assays. The PCA explained 58.2% of the total information and classified microbes into three groups: those considered to be associated with pig and human fecal contamination and others. Infective and gene of genogroup IV (GIV)-FRNA phage were assumed to be specific to pig fecal contamination, while the genes of GII-FRNA phage and crAssphage were identified to be specific to human fecal contamination. However, PMMoV, infective GI-FRNA phage, and FDNA phage were suggested to not be specific to human or pig fecal contamination. FRNA phage genogroups, especially the GIV-FRNA phage, were highly inactivated in the warm months in Japan (i.e., July to November). Comparing the infectivity index of several FRNA phage genogroups or other viruses may provide further insight into viral inactivation in the natural environment and by water treatments.

Host-Associated Bacteroides 16S rDNA-Based Markers for Source Tracking of Fecal Pollution in Laguna Lake, Philippines

Sources of fecal contamination in Laguna Lake, Philippines, were identified using a library-independent microbial source tracking method targeting host-associated Bacteroides 16S rDNA-based markers. Water samples from nine lake stations were assessed for the presence of the fecal markers HF183 (human), BoBac (cattle), Pig-2-Bac (swine), and DuckBac (duck) from August 2019 to January 2020. HF183 (average concentration = 1.91 log₁₀ copies/mL) was the most frequently detected, while Pig-2-Bac (average concentration = 2.47 log₁₀ copies/mL) was the most abundant. The detected marker concentrations in different stations corresponded to the land use patterns around the lake. Generally, all marker concentrations were higher during the wet season (August-October), suggesting the effect of rainfall-associated factors on the movement and retention of markers from sources. There was a significant association (ρ = 0.45; p < 0.001) between phosphate and the concentration of HF183, suggesting domestic sewage-derived pollution. The markers had acceptable sensitivity and specificity, i.e., HF183 (S = 0.88; R = 0.99), Pig-2-Bac (S = 1.00; R = 1.00), and DuckBac (S = 0.94; R = 1.00), and therefore may be used for the continuous monitoring of fecal pollution in the lake and in designing interventions to improve the quality of the lake water.

Fecal pollution source characterization in the surface waters of recharge and contributing zones of a karst aquifer using general and host-associated fecal genetic markers

Fecal pollution of surface waters in the karst-dominated Edwards aquifer is a serious concern as contaminated waters can rapidly transmit to groundwaters, which are used for domestic purposes. Although microbial source tracking (MST) detects sources of fecal pollution, integrating data related to environmental processes (precipitation) and land management practices (septic tanks) with MST can provide better understanding of fecal contamination fluxes to implement effective mitigation strategies. Here, we investigated fecal sources and their spatial origins at recharge and contributing zones of the Edwards aquifer and identified their relationship with nutrients in different environmental/land-use conditions. During March 2019 to March 2020, water samples (n = 295) were collected biweekly from 11 sampling sites across four creeks and analyzed for six physico-chemical parameters and ten fecal indicator bacteria (FIB) and MST-based qPCR assays targeting general (E. coli, Enterococcus, and universal Bacteroidales), human (BacHum and HF183), ruminant (Rum2Bac), cattle (BacCow), canine (BacCan), and avian (Chicken/Duck-Bac and GFD) fecal markers. Among physico-chemical parameters, nitrate-N (NO₃-N) concentrations at several sites were higher than estimated national background concentrations for streams. General fecal markers were detected in the majority of water samples, and among host-associated MST markers, GFD, BacCow, and Rum2Bac were more frequently detected than BacCan, BacHum, and HF183, indicating avian and ruminant fecal contamination is a major concern. Cluster analysis results indicated that sampling sites clustered based on precipitation and septic tank density showed significant correlation (p < 0.05) between nutrients and FIB/MST markers, indicating these factors are influencing the spatial and temporal variations of fecal sources. Overall, results emphasize that integration of environmental/land-use data with MST is crucial for a better understanding of nutrient loading and fecal contamination.

