Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater

Comparison of microbial source tracking efficacy for detection of cattle fecal contamination by quantitative PCR

Identification of fecal contamination sources in surface water has become heavily dependent on quantitative PCR (qPCR) because this technique allows for the rapid enumeration of fecal indicator bacteria as well as the detection and quantification of fecal source-associated genetic markers in the environment. Identification of contamination sources in impaired waters is a prerequisite for developing best management practices to reduce future pollution. Proper management decisions rely on the quality and interpretation of qPCR data. In this study, we developed a method to determine analytical and process lower limits of detection (LLOD) and quantification (LLOQ) using two cattle-associated genetic markers targeting Bacteroidales. Analytical LLOD (A_LLOD) for both CowM2 and CowM3 genetic markers in the qPCR assay were five gene copies per reaction. Using composite fecal DNA, the analytical LLOQ (A_LLOQ) determined for CowM2 and CowM3 were 78 and 195 gene copies/reaction, respectively. When plasmid DNA was used, the A_LLOQ for CowM2 and CowM3 were 46 and 20 gene copies/reaction, respectively. The process LLOD (P_LLOD) for CowM2 and CowM3 were 0.4 and 0.02 mg feces/filter (wet weight), respectively. Using the standard deviation value of 0.25 as a cut-off point for LLOQ in regression analysis, the process LLOQ (P_LLOQ) for CowM2 and CowM3 were 3.2 and 0.3 mg feces/filter, respectively. These results indicate that CowM3 exhibited superior performance characteristics compared with CowM2 for fecal samples collected from our geographical region. Moreover, the method for calculating LLOD and LLOQ developed here can be applied to other microbial source tracking studies.

Lateral flow sand filters are effective for removal of antibiotic resistance genes from domestic wastewater

The ability of lateral flow sand filters, used as on-site wastewater treatment systems (OWTS), to remove antibiotic resistance genes (ARGs), antibiotic resistant bacteria (ARB), and other relevant genetic markers (HF183, 16S rRNA, and int1) was assessed. Municipal wastewater was settled in a septic tank prior to loading into six pilot-scale lateral flow sand filters comprised of three different sand media types, at 5 and 30% slopes. The sand filters were sampled bi-weekly for: 9 ARGs and 3 other complimentary gene markers (sul1, sul2, qnrS, tetO, ermB, bla_TEM, bla_CTX-M, mecA, vanA, int1, HF183, 16S rRNA), and conventional microbial and water quality indicators, from July to November in 2017, and four times in the summer of 2018. The sand filters were observed to attenuate 7 of the ARGs to mostly below 2 log gene copies per mL. Log reductions ranging from 2.9 to 5.4 log were observed for the removal of absolute abundances of ARGs from septic tank effluent in 5 of the 6 sand filters. The fine-grained filter on the 5% slope did not perform as well for ARG attenuation due to hydraulic failure. The apportionment of cell-associated versus cell-free DNA was determined for the gene markers and this indicated that the genes were primarily carried intracellularly. Average log reductions of ARB with resistance to either sulfamethoxazole, erythromycin, or tetracycline were approximately 2.3 log CFU per mL within the filters compared to the septic tank effluent. This field study provides in-depth insights into the attenuation of ARB, ARGs, and their genetic compartmentalization in variably saturated sand OWTS. Overall, this type of OWTS was found to pose little risk of antimicrobial resistance contamination spread into surrounding environments when proper hydraulic function was maintained.

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.

Host Specificity and Sensitivity of Established and Novel Sewage-Associated Marker Genes in Human and Nonhuman Fecal Samples

