Use of a Bacteroides thetaiotaomicron-specific alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water

The host specificity of pilus gene traA in Escherichia coli and its use in tracking human fecal pollution

A reliable and accurate fecal source tracking (FST) approach is important in water quality management and preventing foodborne and waterborne diseases. In this study, a genetic marker of Escherichia coli (E. coli) was identified and utilized to differentiate between human and animal sources of fecal contamination. Nucleotide polymorphisms of 14 genes coding for cellular surface proteins, mainly fimbriae, were analyzed using the 22 draft genomes of E. coli strains from human and three domestic animal sources in Japan. A signature sequence, traAh, within the pilin gene traA, was found to be highly associated with E. coli of human origin. Subsequently, an end-point polymerase chain reaction (PCR) assay, namely PCR-Htra, was developed, specifically targeting traAh. The high association between traAh and E. coli of human origin was validated through the PCR-Htra amplification. This encompassed 1045 E. coli strains isolated from surface water, human feces or sewages, and feces from 12 animal species, including domestic and wild animals in the states of Missouri and Virginia in the United States of America (USA). The data suggested that the sensitivity and specificity of PCR-Htra assay were 49.0 % and 99.5 % respectively in distinguishing human-origin E. coli from nonhuman-source ones. Furthermore, the result of our in silico analysis of GenBank® data suggests that traAh may have a global distribution as the sequence was found in human-origin E. coli isolated from at least 14 countries around the world. Thus, the PCR-Htra may provide a new FST tool for rapid and accurate detection of human-origin E. coli, serving as a means to identify human fecal contamination in water.

Quantitative Assessment of Microbial Pathogens and Indicators of Wastewater Treatment Performance for Safe and Sustainable Water Reuse in India

Currently, there is no data on the molecular quantification of microbial indicators of recycled water quality in India. In this study, multiple microbial pathogens and indicators of water quality were evaluated at three wastewater treatment plants located in two Indian cities (New Delhi and Jaipur) to determine the treatment performance and suitability of recycled water for safe and sustainable reuse applications. Real-time polymerase chain reaction (PCR) was used for the rapid evaluation of six human pathogens and six microbial indicators of fecal contamination. Among the microbial indicators, pepper mild mottle virus (PMMoV), F⁺RNA-GII bacteriophage, Bacteroides thetaiotamicron, and four human pathogens (Norovirus genogroups I & II, Giardia, and Campylobacter coli) were detected in all of the influent samples analyzed. This work suggests that the raw influents contain lower levels of noroviruses and adenoviruses and higher levels of Giardia compared to those reported from other geographic regions. Overall, the efficacy of the removal of microbial targets was over 93% in the final effluent samples, which is consistent with reports from across the world. PMMoV and Giardia were identified as the best microbial targets, from the microbial indicators spanning across bacteria, bacteriophages, DNA/RNA viruses, and protozoan parasites, by which to evaluate treatment performance and recycled water quality in Indian settings, as they were consistently present at high concentrations in untreated wastewater both within and across the sites. Also, they showed a strong correlation with other microbial agents in both the raw influent and in the final effluent. These findings provide valuable insights into the use of culture-independent molecular indicators that can be used to assess the microbial quality of recycled water in Indian settings. IMPORTANCE Wastewater treatment plants (WWTPs) have rapidly increased in India during the last decade. Nonetheless, there are only a few labs in India that can perform culture-based screening for microbial quality. In the last 2 years of the pandemic, India has witnessed a sharp increase in molecular biology labs. Therefore, it is evident that culture-independent real-time PCR will be increasingly used for the assessment of microbial indicators/pathogens in wastewater, especially in resource-limited settings. There is no data available on the molecular quantitation of microbial indicators from India. There is an urgent need to understand and evaluate the performance of widely used microbial indicators via molecular quantitation in Indian WWTPs. Our findings lay the groundwork for the molecular quantitation of microbial indicators in WWTPs in India. We have screened for 12 microbial targets (indicators and human pathogens) and have identified pepper mild mottle virus (PMMoV) and Giardia as the best molecular microbiological indicators in Indian settings.

Connecting microbial, nutrient, physiochemical, and land use variables for the evaluation of water quality within mixed use watersheds

As non-point sources of pollution begin to overtake point sources in watersheds, source identification and complicating variables such as rainfall are growing in importance. Microbial source tracking (MST) allows for identification of fecal contamination sources in watersheds; when combined with data on land use and co-occuring variables (e.g., nutrients, sediment runoff) MST can provide a basis for understanding how to effectively remediate water quality. To determine spatial and temporal trends in microbial contamination and correlations between MST and nutrients, water samples (n = 136) were collected between April 2017 and May of 2018 during eight sampling events from 17 sites in 5 mixed-use watersheds. These samples were analyzed for three MST markers (human - B. theta; bovine - CowM2; porcine - Pig2Bac) along with E. coli, nutrients (nitrogen and phosphorus species), and physiochemical paramaters. These water quality variables were then paired with data on land use, streamflow, precipitation and management practices (e.g., tile drainage, septic tank density, tillage practices) to determine if any significant relationships existed between the observed microbial contamination and these variables. The porcine marker was the only marker that was highly correlated (p value <0.05) with nitrogen and phosphorus species in multiple clustering schemes. Significant relationships were also identified between MST markers and variables that demonstrated temporal trends driven by precipitation and spatial trends driven by septic tanks and management practices (tillage and drainage) when spatial clustering was employed.

Detangling Seasonal Relationships of Fecal Contamination Sources and Correlates with Indicators in Michigan Watersheds

Despite the widely acknowledged public health impacts of surface water fecal contamination, there is limited understanding of seasonal effects on (i) fate and transport processes and (ii) the mechanisms by which they contribute to water quality impairment. Quantifying relationships between land use, chemical parameters, and fecal bacterial concentrations in watersheds can help guide the monitoring and control of microbial water quality and explain seasonal differences. The goals of this study were to (i) identify seasonal differences in Escherichia coli and Bacteroides thetaiotaomicron concentrations, (ii) evaluate environmental drivers influencing microbial contamination during baseflow, snowmelt, and summer rain seasons, and (iii) relate seasonal changes in B. thetaiotaomicron to anticipated gastrointestinal infection risks. Water chemistry data collected during three hydroclimatic seasons from 64 Michigan watersheds were analyzed using seasonal linear regression models with candidate variables including crop and land use proportions, prior precipitation, chemical parameters, and variables related to both wastewater treatment and septic usage. Adaptive least absolute shrinkage and selection operator (LASSO) linear regression with bootstrapping was used to select explanatory variables and estimate coefficients. Regardless of season, wastewater treatment plant and septic system usage were consistently selected in all primary models for B. thetaiotaomicron and E. coli. Chemistry and precipitation-related variable selection depended upon season and organism. These results suggest a link between human pollution (e.g., septic systems) and microbial water quality that is dependent on flow regime.