Occurrence and Reduction of Shiga Toxin-Producing Escherichia coli in Wastewaters in the Kathmandu Valley, Nepal

Inadequately treated effluents discharged from wastewater treatment plants (WWTPs) severely affect the environment and the surrounding population. This study analyzed the presence of the Shiga toxin-producing Escherichia coli (STEC) genes, stx1, and stx2, and the E. coli gene, sfmD, in municipal WWTP A (n = 11) and B (n = 11) where the reductions were also evaluated; hospitals (n = 17), sewage treatment plants (STPs) (n = 4) and non-functional WWTPs (not-working WWTPs) (n = 5) in the Kathmandu Valley, Nepal. The sfmD gene was detected in 100% of the samples in WWTPs, hospitals, and not-working WWTPs and 50% of STP samples. The highest detection of stx1 and stx2 was shown in the WWTP influents, followed by WWTP effluents, not-working WWTP wastewater, hospital wastewater, and STP wastewater. Log10 reduction values of sfmD, stx1, and stx2 in WWTP A were 1.7 log10, 1.7 log10, 1.4 log10, whereas those in WWTP B were 0.5 log10, 0.6 log10, 0.5 log10, respectively, suggesting the ineffective treatment of STEC in the wastewater in the Kathmandu Valley. The high concentrations of the stx genes in the wastewaters suggest the increasing presence of aggressive STEC in the Kathmandu Valley, which should be a major public health concern.

An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

Fecal contamination of water constitutes a serious health risk to humans and environmental ecosystems. This is mainly due to the fact that fecal material carries a variety of enteropathogens, which can enter and circulate in water bodies through fecal pollution. In this respect, the prompt identification of the polluting source(s) is pivotal to guiding appropriate target-specific remediation actions. Notably, microbial source tracking (MST) is widely applied to determine the host origin(s) contributing to fecal water pollution through the identification of zoogenic and/or anthropogenic sources of fecal environmental DNA (eDNA). A wide array of host-associated molecular markers have been developed and exploited for polluting source attribution in various aquatic ecosystems. This review is intended to provide the most up-to-date overview of genetic marker-based MST studies carried out in different water types, such as freshwaters (including surface and groundwaters) and seawaters (from coasts, beaches, lagoons, and estuaries), as well as drinking water systems. Focusing on the latest scientific progress/achievements, this work aims to gain updated knowledge on the applicability and robustness of using MST for water quality surveillance. Moreover, it also provides a future perspective on advancing MST applications for environmental research.

Bacteroides Microbial Source Tracking Markers Perform Poorly in Predicting Enterobacteriaceae and Enteric Pathogen Contamination of Cow Milk Products and Milk-Containing Infant Food

Consumption of microbiologically contaminated food is one of the leading causes of diarrheal diseases. Understanding the source of enteric pathogens in food is important to guide effective interventions. Enterobacteriaceae bacterial assays typically used to assess food safety do not shed light on the source. Source-specific Bacteroides microbial source tracking (MST) markers have been proposed as alternative indicators for water fecal contamination assessment but have not been evaluated as an alternative fecal indicator in animal-derived foods. This study tested various milk products collected from vendors in urban Kenyan communities and infant foods made with the milk (n = 394 pairs) using conventional culture methods and TaqMan qPCR for enteric pathogens and human and bovine-sourced MST markers. Detection profiles of various enteric pathogens and Bacteroides MST markers in milk products differed from that of milk-containing infant foods. MST markers were more frequently detected in infant food prepared by caregivers, indicating recent contamination events were more likely to occur during food preparation at home. However, Bacteroides MST markers had lower sensitivity in detecting enteric pathogens in food than traditional Enterobacteriaceae indicators. Bacteroides MST markers tested in this study were not associated with the detection of culturable Salmonella enterica and Shigella sonnei in milk products or milk-containing infant food. The findings show that while Bacteroides MST markers could provide valuable information about how foods become contaminated, they may not be suitable for predicting the origin of the enteric pathogen contamination sources.