Microbial source tracking (MST) methods measure fecal contamination levels and identify possible sources using quantitative PCR (qPCR) that targets host-associated fecal microorganisms. To date, most established MST assays for human sources, especially bacterial markers, have shown some nonhuman host cross-reactions. Recently developed assays, such as the crAssphage CPQ_056, Lachnospiraceae Lachno3, and Bacteroides BacV6-21, have more limited information on host sensitivity and host specificity for human or sewage sources, particularly in countries other than the United States. In this study, we rigorously evaluated six sewage-associated MST assays (i.e., Bacteroides HF183, human adenovirus [HAdV], human polyomavirus [HPyV], crAssphage CPQ_056, Lachno3, and BacV6-21) to show advantages and disadvantages of their applications for MST. A total of 29 human and 3 sewage samples and 360 nonhuman fecal samples across 14 hosts collected from a subtropical region of Australia were tested for marker host specificity, host sensitivity, and concentrations. All sewage samples were positive for all six marker genes tested in this study. Bacterial markers were more prevalent than viral markers in human feces. Testing against animal hosts showed human feces (or sewage)-associated marker gene specificity was HAdV (1.00) > HPyV (0.99) > crAssphage CPQ_056 (0.98) > HF183 (0.96) > Lachno3 (0.95) > BacV6-21 (0.90), with marker concentrations in some animal fecal samples being 3 to 5 orders of magnitude lower than those in sewage. When considering host specificity, sensitivity, and concentrations in source samples, the HF183, Lachno3, and crAssphage CPQ_056 tests were the most suitable assays in this study for sewage contamination tracking in subtropical waters of Australia.IMPORTANCE Large financial investments are required to remediate fecal contamination sources in waterways, and accurate results from field studies are crucial to build confidence in MST approaches. Host specificity and sensitivity are two main performance characteristics for consideration when choosing MST assays. Ongoing efforts for marker assay validation will improve interpretation of results and could shed light on patterns of occurrence in nontarget hosts that might explain the underlying drivers of cross-reaction of certain markers. For field applications, caution should be taken to choose appropriate MST marker genes and assays based on available host specificity and sensitivity data and background knowledge of the contaminating sources in the study area. Since many waterborne pathogens are viruses, employing both viral and bacterial markers in investigations could provide insight into contamination dynamics and ecological behavior in the environment. Therefore, combined usage of marker assays is recommended for more accurate and informative sewage contamination detection and fecal source resolution.

Application of high-throughput 16S rRNA sequencing to identify fecal contamination sources and to complement the detection of fecal indicator bacteria in rural groundwater

Residents in rural communities across Canada collect potable water from aquifers. Fecal contaminants from sewage and agricultural runoffs can penetrate aquifers, posing a public health risk. Standard methods for detecting fecal contamination test for fecal indicator bacteria (FIB), but the presence of these do not identify sources of contamination. In contrast, DNA-based diagnostic tools can achieve this important objective. We employed quantitative polymerase chain reaction (qPCR) and high-throughput DNA sequencing to trace fecal contamination sources in Wainfleet, a rural Ontario township that has been under the longest active boil water advisory in Canada due to FIB contamination in groundwater wells. Using traditional methods, we identified FIBs indicating persistent fecal pollution in well waters. We used 16S rRNA sequencing to profile groundwater microbial communities and identified Campylobacteraceae as a fecal contamination DNA marker in septic tank effluents (STEs). We also identified Turicibacter and Gallicola as a potential cow and chicken fecal contamination marker, respectively. Using human specific Bacteroidales markers, we identified leaking septic tanks as the likely primary fecal contamination source in some of Wainfleet's groundwater. Overall, the results support the use of sequencing-based methods to augment traditional water quality testing methods and help end-users assess fecal contamination levels and identify point and non-point pollution sources.

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.

Fecal contamination of storm sewers: Evaluating wastewater micropollutants, human-specific Bacteroides 16S rRNA, and mitochondrial DNA genetic markers as alternative indicators of sewer cross connections

A set of fecal indicator bacteria and alternative markers were tested for their use to identify priority sectors of two urban watersheds in the Greater Montreal region with unintended household sewage connections to storm drainage systems. Analyses were performed for thermotolerant (fecal) coliforms (FC), Escherichia coli, human-specific Bacteroidales (HF183) and mitochondrial DNA (Hmt) markers, carbamazepine (CBZ), caffeine (CAF), theophylline (THEO) and acetaminophen (ACE). A high incidence of human fecal contamination was observed, illustrating the need for a method to appropriately prioritize sectors for the rehabilitation of sewer cross-connections. Concentrations of alternative markers were not significantly different between the residential and industrial/commercial/institutional (ICI) sectors. However, median E. coli concentrations were higher in the residential as compared to ICI sectors (p < 0.05). Hmt marker, CAF, and THEO were well correlated to E. coli in the ICI sector (r > 0.61, p < 0.05). Considering all sites, only CAF and THEO were correlated to E. coli (r > 0.59, p < 0.05), possibly as a result of higher E. coli inputs from other sources such as domestic animals or fauna in the residential sector. Thresholds were determined to relate alternative markers to E. coli for use in an index for prioritizing sectors with sewer cross-connections. HF183, Hmt, CAF, THEO, and ACE were identified as suitable markers for identifying sewer cross-connections and are more reliable than E. coli alone, most importantly in residential sectors.