IMPORTANCE In this study, a data set of 64 Michigan watersheds was utilized to gain insights into fecal contamination sources, drivers, and chemical correlates across seasons for general E. coli and human-specific fecal indicators. Results reaffirmed a link between human-specific sources (e.g., septic systems) and microbial water quality. While the importance of human sources of fecal contamination and fate and transport variables (e.g., precipitation) remain important across seasons, this study provides evidence that fate and transport mechanisms vary with seasonal hydrologic condition and microorganism source. This study contributes to a body of research that informs prioritization of fecal contamination source control and surveillance strategy development to reduce the public health burden of surface water fecal contamination.

Technical framework for wastewater-based epidemiology of SARS-CoV-2

Wastewater-based epidemiology (WBE) is expected to become a powerful tool to monitor the dissemination of SARS-CoV-2 at the community level, which has attracted the attention of scholars all over the world. However, there is not yet a standard protocol to guide its implementation. In this paper, we proposed a comprehensive technical and theoretical framework of relative quantification via qPCR for determining the virus abundance in wastewater and estimating the infection ratio in corresponding communities, which is expected to achieve horizontal and vertical comparability of the data using a human-specific biomarker as the internal reference. Critical factors affecting the virus detectability and the estimation of infection ratio include virus concentration methods, lag-period, per capita virus shedding amount, sewage generation rate, temperature-related decay kinetics of virus/biomarker in wastewater, and hydraulic retention time (HRT), etc. Theoretical simulation shows that the main factors affecting the detectability of virus in sewage are per capita virus shedding amount and sewage generation rate. While the decay of SARS-CoV-2 RNA in sewage is a relatively slow process, which may have limited impact on its detection. Under the ideal condition of high per capita virus shedding amount and low sewage generation rate, it is expected to detect a single infected person within 400,000 people.

A Double-Blind, Placebo-Controlled Trial to Assess Safety and Tolerability of (Thetanix) Bacteroides thetaiotaomicron in Adolescent Crohn's Disease

INTRODUCTION

Thetanix (gastroresistant capsules containing lyophilized Bacteroides thetaiotaomicron) is a live biotherapeutic, under development for Crohn's disease, that antagonizes transcription factor nuclear factor kappa B, reducing proinflammatory cytokines, particularly tumor necrosis factor alpha. We aimed to assess safety and tolerability in adolescents with Crohn's disease in remission.

METHODS

Subjects who were 16-18 years with Crohn's in remission (weighted pediatric Crohn's disease activity index <12.5) were recruited. Each active dose comprised ∼108.2±1.4 colony forming units of B. thetaiotaomicron (randomized 4:1 active:placebo). Part A was single dose. Part B involved 7.5 days twice daily dosing. Serial stools were analyzed for calprotectin, 16S rRNA sequencing, and B. thetaiotaomicron real-time polymerase chain reaction. Bloods were taken serially. Subjects reported adverse events and recorded temperature twice daily.

RESULTS

Fifteen subjects were treated-8 in part A (75% men, median 17.1 years) and 10 in part B, including 3 from part A (80% men, median 17.1 years); all 18 completed. Seventy percent took concurrent immunosuppression. Reported compliance was >99% in part B. Two subjects reported adverse events deemed related-one in part A with eructation, flatulence, and reflux; one in part B with dizziness, abdominal pain, and headache. No serious adverse events were reported. There was no significant change in median calprotectin across part B (87.8 [4.4-447] to 50.5 [5.3-572], P = 0.44 by the Fisher exact test in the active group). No significant differences were found in microbiota profiles, but diversity seemed to increase in treated subjects.

DISCUSSION

Thetanix, after single and multiple doses, was well tolerated. Although the numbers in this study were small, the safety profile seems good. Future studies should explore efficacy.

Occurrence of a human-associated microbial source tracking marker and its relationship with faecal indicator bacteria in an urban estuary

One of the main impacts of urban sprawl in rapidly growing countries has been contamination of coastal environments by waterborne pathogens, posing a critical risk to ecosystem and human health. Microbial source tracking (MST) has been a robust tool to identify the origin of these pathogens globally. This study compared the occurrence of a human-associated Bacteroides marker (BT-α) with faecal indicator bacteria (FIB) in an urban estuary (Golden Horn, Istanbul, Turkey). Faecal coliform (culture method), enterococci (both culture and qPCR method) concentrations and physicochemical variables were compared with the BT-α concentrations in monthly collected samples for a year (n = 108). Enterococci concentrations detected by culture and qPCR were positively correlated (r = 0·86, P < 0·01) suggesting that qPCR can be an alternative method for monitoring. BT-α marker was positive for 30% of the samples and positively correlated with enterococci (r = 0·61 and r = 0·64 for culture and qPCR methods respectively, P < 0·01). Rainfall had a moderate positive correlation with all faecal/MST indicators suggesting combined sewer overflows also severely impacted estuarine water quality. The high FIB and BT-α concentrations at upper estuary suggested that faecal pollution mainly originated from the peri-urban settlements around two creeks entering the estuary.

Fecal indicator bacteria, fecal source tracking markers, and pathogens detected in two Hudson River tributaries

Volunteer monitoring in the Hudson River watershed since 2012 has identified that the Wallkill River and Rondout Creek tributary complex have elevated concentrations of the fecal indicator bacteria, enterococci. Concentrations of enterococci do not provide insight into the sources of pollution and are imperfect indicators of health risks. In 2017, the regular monthly volunteer monitoring campaign for culturable enterococci at 24 sites on the Wallkill and Rondout expanded to include: (1) culturable measurements of E. coli and quantification of E. coli and Enterococcus specific markers vis nanoscale qPCR, (2) microbial source tracking (MST) assays (avian, human, bovine, and equine) via real time PCR and nanoscale qPCR, and 3) quantification of 12 gastrointestinal pathogens including viruses, bacteria, and protozoa via nanoscale qPCR. Three human associated MST markers (HumM2, HF183, and B. theta) corroborated that human pollution was present in Rondout Creek and widespread in the Wallkill River. The presence of B. theta was associated with increased concentrations of culturable E. coli. Genes for adenovirus 40 and 41 conserved region, rotavirus A NSP3, E. coli eae and stx1, and Giardia lamblia 18S rRNA were detected in >45% of samples. Abundance of rotavirus A NSP3 genes was significantly correlated to the bovine marker gene, CowM3, though wild bird sources cannot be ruled out. This is the first study to investigate potential fecal pollution sources and pathogen concentrations in Hudson tributaries during the months of peak recreational use.