Quantitative detection of human- and canine-associated Bacteroides genetic markers from an urban coastal lagoon

The contamination of water catchments by nonpoint source faecal pollution is a major issue affecting the microbial quality of receiving waters and is associated with the occurrence of a range of enteric illnesses in humans. The potential sources of faecal pollution in surface waters are diverse, including urban sewage leaks, surface runoff and wildlife contamination originating from a range of hosts. The major contributing hosts require identification to allow targeted management of this public health concern. In this study, two high-performing Microbial Source Tracking (MST) assays, HF183/Bac242 and BacCan-UCDmodif, were used for their ability to detect host-specific Bacteroides 16Sr RNA markers for faecal pollution in a 12-month study on an urban coastal lagoon in Sydney, Australia. The lagoon was found to contain year-round high numbers of human and canine faecal markers, as well as faecal indicator bacteria counts, suggesting considerable human and animal faecal pollution. The high sensitivity and specificity of the HF183/Bac242 and BacCan-UCDmodif assays, together with the manageable levels of PCR inhibition and high level DNA extraction efficiency obtained from lagoon water samples make these markers candidates for inclusion in an MST 'toolbox' for investigating host origins of faecal pollution in urban surface waters.

Impacts of rapid urbanization on characteristics, sources and variation of fecal coliform at watershed scale

Microbial pollution is an environmental problem of growing concern for threatening human health. However, the impacts of rapid urbanization on characteristics, sources and variation of fecal coliform (FC) at watershed scale have not been fully explored. In this study, FC characteristics were monitored monthly for 2 years at 21 river sections in an urbanizing watershed, while the sources and continuously annual variation were quantified by integrating two commonly-used models. The results showed that FC varied from 10³ to 10⁶ MPN/L, indicating a great spatiotemporal variation at watershed scale. Peak FC occurred in summer and autumn among upstream and downstream areas, respectively. Besides, 65% impermeable surface was identified as the threshold of urban level, beyond which the key FC source would shift from agriculture to urban. It was also found that the changes of urban landscape patterns had poor correlation with annual variation of FC. In comparison, urbanization speed was identified as the major driver with the threshold of 30% for deteriorating FC pollution. The Low Impact Development could result in a 5.13%-97.59% reduction of FC at watershed scale.

Associations among Household Animal Ownership, Infrastructure, and Hygiene Characteristics with Source Attribution of Household Fecal Contamination in Peri-Urban Communities of Iquitos, Peru

Using previously validated microbial source tracking markers, we detected and quantified fecal contamination from avian species and avian exposure, dogs, and humans on household cooking tables and floors. The association among contamination, infrastructure, and socioeconomic covariates was assessed using simple and multiple ordinal logistic regressions. The presence of Campylobacter spp. in surface samples was linked to avian markers. Using molecular methods, animal feces were detected in 75.0% and human feces in 20.2% of 104 households. Floors were more contaminated than tables as detected by the avian marker Av4143, dog marker Bactcan, and human marker Bachum. Wood tables were consistently more contaminated than non-wood surfaces, specifically with the mitochondrial avian markers ND5 and CytB, fecal marker Av4143, and canine marker Bactcan. Final multivariable models with socioeconomic and infrastructure characteristics included as covariates indicate that detection of avian feces and avian exposure was associated with the presence of chickens, maternal age, and length of tenancy, whereas detection of human markers was associated with unimproved water source. Detection of Campylobacter in surface samples was associated with the avian fecal marker Av4143. We highlight the critical need to detect and measure the burden of animal fecal waste when evaluating household water, hygiene, and sanitation interventions, and the possibility of decreasing risk of exposure through the modification of surfaces to permit more effective household disinfection practices. Animals may be a more important source of household fecal contamination than humans in many low-resource settings, although interventions have historically focused almost exclusively on managing human waste.

Assessing the faecal source sensitivity and specificity of ruminant and human genetic microbial source tracking markers in the central Ethiopian highlands