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.

Presence of bacteroidales as a predicator of human enteric viruses in Haihe River of Tianjin City, China

Traditional microbe indicators including total bacteria, total coliforms, fecal coliforms, Escherichia coli, enterococci, and F+ coliphage are all frequently used to characterize the microbial contamination state of water bodies for their correlation with pathogenic bacteria. However, these indicators have a poor relationship with viruses, which pose serious threat to economic and human health. Alternative indicators such as bacteroidales may be suitable complementary alternatives to traditional microbe indicators and are being increasingly reported. In the present study, water was analyzed for selected sites along Haihe River in Tianjin for traditional indicators, an alternative indicator (bacteroidales), pathogenic bacteria (Salmonella, Escherichia coli (E. coli) O157:H7, and Vibrio parahaemolyticus), viruses (enteric adenovirus, norovirus, enterovirus, poliovirus and rotavirus), and physicochemical parameters. Results indicated that traditional microbe indicators detected in this study showed good correlation with pathogenic bacteria, and the alternative indicator (bacteroidales) had a surprisingly good relationship with viral presence. We propose that bacteroidales might be a suitable complementary indicator for viral contamination in water bodies.

Determination of wild animal sources of fecal indicator bacteria by microbial source tracking (MST) influences regulatory decisions

Fecal indicator bacteria (FIB) are used to assess fecal pollution levels in surface water and are among the criteria used by regulatory agencies to determine water body impairment status. While FIB provide no information about pollution source, microbial source tracking (MST) does, which contributes to more direct and cost effective remediation efforts. We studied a watershed in Florida managed for wildlife conservation that historically exceeded the state regulatory guideline for fecal coliforms. We measured fecal coliforms, enterococci, a marker gene for avian feces (GFD), and a marker gene for human-associated Bacteroides (HF183) in sediment, vegetation, and water samples collected monthly from six sites over two years to: 1) assess the influence of site, temporal factors, and habitat (sediment, vegetation, and water) on FIB and MST marker concentrations, 2) test for correlations among FIB and MST markers, and 3) determine if avian feces and/or human sewage contributed to FIB levels. Sediment and vegetation had significantly higher concentrations of FIB and GFD compared to water and thus may serve as microbial reservoirs, providing unreliable indications of recent contamination. HF183 concentrations were greatest in water samples but were generally near the assay limit of detection. HF183-positive results were attributed to white-tailed deer (Odocoileus virginianus) feces, which provided a false indication of human sewage in this water body. FIB and GFD were positively correlated while FIB and HF183 were negatively correlated. We demonstrated that birds, not sewage, were the main source of FIB, thus avoiding implementation of a total maximum daily load program (TMDL). Our results demonstrate that the concomitant use of FIB and MST can improve decision-making and provide direction when water bodies are impaired, and provides a strategy for natural source exclusion in water bodies impacted by wild animal feces.

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.

Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds - A review

In New Zealand, there is substantial potential for microbial contaminants from agricultural fecal sources to be transported into waterways. The flow and transport pathways for fecal contaminants vary at a range of scales and is dependent on chemical, physical and biological attributes of pathways, soils, microorganisms and landscape characteristics. Understanding contaminant transport pathways from catchment to stream can aid water management strategies. It is not practical, however to conduct direct field measurement for all catchments on the fate and transport of fecal pathogens due to constraints on time, personnel, and material resources. To overcome this problem, fecal source tracking can be utilised to link catchment characteristics to fecal signatures identifying critical sources. In this article, we have reviewed approaches to identifying critical sources and pathways for fecal microorganisms from agricultural sources, and make recommendations for the appropriate use of these fecal source tracking (FST) tools.