Ecological and Technical Mechanisms for Cross-Reaction of Human Fecal Indicators with Animal Hosts

Quantitative PCR (qPCR) assays for human/sewage marker genes have demonstrated sporadic positive results in animal feces despite their high specificities to sewage and human feces. It is unclear whether these positive reactions are caused by true occurrences of microorganisms containing the marker gene (i.e., indicator organisms) or nonspecific amplification (false positive). The distribution patterns of human/sewage indicator organisms in animals have not been explored in depth, which is crucial for evaluating a marker gene's true- or false-positive reactions. Here, we analyzed V6 region 16S rRNA gene sequences from 257 animal fecal samples and tested a subset of 184 using qPCR for human/sewage marker genes. Overall, specificities of human/sewage marker genes within sequencing data were 99.6% (BacV6-21), 96.9% (Lachno3), and 96.1% (HF183, indexed by its inferred V6 sequence). Occurrence of some true cross-reactions was associated with atypical compositions of organisms within the genera Blautia or Bacteroides For human/sewage marker qPCR assays, specificities were 96.7% (HF183/Bac287R), 96.2% (BacV6-21), 95.6% (human Bacteroides [HB]), and 94.0% (Lachno3). Select assays duplexed with either Escherichia coli or Enterococcus spp. were also validated. Most of the positive qPCR results in animals were low level and, on average, 2 orders of magnitude lower than the copy numbers of E. coli and Enterococcus spp. The lower specificity in qPCR assays compared to sequencing data was mainly caused by amplification of sequences highly similar to the marker gene and not the occurrence of the exact marker sequence in animal fecal samples.IMPORTANCE Identifying human sources of fecal pollution is critical to remediate sanitation concerns. Large financial investments are required to address these concerns; therefore, a high level of confidence in testing results is needed. Human fecal marker genes validated in this study showed high specificity in both sequencing data and qPCR results. Human marker sequences were rarely found in individual animals, and in most cases, the animals had atypical microbial communities. Sequencing also revealed the presence of closely related organisms that could account for nonspecific amplification in certain assays. Both the true cross-reactions and the nonspecific amplification had low signals well below E. coli or Enterococcus levels and likely would not impact the assay's ability to reliably detect human fecal pollution. No animal source had multiple human/sewage marker genes present; therefore, using a combination of marker genes would increase the confidence of human fecal pollution detection.

Microbial Source-Tracking Reveals Origins of Fecal Contamination in a Recovering Watershed

Fecal contamination of waterbodies due to poorly managed human and animal waste is a pervasive problem that can be particularly costly to address, especially if mitigation strategies are ineffective at sufficiently reducing the level of contamination. Identifying the most worrisome sources of contamination is particularly difficult in periurban streams with multiple land uses and requires the distinction of municipal, agricultural, domestic pet, and natural (i.e., wildlife) wastes. Microbial source-tracking (MST) methods that target host-specific members of the bacterial order Bacteroidales and others have been used worldwide to identify the origins of fecal contamination. We conducted a dry-weather study of Onondaga Creek, NY, where reducing fecal contamination has been approached mainly by mitigating combined sewer overflow events (CSOs). Over three sampling dates, we measured in-stream concentrations of fecal indicator bacteria; MST markers targeting human, ruminant, and canine sources; and various physical–chemical parameters to identify contaminants not attributable to CSOs or stormwater runoff. We observed that despite significant ruminant inputs upstream, these contaminants eventually decayed and/or were diluted out and that high levels of urban bacterial contamination are most likely due to failing infrastructure and/or illicit discharges independent of rain events. Similar dynamics may control other streams that transition from agricultural to urban areas with failing infrastructure.

Variably improved microbial source tracking with digital droplet PCR

This study addressed whether digital droplet PCR (ddPCR) could improve sensitivity and specificity of human-associated Bacteroidales genetic markers, BacHum and B. theta, and their quantification in environmental and fecal composite samples. Human markers were quantified by qPCR and ddPCR platforms obtained from the same manufacturer. A total of 180 samples were evaluated by each platform including human and animal feces, sewage, and environmental water. The sensitivity of ddPCR and qPCR marker assays in sewage and human stool was 0.85-1.00 with marginal reduction in human stool by ddPCR relative to qPCR (<10%). The prevalence and distribution of markers across complex sample types was similar (74-100% agreement) by both platforms with qPCR showing higher sensitivity for markers in environmental and composite samples and ddPCR showing greater reproducibility for marker detection in fecal composites. Determination of BacHum prevalence in fecal samples by ddPCR increased specificity relative to qPCR (from 0.58 to 0.88) and accuracy (from 0.77 to 0.94), while the B. theta assay performed similarly on both platforms (specificity = 0.98). In silico analysis indicated higher specificity of ddPCR for BacHum was not solely attributed to reduced sensitivity relative to qPCR. Marker concentrations measured by ddPCR for all sample types were consistently lower than those measured by qPCR, by a factor of 2.6 ± 2.8 for B. theta and 18.7 ± 10.0 for BacHum. We suggest that differences in assay performance on ddPCR and qPCR platforms may be linked to the characteristics of the assay targets (that is, genes with multiple versus single copies and encoding proteins versus ribosomal RNA) however further work is needed to validate these ideas. We conclude that ddPCR is a suitable tool for microbial source tracking, however, other factors such as cost-effectiveness and assay-specific performance should be considered.

Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed

Fecal pollution management remains one of the biggest challenges for water quality authorities worldwide. Advanced fecal pollution source identification technologies are now available that can provide quantitative information from many animal groups. As public interest in these methodologies grows, it is vital to use standardized procedures with clearly defined data acceptance metrics and conduct field studies demonstrating the use of these techniques to help resolve real-world water quality challenges. Here we apply recently standardized human-associated qPCR methods with custom data acceptance metrics (HF183/BacR287 and HumM2), along with established procedures for ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution sources to (i) demonstrate the feasibility of implementing standardized qPCR procedures in a large-scale field study, and (ii) characterize trends in fecal pollution sources in the research area. A total of 602 water samples were collected over a one-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries in the Tillamook Bay Watershed (OR, USA). Host-associated qPCR results were combined with high-resolution geographic information system (GIS) land use and general indicator bacteria (E. coli) measurements to elucidate water quality fecal pollution trends. Results demonstrate the feasibility of implementing standardized fecal source identification qPCR methods with established data acceptance metrics in a large-scale field study leading to new investigative leads suggesting that elevated E. coli levels may be linked to specific pollution sources and land use activities in the Tillamook Bay Watershed.

Highly Specific Sewage-Derived Bacteroides Quantitative PCR Assays Target Sewage-Polluted Waters

The identification of sewage contamination in water has primarily relied on the detection of human-associated Bacteroides using markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e., Bacteroides dorei) and other Bacteroides organisms (e.g., Bacteroides thetaiota omicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined the Bacteroides population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundant Bacteroides in untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. Freshwater Bacteroides were also identified in uncontaminated water samples, demonstrating that measures of total Bacteroides do not reflect fecal pollution. A comparison of two previously described human Bacteroides assays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derived Bacteroides provided an independent measure of sewage-impacted waters.IMPORTANCE Bacteroides are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundant Bacteroides in sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.