This study tested genetic microbial source tracking (MST) methods for identifying ruminant‐ (BacR) and human‐associated (HF183/BacR287, BacHum) bacterial faecal contaminants in Ethiopia in a newly created regional faecal sample bank (n = 173). BacR performed well, and its marker abundance was high (100% sensitivity (Sens), 95% specificity (Spec), median log₁₀ 8·1 marker equivalents (ME) g⁻¹ ruminant faeces). Human‐associated markers tested were less abundant in individual human samples (median: log₁₀ 5·4 and 4·2 (ME + 1) g⁻¹) and were not continuously detected (81% Sens, 91% Spec for BacHum; 77% Sens, 91% Spec for HF183/BacR287). Furthermore, the pig‐associated Pig2Bac assay was included and performed excellent (100% Sens, 100% Spec). To evaluate the presence of MST targets in the soil microbiome, representative soil samples were tested during a whole seasonal cycle (n = 60). Only BacR could be detected, but was limited to the dry season and to sites of higher anthropogenic influence (log₁₀ 3·0 to 4·9 (ME + 1) g⁻¹ soil). In conclusion, the large differences in marker abundances between target and non‐target faecal samples (median distances between distributions ≥log₁₀ 3 to ≥log₁₀ 7) and their absence in pristine soil indicate that all tested assays are suitable candidates for diverse MST applications in the Ethiopian area.

Validation of microbial source tracking markers for the attribution of fecal contamination in indoor-household environments of the Peruvian Amazon

The performance of eight microbial source tracking (MST) markers was evaluated in a low-resource, tropical community located in Iquitos, Peru. Fecal samples from humans, dogs, cats, rats, goats, buffalos, guinea-pigs, chickens, ducks, pigeons, and parrots were collected (n = 117). All samples were tested with human (BacHum, HF183-Taqman), dog (BactCan), pig (Pig-2-Bac), and avian (LA35, Av4143, ND5, cytB) markers using quantitative PCR (qPCR). Internal validity metrics were calculated using all animal fecal samples, as well as animal fecal samples contextually relevant for the Peruvian Amazon. Overall, Pig-2-Bac performed best, with 100% sensitivity and 88.5% specificity to detect the correct fecal source. Human-associated markers showed a sensitivity of 80.0% and 76.7%, and specificity of 66.2% and 67.6%. When limiting the analysis to contextually relevant animal fecal samples for the Peruvian Amazon, Av143 surpassed cytB with 95.7% sensitivity and 81.8% specificity. BactCan demonstrated 100% sensitivity and 47.4% specificity. The gene copy number detected by BacHum and HF183-Taqman were positively correlated (Pearson's correlation coefficient: 0.785), as well as avian markers cytB with Av4143 (Pearson's correlation coefficient: 0.508) and nd5 (Pearson's correlation coefficient: 0.949). These findings suggest that markers such as Av4143, Pig2Bac, cytb and BacHum have acceptable performance to be impactful in source attribution studies for zoonotic enteric disease transmission in this and similar low-resource communities.

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

PURPOSE OF REVIEW

Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination.

RECENT FINDINGS

This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.

Performance of host-associated genetic markers for microbial source tracking in China

Numerous genetic markers have been developed to establish microbial source tracking (MST) assays in the last decade. However, the selection of suitable markers is challenging due to a lack of understanding of fundamental factors such as sensitivity, specificity, and concentration in target/nontarget hosts, especially in East Asia. In this study, a total of 506 faecal samples comprised of human and 12 nonhuman hosts were collected from 28 cities across China and tested for marker performance characteristics. We firstly tested 40 host-associated markers based on a binary (presence/absence) criterion. Here, 15 markers (7 human-associated, 4 pig-associated, 3 ruminant-associated, and 1 poultry-associated) showed potential applicability in our study area. The selected 15 markers were then tested using qualitative and quantitative methods to characterise their performance. Overall, Bacteroidales markers presented higher sensitivity and concentrations in target samples compared to other bacterial or viral markers, but their specificity was low. Among nontarget samples, pets accounted for 43.7% and 35.7% of cross-reactivity with human-associated and poultry-associated markers, respectively. Noncommon animals, including horse and donkey, contributed 61.3% of cross-reactivity with ruminant-associated markers. When considering the quantitative distribution of markers, their concentration in nontarget samples were 1-3 orders of magnitude lower than in target samples. Moreover, a novel classification method was proposed to classify the nontarget hosts into four groups spanning "no cross-reactivity", "weak cross-reactivity", "moderate cross-reactivity", and "strong cross-reactivity" animal hosts. There were 77.9% nontarget samples identified as no cross-reactivity and weak cross-reactivity hosts, suggesting that these nontarget hosts produce little interference for corresponding markers. Our findings elucidate the performance of host-associated markers around China in a qualitative and quantitative manner, and reveal the interference degree of cross-reactivity from nontarget animals to genetic markers, which will facilitate tracking of multiple faecal pollution sources and planning timely remedial strategies in China.