Occurrence of microbial indicators, pathogenic bacteria and viruses in tropical surface waters subject to contrasting land use

Fecal indicator bacteria, such as Escherichia coli (E.coli) and Enterococcus, have been widely used to indicate the presence of pathogens. However, the suitability of fecal indicator bacteria to represent health risks is still being challenged, particularly in tropical aquatic environments. The objective of this study is to understand the occurrence and prevalence of indicators and pathogens in areas with contrasting land use, as well as to identify the major correlations between indicators, pathogens and environmental parameters. The spatial and temporal variation of indicators and pathogens was studied to examine the distribution patterns for areas with different land use, and the impact of seasonal changes on microbial populations. A total of 234 water samples were sampled for two years from reservoirs and their tributaries, and tested for fecal indicator bacteria, coliphages, human specific markers, pathogenic bacteria and viruses. The prevalence of indicators and pathogens in reservoirs were generally low, while relatively high concentrations were observed in tributaries to varying degrees. Of the enteric viruses, norovirus GII was among the most prevalent and had the highest concentration. Although strong correlations were found between indicators, only relatively weak correlations were found between indicators and pathogens. The results in this study showed that none of the bacteria/phage indicators were universal predictors for pathogens. Inclusion of the alternative indicators, Methanobrevibacter smithii, Bacteroides and human polyomaviruses (HPyVs) to monitoring programs could help to determine whether the fecal source was human. The microbial distribution patterns allow the classification of sampling sites to different clusters and thus, help to identify sites which have poor water quality. This approach will be useful for water quality management to pinpoint factors that influence water quality and help to prioritize sites for restoration of water quality.

Pathogens, faecal indicators and human-specific microbial source-tracking markers in sewage

The objective of this review is to assess the current state of knowledge of pathogens, general faecal indicators and human-specific microbial source tracking markers in sewage. Most of the microbes present in sewage are from the microbiota of the human gut, including pathogens. Bacteria and viruses are the most abundant groups of microbes in the human gut microbiota. Most reports on this topic show that raw sewage microbiological profiles reflect the human gut microbiota. Human and animal faeces share many commensal microbes as well as pathogens. Faecal-orally transmitted pathogens constitute a serious public health problem that can be minimized through sanitation. Assessing both the sanitation processes and the contribution of sewage to the faecal contamination of water bodies requires knowledge of the content of pathogens in sewage, microbes indicating general faecal contamination and microbes that are only present in human faecal remains, which are known as the human-specific microbial source-tracking (MST) markers. Detection of pathogens would be the ideal option for managing sanitation and determining the microbiological quality of waters contaminated by sewage; but at present, this is neither practical nor feasible in routine testing. Traditionally, faecal indicator bacteria have been used as surrogate indicators of general faecal residues. However, in many water management circumstances, it becomes necessary to detect both the origin of faecal contamination, for which MST is paramount, and live micro-organisms, for which molecular methods are not suitable. The presence and concentrations of pathogens, general faecal indicators and human-specific MST markers most frequently reported in different areas of the world are summarized in this review.

Multi-tiered approach utilizing microbial source tracking and human associated-IMS/ATP for surveillance of human fecal contamination in Baja California, Mexico

As both the need for reuse of reclaimed wastewater and the burden placed on existing wastewater treatment plants increase, so does the need for methods that can reliably, rapidly and economically identify human-associated contamination. A survey of surface water quality was conducted in Baja California, Mexico where inadequate infrastructure or its inefficient operation leads to poor water quality. The HF183 and Bacteroides thetaiotaomicron (B. theta) human-associated gene markers were detected in 84% and 82% of samples collected during dry weather, illustrating evidence of widespread human fecal contamination. In addition, an inversely-coupled (Inv-IMS/ATP) viability-based assay for detection of B. theta was developed and applied for rapid detection and screening of human-associated fecal contamination. The Inv-IMS/ATP assay was able to effectively differentiate between surface waters impacted with human fecal contamination, and B. theta levels measured by Inv-IMS/ATP were highly correlated with HF183 and B. theta human marker measurements (r = 0.76; r = 0.82) in complex surface water samples. In areas with widespread human fecal contamination and limited access to more expensive methods, a multi-pronged approach utilizing a combination of methods including the Inv-IMS/ATP assay for rapid evaluation and screening of surface water quality alongside human-associated genetic markers may improve risk assessment and surveillance capabilities.

Impact of nutrient addition on diversity and fate of fecal bacteria

Understanding the variations in the microorganisms associated with human fecal pollution in different types of water is necessary to manage water quality and predict human health risks. Using an Illumina sequencing method, we investigated variations in the fecal bacteria originating from fresh human feces and their decay trends in nutrient-supplemented water and natural river water. Nutrient addition contributed to the growth of heterotrophic bacteria like Comamonadaceae, Cytophagaceae, and Sphingobacteriaceae, but led to lower concentrations for Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae. This result suggests that the utilization of nutrients by high-activity bacteria may suppress other bacteria via depletion of the available nutrient resources. As we did not observe proliferation of Bacteroidales, Lactobacillales, Clostridiales, or Ruminococcaceae in either supplemented or river water, we consider these groups suitable for use as indicators to determine the level of fecal pollution. Moreover, we tested the persistence of Bacteroidales markers, including general-Bacteroidales marker GenBac and human-specific Bacteroidales marker qHS601, by quantitative PCR. We observed similar trends in the decay of the Bacteroidales markers GenBac and qHS601 in the nutrient-supplemented water and natural river water, and the high R² values of the GenBac (R²_{nutrient-supplemented} = 0.93, R²_{natural river} = 0.81) and qHS601 (R²_{nutrient-supplemented} = 0.93, R²_{natural river} = 0.91) suggests they are a good fit for the first-order decay model. We also found stronger correlations between the markers and potential pathogenic anaerobes in the different types of water, demonstrating the validity of the use of GenBac and qHS601 from Bacteroidales for the identification of human-associated pollution sources.

The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients

Anti-PD-1-based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients' microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria. A significant association was observed between commensal microbial composition and clinical response. Bacterial species more abundant in responders included Bifidobacterium longum, Collinsella aerofaciens, and Enterococcus faecium. Reconstitution of germ-free mice with fecal material from responding patients could lead to improved tumor control, augmented T cell responses, and greater efficacy of anti-PD-L1 therapy. Our results suggest that the commensal microbiome may have a mechanistic impact on antitumor immunity in human cancer patients.

Bacteroidales markers for microbial source tracking in Southeast Asia

The island city country of Singapore served as a model to validate the use of host-associated Bacteroidales 16S rRNA gene marker assays for identifying sources of fecal pollution in the urban tropical environment of Southeast Asia. A total of 295 samples were collected from sewage, humans, domesticated animals (cats, dogs, rabbits and chicken), and wild animals (birds, monkeys and wild boars). Samples were analyzed by real time PCR using five human-associated assays (HF183-SYBR Green, HF183, BacHum, BacH and B. thetaiotaomicron α-1-6, mannanase (B. theta), one canine-associated assay (BacCan), and a total Bacteroidales assay (BacUni). The best performing human-associated assay was B. theta with a diagnostic sensitivity of 69% and 100% in human stool and sewage, respectively, and a specificity of 98%. BacHum achieved the second highest sensitivity and specificity for human stool at 65% and 91%, respectively. The canine-associated Bacteroidales assay (BacCan) had a sensitivity and specificity above 80% and was validated for tracking fecal pollution from dogs. BacUni demonstrated a sensitivity and specificity of 100% for mammals, thus BacUni was confirmed for total Bacteroidales detection in the region. We showed for the first time that rabbit fecal samples cross-react with human-associated assays (HF183-SYBR Green, HF183, BacHum and BacH) and with BacCan. Our findings regarding the best performing human-associated assays differ from those reported in Bangladesh and India, which are geographically close to Southeast Asia, and where HF183 and BacHum were the preferred assays, respectively.

Sources and persistence of fecal indicator bacteria and Bacteroidales in sand as measured by culture-based and culture-independent methods: A case study at Santa Monica Pier, California

This study investigated causes of persistent fecal indicator bacteria (FIB) in beach sand under the pier in Santa Monica, CA. FIB levels were up to 1,000 times higher in sand underneath the pier than that collected from adjacent to the pier, with the highest concentrations under the pier in spring and fall. Escherichia coli (EC) and enterococci (ENT) under the pier were significantly positively correlated with moisture (ρ = 0.61, p < 0.001, n = 59; ρ = 0.43, p < 0.001, n = 59, respectively), and ENT levels measured by qPCR (qENT) were much higher than those measured by membrane filtration (cENT). Microcosm experiments tested the ability of EC, qENT, cENT, and general Bacteroidales (GenBac) to persist under in-situ moisture conditions (10% and 0.1%). Decay rates of qENT, cENT, and GenBac were not significantly different from zero at either moisture level, while decay rates for EC were relatively rapid during the microcosm at 10% moisture (k = 0.7 days-1). Gull/pelican marker was detected at eight of 12 sites and no human-associated markers (TaqHF183 and HumM2) were detected at any site during a one-day site survey. Results from this study indicate that the high levels of FIB observed likely stem from environmental sources combined with high persistence of FIB under the pier.

Decay kinetics of microbial source tracking (MST) markers and human adenovirus under the effects of sunlight and salinity

Artificial seawater and freshwater microcosms inoculated with raw sewage were set up to compare the persistence of microbial source tracking (MST) markers (i.e. Bacteroides thetaiotaomicron (B. theta), Methanobrevibacter smithii (M. smithii), human polyomaviruses JC and BK (HPyVs)) and human adenoviruses under different sunlight intensity and salinity. PMA pretreatment successfully eliminated the false-positive detection of dead bacterial cells in the model-development experiment. The results were then validated using real environmental matrices in microcosms inoculated with raw sewage. The genome concentrations of the targets followed a first-order decay pattern with 90% reduction of the initial amounts in <5days for both artificial and natural surface waters. Decay rate constant (k₁) were developed microorganisms in artificial water matrices. Due to the different water environment conditions, improved decay rates (k₂) incorporated with sunlight, TSS and TOC adjustment coefficients were used for validation of the natural water matrices. Based on the predictive squared correlation coefficient (Q²_F) and root-mean-square error (RMSE) validation criteria, the improved k₂ were able to provide better prediction on the survival of target microorganisms in environmental surface waters (Q²_F>0.6 and RMSE ranged from 0.05 to 1.81). For microbial source tracking purposes, HPyVs are suggested to be better MST markers in freshwater, while B. theta is recommended for seawater based on the decay models developed in this study. The targeted DNA of M. smithii should only be used to indicate recent human faecal pollution in surface waters due to their faster decay than human adenoviruses.

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (no-template and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria proposed in this study should help scientists, managers, reviewers, and the public evaluate the technical quality of future findings against an established benchmark.

Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces

The aim of this study was to judge the legal duty of pollution liabilities by assessing a duck faeces-specific marker, which can exclude distractions of residual bacteria from earlier contamination accidents. With the gene sequencing technology and bioinformatics method, we completed the comparative analysis of Faecalibacterium sequences, which were associated with ducks and other animal species, and found the sequences unique to duck faeces. Polymerase chain reaction (PCR) and agarose gel electrophoresis techniques were used to verify the reliability of both human and duck faeces-specific primers. The duck faeces-specific primers generated an amplicon of 141 bp from 43.3 % of duck faecal samples, 0 % of control samples and 100 % of sewage wastewater samples that contained duck faeces. We present here the initial evidence of Faecalibacterium-based applicability as human faeces-specificity in China. Meanwhile, this study represents the initial report of a Faecalibacterium marker for duck faeces and suggests an independent or supplementary environmental biotechnology of microbial source tracking (MST).

Well water quality in rural Nicaragua using a low-cost bacterial test and microbial source tracking

Water-related diseases, particularly diarrhea, are major contributors to morbidity and mortality in developing countries. Monitoring water quality on a global scale is crucial to making progress in terms of population health. Traditional analytical methods are difficult to use in many regions of the world in low-resource settings that face severe water quality issues due to the inaccessibility of laboratories. This study aimed to evaluate a new low-cost method (the compartment bag test (CBT)) in rural Nicaragua. The CBT was used to quantify the presence of Escherichia coli in drinking water wells and aimed to determine the source(s) of any microbial contamination. Results indicate that the CBT is a viable method for use in remote rural regions. The overall quality of well water in Pueblo Nuevo, Nicaragua was deemed unsafe, and results led to the conclusion that animal fecal wastes may be one of the leading causes of well contamination. Elevation and depth of wells were not found to impact overall water quality. However rope-pump wells had a 64.1% reduction in contamination when compared with simple wells.

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

The emerging microbial source tracking (MST) methodologies aim to identify fecal contamination originating from domestic and wild animals, and from humans. Avian MST is especially challenging, primarily because the Aves class includes both domesticated and wild species with highly diverse habitats and dietary characteristics. The quest for specific fecal bacterial MST markers can be difficult with respect to attaining sufficient assay sensitivity and specificity. The present study utilizes high throughput sequencing (HTS) to screen bacterial 16S rRNA genes from fecal samples collected from both domestic and wild avian species. Operational taxonomic unit (OTU) analysis was then performed, from which sequences were retained for downstream quantitative polymerase chain reaction (qPCR) marker development. Identification of unique avian host DNA sequences, absent in non-avian hosts, was then carried out using a dedicated database of bacterial 16S rRNA gene taken from the Ribosomal Database Project. Six qPCR assays were developed targeting the 16S rRNA gene of Lactobacillus, Gallibacterium, Firmicutes, Fusobacteriaceae, and other bacteria. Two assays (Av4143 and Av163) identified most of the avian fecal samples and demonstrated sensitivity values of 91 and 70%, respectively. The Av43 assay only identified droppings from battery hens and poultry, whereas each of the other three assays (Av24, Av13, and Av216) identified waterfowl species with lower sensitivities values. The development of an MST assay-panel, which includes both domestic and wild avian species, expands the currently known MST analysis capabilities for decoding fecal contamination.