Comparative fate of CrAssphage with culturable and molecular fecal pollution indicators during activated sludge wastewater treatment

Wastewater treatment plants are typically monitored using fecal indicator bacteria to ensure adequate microbial water quality of the treated effluent. Fecal indicator bacteria exhibit poor correlation with virus fate in the environment, including during wastewater treatment. Viral-based microbial source tracking methods have the potential to overcome this limitation. The recently discovered human gut bacteriophage crAssphage is a promising viral human fecal indicator. In this current study, primary influent, primary effluent, secondary effluent, and final effluent of a conventional activated sludge wastewater treatment plant were analyzed for a suite of fecal indicators to evaluate the suitability of crAssphage as a wastewater process indicator for virus removal. CrAssphage was the most abundant fecal indicator measured through the wastewater treatment process. Culturable and molecular bacterial fecal pollution indicators showed higher removal than viral fecal pollution indicators, including crAssphage, confirming the necessity of a viral-specific fecal monitoring target. CrAssphage was strongly correlated with adenovirus and polyomavirus molecular indicators through the wastewater treatment process. Literature comparison demonstrated site-specific removal of molecular fecal indicators during wastewater treatment highlighting the need for local performance validation. The high abundance of crAssphage and correlation with pathogenic viruses suggests the potential suitability of crAssphage as a viral fecal pollution process indicator during wastewater treatment.

Tracking faecal microorganisms using the qPCR method in a typical urban catchment in China

Faecal microorganisms represent a key threat to human health. Potential origins of faecal microbial contamination in a typical urban-representative micro-scale were evaluated. The quantitative polymerase chain reaction (qPCR) method was used in this study. The Bacteroidetes is selected as the indicative microorganism in runoff samples that are collected during four representative stormwater events in north China. The principal component analysis (PCA) method indicated the distribution feature of the environmental factors. The largest contributor is dog, followed by bird and human to the faecal pollution in stormwater runoff. The output of human and dog faecal pollutants in response to the first flush effect of nonpoint source pollution while the transmit time of bird faecal pollutant is relatively longer. In addition, the number of antecedent drying days represents the key factor for dog faecal pollution, while human faecal pollution is impacted by more factors. The results of this study will provide sound evidence for the tracking and management of nonpoint source faecal pollution in urban catchment areas.

Performance Evaluation of Human-Specific Viral Markers and Application of Pepper Mild Mottle Virus and CrAssphage to Environmental Water Samples as Fecal Pollution Markers in the Kathmandu Valley, Nepal

Monitoring of environmental water is crucial to protecting humans and animals from possible health risks. Although numerous human-specific viral markers have been designed to track the presence of human fecal contamination in water, they lack adequate sensitivity and specificity in different geographical regions. We evaluated the performances of six human-specific viral markers [Aichi virus 1 (AiV-1), human adenoviruses (HAdVs), BK and JC polyomaviruses (BKPyVs and JCPyVs), pepper mild mottle virus (PMMoV), and crAssphage] using 122 fecal-source samples collected from humans and five animal hosts in the Kathmandu Valley, Nepal. PMMoV and crAssphage showed high sensitivity (90-100%) with concentrations of 4.5-9.1 and 6.2-7.0 log₁₀ copies/g wet feces (n = 10), respectively, whereas BKPyVs, JCPyVs, HAdVs, and AiV-1 showed poor performances with sensitivities of 30-40%. PMMoV and crAssphage were detected in 40-100% and 8-90%, respectively, of all types of animal fecal sources and showed no significantly different concentrations among most of the fecal sources (Kruskal-Wallis test, P > 0.05), suggesting their applicability as general fecal pollution markers. Furthermore, a total of 115 environmental water samples were tested for PMMoV and crAssphage to identify fecal pollution. PMMoV and crAssphage were successfully detected in 62% (71/115) and 73% (84/115) of water samples, respectively. The greater abundance and higher mean concentration of crAssphage (4.1 ± 0.9 log₁₀ copies/L) compared with PMMoV (3.3 ± 1.4 log₁₀ copies/L) indicated greater chance of detection of crAssphage in water samples, suggesting that crAssphage could be preferred to PMMoV as a marker of fecal pollution.