Polymorphism of the glucosyltransferase gene (ycjM) in Escherichia coli and its use for tracking human fecal pollution in water

This study examined polymorphism of the glucosyltransferase gene (ycjM) in fecal Escherichia coli isolates and evaluated the use of the sequence polymorphism for measuring human fecal pollution in water. Significant nucleotide variations were observed through comparative analysis of the ycjM sequences of 70 E. coli strains isolated from the feces of humans, domestic livestock, and wild animals. Three distinct types of ycjM sequences were found: universal-ycjM, human/chicken-ycjM, and human-ycjM. Using the human-ycjM sequences, both a polymerase chain reaction (PCR), Hycj-PCR and a quantitative PCR, Hycj-qPCR, were developed. As shown by the Hycj-PCR amplification, the human-ycjM marker appeared to be highly associated with the E. coli strains isolated from human feces, based on the analysis of 370 E. coli strains isolated from humans and seven other animal species. Similarly, the human-ycjM marker was highly linked with human feces, as demonstrated by the Hycj-PCR assay, when using 337 fecal DNA samples from 16 host animal sources, including both domestic and wild animals. Overall, the specificity and sensitivity of the human-ycjM marker for differentiating between the feces of humans and those of nonhuman groups were 99.7% and 100%, respectively; the prevalence of the marker appeared to be greater than 50% in the human-feces-associated E. coli population. In addition, our study showed that the quantification of human E. coli by the Hycj-qPCR was linearly correlated with the anthropogenic activity within a watershed. Our study suggests that this novel human-ycjM marker and the resulting PCR-based methods developed should be useful for measuring human-associated E. coli and human fecal pollution in water.

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

Linking fecal bacteria in rivers to landscape, geochemical, and hydrologic factors and sources at the basin scale

Linking fecal indicator bacteria concentrations in large mixed-use watersheds back to diffuse human sources, such as septic systems, has met limited success. In this study, 64 rivers that drain 84% of Michigan's Lower Peninsula were sampled under baseflow conditions for Escherichia coli, Bacteroides thetaiotaomicron (a human source-tracking marker), landscape characteristics, and geochemical and hydrologic variables. E. coli and B. thetaiotaomicron were routinely detected in sampled rivers and an E. coli reference level was defined (1.4 log10 most probable number⋅100 mL(-1)). Using classification and regression tree analysis and demographic estimates of wastewater treatments per watershed, septic systems seem to be the primary driver of fecal bacteria levels. In particular, watersheds with more than 1,621 septic systems exhibited significantly higher concentrations of B. thetaiotaomicron. This information is vital for evaluating water quality and health implications, determining the impacts of septic systems on watersheds, and improving management decisions for locating, constructing, and maintaining on-site wastewater treatment systems.

Analysis of the persistence of enteric markers in sewage polluted water on a solid matrix and in liquid suspension

Addressing the persistence of bacterial indicators using qPCR and their respective DNA targets under various conditions is a critical part of risk assessment for water quality monitoring. The goal of this study was to examine the persistence of fecal indicator bacteria (FIB) via Escherichia coli uidA, enterococci 23S rDNA and Bacteroides thetataiotaomicron 1,6 alpha mannanase from cells attached to a solid matrix and in suspension. Raw sewage (10% vol/vol) was seeded into autoclaved river water with half of the sample volume in suspension and the other half was filtered onto membranes and stored at 4°, 27° and 37°C for up to 28 days. At various time points, DNA from cells was extracted, markers were quantified, and were fit to linear and non-linear models (first order exponential, biphasic (double) exponential, two-staged, log-logistic, and Gompertz 3-parameter). First order and biphasic exponential models fit 73% of the experimental data. Persistence increased significantly when the cells were stored in an attached state (p < 0.001). Increasing temperature had an inverse effect on persistence for the cells in suspension. Bacterial cells could be stored on a solid matrix at 4°, 27° and 37 °C for up to 27, 18, and 3 days, respectively, with <90% decay. The least stable indicator at 4°, 27° and 37 °C was B. thetataiotaomicron in suspension with T90 = 9.6, 1.8, and 1.1 days, respectively. The most persistent indicator was enterococci, with T90 > 28 days in an attached state at all temperatures.

Alternative fecal indicators and their empirical relationships with enteric viruses, Salmonella enterica, and Pseudomonas aeruginosa in surface waters of a tropical urban catchment

The suitability of traditional microbial indicators (i.e., Escherichia coli and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (Bacteroides thetaiotaomicron, Methanobrevibacter smithii, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (Salmonella spp., Pseudomonas aeruginosa, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore. Salmonella and P. aeruginosa had significant positive correlations with most of the microbial indicators, especially E. coli and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e., B. thetaiotaomicron, M. smithii, and HPyVs) with E. coli and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of M. smithii and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions.

Environmental fate of tetracycline resistance genes originating from swine feedlots in river water

Tetracyclines are antibiotics commonly used in swine farms to treat disease and promote growth. However, there are growing concerns regarding the discharge of animal feces into the environment owing to the potential for development and dissemination of tetracycline resistance genes (TRGs). In this study, farming wastewater from one Chinese swine farm as well as river water from seven locations downstream of the farm was sampled. Polymerase chain reaction (PCR) showed that 12 TRGs, including six efflux pump genes (tet(B), tet(C), tet(D), tet(E), tet(G) and tet(L)), five ribosomal protection proteins (RPPs) genes (tet(O), tet(M), tet(Q), tet(W) and tet(S)), and one enzymatic modification gene (tet(X)), were present in all wastewater and river water samples. Quantitative real-time PCR (qPCR) showed that the abundance of tet(C), tet(X), tet(O), tet(M), tet(Q) and tet(W) decreased with downstream flow. Among the detected TRGs, tet(C) had the highest abundance, ranging from 459.5 copies/16S rRNA gene copies in wastewater to 33.8 copies/16S rRNA gene copies in river water samples collected from the last location. Furthermore, pig-specific Bacteroidales 16S rRNA genetic marker was quantified by qPCR to determine the level of fecal pollution in the river water. Bivariate correlation analysis confirmed that the total relative abundance of the six TRGs was significantly correlated with the level of swine feces in the aquatic environment (R(2) = 0.63, P < 0.05), suggesting that swine feces mainly contributed to the spread of TRGs in the river water.

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman(®), HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman(®) was found to be the most effective marker of human fecal contamination in this California-based study.

Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study

The last decade has seen development of numerous new microbial source tracking (MST) methodologies, but many of these have been tested in just a few laboratories with a limited number of fecal samples. This method evaluation study examined the specificity and sensitivity of 41 MST methodologies by analyzing data generated in 27 laboratories. MST methodologies that targeted human, cow, ruminant, dog, gull, pig, horse, and sheep were tested against sewage, septage, human, cow, dog, deer, pig, chicken, pigeon, gull, horse, and goose fecal samples. Each laboratory received 64 blind samples containing a single source (singletons) or two sources (doubletons), as well as diluted singleton samples to assess method sensitivity. Laboratories utilized their own protocols when performing the methods and data were deposited in a central database before samples were unblinded. Between one and seven laboratories tested each method. The most sensitive and specific assays, based on an analysis of presence/absence of each marker in target and non-target fecal samples, were HF183 endpoint and HF183SYBR (human), CF193 and Rum2Bac (ruminant), CowM2 and CowM3 (cow), BacCan (dog), Gull2SYBR and LeeSeaGull (gull), PF163 and pigmtDNA (pig), HoF597 (horse), PhyloChip (pig, horse, chicken, deer), Universal 16S TRFLP (deer), and Bacteroidales 16S TRFLP (pig, horse, chicken, deer); all had sensitivity and specificity higher than 80% in all or the majority of laboratories. When the abundance of MST markers in target and non-target fecal samples was examined, some assays that performed well in the binary analysis were found to not be sensitive enough as median concentrations fell below a minimum abundance criterion (set at 50 copies per colony forming units of enterococci) in target fecal samples. Similarly, some assays that cross-reacted with non-target fecal sources in the binary analysis were found to perform well in a quantitative analysis because the cross-reaction occurred at very low levels. Based on a quantitative analysis, the best performing methods were HF183Taqman and BacH (human), Rum2Bac and BacR (ruminant), LeeSeaGull (gull), and Pig2Bac (pig); no cow or dog-specific assay met the quantitative specificity and sensitivity criteria. Some of the best performing assays in the study were run by just one laboratory so further testing of assay portability is needed. While this study evaluated the marker performance in defined samples, further field testing as well as development of frameworks for fecal source allocation and risk assessment are needed.

Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces

This study was designed to identify poultry feces-specific marker(s) within sequences of Faecalibacterium 16S rDNA for detecting poultry fecal pollution in water. Bioinformatics tools were used in the comparative analysis of 7,458 sequences of Faecalibacterium 16S rDNA, reportedly associated with various poultry (chicken and turkey) and animal species. One intervening sequence (IVS) within between the hypervariable region 1 and the conserved region 2, designated as IVS-p, was found to be unique to poultry feces. Based on this sequence, a PCR assay (PCR-p) was developed. The PCR-p produced an amplicon of 132 bp only in the test when fecal or wastewater samples from poultry were used, but not when using fecal or wastewater samples from other sources. The non-poultry sources included feces of beef or dairy cattle, dog, horse, human, domestic or wild geese, seagull, sheep, swine, and wild turkey. These data indicate that IVS-p may prove to be a useful genetic marker for the specific identification of poultry fecal pollution in environmental waterways. Furthermore, results of data mining and PCR assay indicate that the IVS-p may have a broad geographic distribution. This report represents initial evidence of the potential utility of ribosomal intervening sequences as genetic markers for tracking host sources of fecal pollution in waterways.

Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes

Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.

Identification of feces by detection of Bacteroides genes

In forensic science, the identification of feces is very important in a variety of crime investigations. However, no sensitive and simple fecal identification method using molecular biological techniques has been reported. Here, we focused on the fecal bacteria, Bacteroides uniformis, Bacteroides vulgatus and Bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, urine, vaginal fluids and skin surfaces) and forensic (anal adhesions) specimens. Bacterial gene detection was performed by real-time PCR using a minor groove binding probe to amplify the RNA polymerase β-subunit gene of B. uniformis and B. vulgatus, and the α-1-6 mannanase gene of B. thetaiotaomicron. At least one of these bacteria was detected in the feces of 20 donors; the proportions of B. uniformis, B. vulgatus and B. thetaiotaomicron were 95, 85 and 60%, respectively. Bacteroides vulgatus was also detected in one of six vaginal fluid samples, but B. thetaiotaomicron and B. uniformis were not detected in body samples other than feces. Further, we applied this method to forensic specimens from 18 donors. Eighteen anal adhesions also contained at least one of three bacteria; B. uniformis, B. vulgatus and B. thetaiotaomicron were detected in 89, 78 and 56%, respectively, of the specimens. Thus, these bacteria were present at a high frequency in the fecal and forensic specimens, while either B. uniformis or B. vulgatus was detected in all samples. Therefore, B. uniformis and B. vulgatus represent more appropriate target species than B. thetaiotaomicron for the identification of fecal material. If B. vulgatus and/or B. uniformis are detected, it is likely that the sample contains feces. Taken together, our results suggest that the use of molecular biological techniques will aid the detection of feces in forensic practice, although it is possible that the samples contained both feces and vaginal fluid.

A perspective on the prevalence of DNA enteric virus genomes in anaerobic-digested biological wastes

The major goal of this study is to gain a perspective on the prevalence of DNA enteric virus genomes in mesophilic anaerobic-digested (MAD) sewage sludge and manure by comparing their quantitative PCR (qPCR) concentrations and removals with traditional fecal indicators (Escherichia coli, enterococci, and Bacteroidetes). In addition, relationships between qPCR and culture measurements of fecal indicators (FIs) were determined. There was no significant difference between the qPCR concentrations of human adenovirus and E. coli/enterococci in MAD sewage sludge; however, the qPCR concentrations of bovine adenovirus were significantly lower than FIs and bovine polyomavirus (BPyV) in MAD manure. The qPCR concentrations of human polyomavirus were slightly lower than E. coli and enterococci (p  ≤  0.05), but no significant difference was observed between the qPCR concentrations of BPyV and FIs. The digestion treatment achieved higher genome removal of bovine DNA enteric viruses than FIs (p  ≤  0.05). Significant correlations were observed between qPCR and culture measurements of FIs, but the concentrations and removals of FIs determined by qPCR assays were still significantly different than those determined by culture assays. Overall, we determined that the prevalence of DNA enteric virus genomes in MAD biological wastes was high due to their comparable in qPCR concentrations to FIs, indicating that mesophilic anaerobic digestion treatment alone may not be effective enough to remove DNA viral pathogens in biological wastes.

Escherichia coli, enterococci, and Bacteroides thetaiotaomicron qPCR signals through wastewater and septage treatment

Fecal indicators such as Escherichia coli and enterococci are used as regulatory tools to monitor water with 24 h cultivation techniques for possible input of sewage or feces and presence of potential enteric pathogens yet their source (human or animal) cannot be determined with routine methods. This critical uncertainty has furthered water pollution science toward new molecular approaches. Members of Bacteroides genus, such as Bacteroides thetaiotaomicron are found to have features that allow their use as alternative fecal indicators and for Microbial Source Tracking (MST). The overall aim of this study was to evaluate the concentration and fate of B. thetaiotaomicron, throughout a wastewater treatment facility and septage treatment facility. A large number of samples were collected and tested for E. coli and enterococci by both cultivation and qPCR assays. B. thetaiotaomicron qPCR equivalent cells (mean: 1.8 × 10(7)/100 mL) were present in significantly higher concentrations than E. coli or enterococci in raw sewage and at the same levels in raw septage. The removal of B. thetaiotaomicron target qPCR signals was similar to E. coli and enterococci DNA during the treatment of these wastes and ranged from 3 to 5 log(10) for wastewater and was 7 log(10) for the septage. A significant correlation was found between B. thetaiotaomicron marker and each of the conventional indicators throughout the waste treatment process for both raw sewage and septage. A greater variability was found with enterococci when compared to E. coli, and CFU and equivalent cells could be contrasted by various treatment processes to examine removal and inactivation via septage and wastewater treatment. These results are compared and contrasted with other qPCR studies and other targets in wastewater samples providing a view of DNA targets in such environments.