Identification of 16S rRNA and Virulence-Associated Genes of Arcobacter in Water Samples in the Kathmandu Valley, Nepal

This study aimed to determine the prevalence of Arcobacter and five associated virulence genes (cadF, ciaB, mviN, pldA, and tlyA) in water samples in the Kathmandu Valley, Nepal. A total of 286 samples were collected from deep tube wells (n = 30), rivers (n = 14), a pond (n = 1), shallow dug wells (n = 166), shallow tube wells (n = 33), springs (n = 21), and stone spouts (n = 21) in February and March (dry season) and August (wet season), 2016. Bacterial DNA was extracted from the water samples and subjected to SYBR Green-based quantitative PCR for 16S rRNA and virulence genes of Arcobacter. The 16S rRNA gene of Arcobacter was detected in 36% (40/112) of samples collected in the dry season, at concentrations ranging from 5.7 to 10.2 log copies/100 mL, and 34% (59/174) of samples collected in the wet season, at concentrations of 5.4–10.8 log copies/100 mL. No significant difference in Arcobacter 16S rRNA gene-positive results was observed between samples collected in the two seasons (p > 0.05). Seventeen (17%), 84 (84%), 19 (19%), 23 (23%), and 17 (17%) of the 99 Arcobacter 16S rRNA gene-positive samples were also positive for cadF, ciaB, mviN, pldA, and tlyA, respectively. At least one virulence gene was detected in 87 (88%) of the 99 Arcobacter 16S rRNA gene-positive samples. The presence of Arcobacter and the virulence genes in these samples illustrates the persistence of pathogenic bacteria in the environment and highlights the importance of regular monitoring of water for pathogens.

Detection of Pathogenic Viruses, Pathogen Indicators, and Fecal-Source Markers within Tanker Water and Their Sources in the Kathmandu Valley, Nepal

Tanker water is used extensively for drinking as well as domestic purposes in the Kathmandu Valley of Nepal. This study aimed to investigate water quality in terms of microbial contamination and determine sources of fecal pollution within these waters. Thirty-one samples from 17 tanker filling stations (TFSs) and 30 water tanker (WT) samples were collected during the dry and wet seasons of 2016. Escherichia coli was detected in 52% of the 31 TFS samples and even more frequently in WT samples. Of the six pathogenic viruses tested, enteroviruses, noroviruses of genogroup II (NoVs-GII), human adenoviruses (HAdVs), and group A rotaviruses were detected using quantitative PCR (qPCR) at 10, five, four, and two TFSs, respectively, whereas Aichi virus 1 and NoVs-GI were not detected at any sites. Index viruses, such as pepper mild mottle virus and tobacco mosaic virus, were detected using qPCR in 77% and 95% out of 22 samples, respectively, all of which were positive for at least one of the tested pathogenic viruses. At least one of the four human-associated markers tested (i.e., BacHum, HAdVs, and JC and BK polyomaviruses) was detected using qPCR in 39% of TFS samples. Ruminant-associated markers were detected at three stations, and pig- and chicken-associated markers were found at one station each of the suburbs. These findings indicate that water supplied by TFSs is generally of poor quality and should be improved, and proper management of WTs should be implemented.

Quantification of Microbial Source Tracking and Pathogenic Bacterial Markers in Water and Sediments of Tiaoxi River (Taihu Watershed)