Bifidobacterial diversity and the development of new microbial source tracking indicators

Many studies suggest a close relationship between species of Bifidobacterium and their hosts. Thus, species such as B. adolescentis and B. thermacidophilum subsp. porcinum have been proposed as potential indicators of human and porcine fecal pollution. The diversity of bifidobacteria in wastewaters (human and animal) and slurries is analyzed using nested PCR followed by denaturant gradient gel electrophoresis (DGGE). The sewage samples showed similar DGGE patterns. The predominant bands were recognized as B. adolescentis, B. longum, and two unidentified species related to B. adolescentis. A single band detected in poultry samples was identified as B. saeculare. Bifidobacterial diversity was higher within porcine and bovine samples. The main bands in porcine samples were identified as B. minimum, an unknown species, and B. thermophilum/B. thermacidophilum subsp. porcinum. The latter species was also identified among the main bands in bovine samples together with B. pseudolongum and B. ruminantium. We then attempted to isolate the host-specific strains. DGGE bands were examined to develop specific probes to screen environmental samples by colony hybridization and further isolation of strains from positively hybridized colonies. Bifidobacterial strains that are host associated by DGGE bands to human and pig were successfully isolated from the environment: B. adolescentis from human sewage samples and the unidentified species related to pig from slurries and slaughterhouse wastewater. Neither the poultry-associated B. saeculare nor the ruminant-associated B. pseudolongum could be isolated with the current methodology, suggesting either a low prevalence in the samples or failure of the culture to grow in the media used.

Efficacy of hollow-fiber ultrafiltration for microbial sampling in groundwater

The goal of this study was to test hollow-fiber ultrafiltration as a method for concentrating in situ bacteria and viruses in groundwater samples. Water samples from nine wells tapping a shallow sandy aquifer in a densely populated village in Bangladesh were reduced in volume approximately 400-fold using ultrafiltration. Culture-based assays for total coliforms and Escherichia coli, as well as molecular-based assays for E. coli, Bacteroides, and adenovirus, were used as microbial markers before and after ultrafiltration to evaluate performance. Ultrafiltration increased the concentration of the microbial markers in 99% of cases. However, concentration factors (CF = post-filtration concentration/pre-filtration concentration) for each marker calculated from geometric means ranged from 52 to 1018 compared to the expected value of 400. The efficiency was difficult to quantify because concentrations of some of the markers, especially E. coli and total coliforms, in the well water (WW) collected before ultrafiltration varied by several orders of magnitude during the period of sampling. The potential influence of colloidal iron oxide precipitates in the groundwater was tested by adding EDTA to the pre-filtration water in half of the samples to prevent the formation of precipitates. The use of EDTA had no significant effect on the measurement of culturable or molecular markers across the 0.5 to 10 mg/L range of dissolved Fe(2+) concentrations observed in the groundwater, indicating that colloidal iron did not hinder or enhance recovery or detection of the microbial markers. Ultrafiltration appears to be effective for concentrating microorganisms in environmental water samples, but additional research is needed to quantify losses during filtration.

Persistence of Bacteroides species populations in a river as measured by molecular and culture techniques

Given the interest in Bacteroides species as microbial source tracking (MST) markers, and the limited knowledge of the survival of Bacteroides species in the environment, here we examine the survival of Bacteroides fragilis, B. thetaiotaomicron, and environmental species of Bacteroides by use of culture techniques and molecular tools. Two kinds of experiments were performed: (i) on-site experiments, in which bacteria were exposed to changes in the levels of several environmental parameters in a river, and (ii) microcosm assays in the laboratory, with controlled temperatures. On-site experiments showed different survival patterns for the cultivable Bacteroides strains. B. fragilis die-off rate was strongly affected by the combined effect of high temperatures and grazing predators, which were more active under warmer conditions. However, the survival rates of cultivable B. thetaiotaomicron and environmental Bacteroides spp. were more affected by dissolved oxygen (DO) concentration in water. Environmental Bacteroides strains survived longer than either type strain, due to better adaptation to environmental conditions. However, the period of their survival was shorter than that observed for fecal coliforms and enterococci, suggesting Bacteroides species as markers of recent fecal pollution. The total Bacteroides species were detected by molecular techniques throughout the experiment in winter, but they were detected on only two or three days in the summer. This indicates that temperature is the main factor affecting DNA degradation, regardless of species. The use of microcosms in the laboratory also pointed to temperature as the main factor affecting Bacteroides survival, regardless of species. However, the conditions in the laboratory may mask the effects of the environmental factors and their interactions. The observed variability in die-off rate as a function of the species analyzed, the experimental conditions, and the methodology used should be taken into consideration in future persistence studies.

Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces

AIMS

The focus of this study was to identify a bacterial 16S rRNA gene sequence, unique to microbiota in the human gut, for use in development of a dependable PCR assay to detect human faecal pollution in water.

METHODS AND RESULTS

Suppression subtractive hybridization (SSH) and bioinformatics were used to identify a genetic marker, within the 16S rRNA gene of Faecalibacterium, for the detection of human faeces. DNA sequencing analysis demonstrated that a majority (16) of 74 clones of the SSH library contained insertion sequences identified as Faecalibacterium 16S rRNA genes. Human faeces-specific sequences were derived and six PCR primer sets designed and tested against faecal DNA samples from human and nonhuman sources. One PCR primer set, HFB-F3 and HFB-R5, was exclusively associated with human faeces. These primers generated a human faeces-specific amplicon of 399 bp from 60.2% of human faecal samples and 100% of sewage samples.

CONCLUSIONS

The subject Faecalibacterium marker is specific for sewage.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study represents the initial report of a Faecalibacterium marker for human faeces, which may prove useful for microbial source tracking.

Molecular indicators used in the development of predictive models for microbial source tracking

A number of chemical, microbial, and eukaryotic indicators have been proposed as indicators of fecal pollution sources in water bodies. No single one of the indicators tested to date has been able to determine the source of fecal pollution in water. However, the combined use of different indicators has been demonstrated to be the best way of defining predictive models suitable for determining fecal pollution sources. Molecular methods are promising tools that could complement standard microbiological water analysis. In this study, the feasibility of some proposed molecular indicators for microbial source tracking (MST) was compared (names of markers are in parentheses): host-specific Bacteroidetes (HF134, HF183, CF128, and CF193), Bifidobacterium adolescentis (ADO), Bifidobacterium dentium (DEN), the gene esp of Enterococcus faecium, and host-specific mitochondrial DNA associated with humans, cattle, and pigs (Humito, Bomito, and Pomito, respectively). None of the individual molecular markers tested enabled 100% source identification. They should be combined with other markers to raise sensitivity and specificity and increase the number of sources that are identified. MST predictive models using only these molecular markers were developed. The models were evaluated by considering the lowest number of molecular indicators needed to obtain the highest rate of identification of fecal sources. The combined use of three molecular markers (ADO, Bomito, and Pomito) enabled correct identification of 75.7% of the samples, with differentiation between human, swine, bovine, and poultry sources. Discrimination between human and nonhuman fecal pollution was possible using two markers: ADO and Pomito (84.6% correct identification). The percentage of correct identification increased with the number of markers analyzed. The best predictive model for distinguishing human from nonhuman fecal sources was based on 5 molecular markers (HF134, ADO, DEN, Bomito, and Pomito) and provided 90.1% correct classification.