Taihu Lake is one of the largest freshwater lakes in China, serving as an important source of drinking water; >60% of source water to this lake is provided by the Tiaoxi River. This river faces serious fecal contamination issues, and therefore, a comprehensive investigation to identify the sources of fecal contamination was carried out and is presented here. The performance of existing universal (BacUni and GenBac), human (HF183-Taqman, HF183-SYBR, BacHum, and Hum2), swine (Pig-2-Bac), ruminant (BacCow), and avian (AV4143 and GFD) associated microbial source tracking (MST) markers was evaluated prior to their application in this region. The specificity and sensitivity results indicated that BacUni, HF183-TaqMan, Pig-2-Bac, and GFD assays are the most suitable in identifying human and animal fecal contamination. Therefore, these markers along with marker genes specific to selected bacterial pathogens were quantified in water and sediment samples of the Tiaoxi River, collected from 15 locations over three seasons during 2014 and 2015. Total/universal Bacteroidales markers were detected in all water and sediment samples (mean concentration 6.22 log10 gene copies/100 ml and 6.11 log10 gene copies/gram, respectively), however, the detection of host-associated MST markers varied. Human and avian markers were the most frequently detected in water samples (97 and 89%, respectively), whereas in sediment samples, only human-associated markers were detected more often (86%) than swine (64%) and avian (8.8%) markers. The results indicate that several locations in the Tiaoxi River are heavily polluted by fecal contamination and this correlated well with land use patterns. Among the five bacterial pathogens tested, Shigella spp. and Campylobacter jejuni were the most frequently detected pathogens in water (60% and 62%, respectively) and sediment samples (91% and 53%, respectively). Shiga toxin-producing Escherichia coli (STEC) and pathogenic Leptospira spp. were less frequently detected in water samples (55% and 33%, respectively) and sediment samples (51% and 13%, respectively), whereas E. coli O157:H7 was only detected in sediment samples (11%). Overall, the higher prevalence and concentrations of Campylobacter jejuni, Shigella spp., and STEC, along with the MST marker detection at a number of locations in the Tiaoxi River, indicates poor water quality and a significant human health risk associated with this watercourse. GRAPHICAL ABSTRACTTracking fecal contamination and pathogens in watersheds using molecular methods.

Identification of Human and Animal Fecal Contamination in Drinking Water Sources in the Kathmandu Valley, Nepal, Using Host-Associated Bacteroidales Quantitative PCR Assays

This study identified the sources of fecal contamination in the groundwater of different land covers. A total of 300 groundwater samples were collected in the Kathmandu Valley, Nepal, in the dry (n = 152) and wet (n = 148) seasons of 2016. Fecal indicator bacteria were initially enumerated, and then fecal contamination sources were identified using human (BacHum), ruminant (BacR), and pig-associated (Pig2Bac) Bacteroidales quantitative polymerase chain reaction assays. Sixty-six percent (197/300) of the tested groundwater samples had Escherichia coli concentrations higher than the World Health Organization threshold for drinking (<1 most probable number/100 mL). The fecal contamination of the groundwater was of human (22%, 55/250), ruminant (11%, 28/250), and pig (3%, 8/250) origin. Deep tube wells were less likely to be positive for E. coli and fecal markers compared to shallow dug wells. The human fecal marker was more likely to be detected in sources from built-up as compared to agricultural areas (Adjusted odds ratio (AOR) = 3.60, p = 0.002). Likewise, the ruminant fecal marker was more likely to be detected in sources from agricultural as compared to built-up areas (AOR = 2.90, p = 0.018). These findings suggest the preparation of mitigation strategies for controlling fecal pollution based on land cover and well types.

Assessment and application of host-specific Bacteroidales genetic markers for microbial source tracking of river water in Japan

Microbial source tracking using host-specific microbial genetic markers is considered a promising approach to determine fecal contamination sources of aquatic environments. This study aimed to assess the application of previously developed host-specific Bacteroidales quantitative PCR assays to microbial source tracking of river water samples in Yamanashi Prefecture, Japan. Various types of fecal-source samples, such as raw sewage, secondary-treated sewage of a wastewater treatment plant, and cattle feces, were used for three human-, two ruminant- and two pig-specific Bacteroidales quantitative PCR assays. Our results demonstrated that BacHum, BacR and Pig2Bac assays as suitable human-, ruminant- and pig-specific assays, with an accuracy of 86%, 94% and 77%, respectively. These selected assays were used for microbial source tracking of 63 river water samples collected at nine sites in two river basins. From these sites, there were 48 (76%), 34 (54%) and 9 (14%) positive samples using the BacHum, BacR and Pig2Bac assays, respectively. These assays revealed the effects of humans and animals on fecal contamination of river water.