Can We Swim Yet? Systematic Review, Meta-Analysis, and Risk Assessment of Aging Sewage in Surface Waters

This study investigated the risk of gastrointestinal illness associated with swimming in surface waters with aged sewage contamination. First, a systematic review compiled 333 first order decay rate constants ( k) for human norovirus and its surrogates feline calicivirus and murine norovirus, Salmonella, Campylobacter, Escherichia coli O157:H7, Giardia, and Cryptosporidium, and human-associated indicators in surface water. A meta-analysis investigated effects of sunlight, temperature, and water matrix on k. There was a relatively large number of k for bacterial pathogens and some human-associated indicators ( n > 40), fewer for protozoans ( n = 14-22), and few for human norovirus and its Caliciviridae surrogates ( n = 2-4). Average k ranked: Campylobacter > human-associated markers > Salmonella> E. coli O157:H7 > norovirus and its surrogates > Giardia > Cryptosporidium. Compiled k values were used in a quantitative microbial risk assessment (QMRA) to simulate gastrointestinal illness risk associated with swimming in water with aged sewage contamination. The QMRA used human-associated fecal indicator HF183 as an index for the amount of sewage present and thereby provided insight into how risk relates to HF183 concentrations in surface water. Because exposure to norovirus contributed the majority of risk, and HF183 k is greater than norovirus k, the risk associated with exposure to a fixed HF183 concentration increases with the age of contamination. Swimmer exposure to sewage after it has aged ∼3 days results in median risks less than 30/1000. A risk-based water quality threshold for HF183 in surface waters that takes into account uncertainty in contamination age is derived to be 4100 copies/100 mL.

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems

Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.

Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing

In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.

Exposure to Human-Associated Chemical Markers of Fecal Contamination and Self-Reported Illness among Swimmers at Recreational Beaches

Anthropogenic chemicals have been proposed as potential markers of human fecal contamination in recreational water. However, to date, there are no published studies describing their relationships with illness risks. Using a cohort of swimmers at seven U.S. beaches, we examined potential associations between the presence of chemical markers of human fecal pollution and self-reported gastrointestinal (GI) illness, diarrhea, and respiratory illness. Swimmers were surveyed about their beach activities, water exposure, and baseline symptoms on the day of their beach visit, and about any illness experienced 10-12 days later. Risk differences were estimated using model-based standardization and adjusted for the swimmer's age, beach site, sand contact, rainfall, and water temperature. Sixty-two chemical markers were analyzed from daily water samples at freshwater and marine beaches. Of those, 20 were found consistently. With the possible exception of bisphenol A and cholesterol, no chemicals were consistently associated with increased risks of illness. These two chemicals were suggestively associated with 2% and 1% increased risks of GI illness and diarrhea in both freshwater and marine beaches. Additional research using the more sensitive analytic methods currently available for a wider suite of analytes is needed to support the use of chemical biomarkers to quantify illness risk and identify fecal pollution sources.

Human-Associated Lachnospiraceae Genetic Markers Improve Detection of Fecal Pollution Sources in Urban Waters

The human microbiome contains many organisms that could potentially be used as indicators of human fecal pollution. Here we report the development of two novel human-associated genetic marker assays that target organisms within the family Lachnospiraceae Next-generation sequencing of the V6 region of the 16S rRNA gene from sewage and animal stool samples identified 40 human-associated marker candidates with a robust signal in sewage and low or no occurrence in samples from nonhuman hosts. Two were chosen for quantitative PCR (qPCR) assay development using longer sequences (the V2 to V9 regions) generated from clone libraries. Validation of these assays with these markers, designated Lachno3 and Lachno12, was performed using fecal samples (n = 55) from cat, dog, pig, cow, deer, and gull sources, and the results were compared with those of established host-associated assays (the Lachno2 marker and two human Bacteroides markers, the HB and HF183/BacR287). Each of the established assays cross-reacted with samples from at least one other animal species, including animals common in urban areas. The Lachno3 and Lachno12 markers were primarily human associated; however, the Lachno12 marker demonstrated low levels of cross-reactivity with samples from select cows and nonspecific amplification with samples from pigs. This limitation may not be problematic when testing urban waters. These novel markers resolved ambiguous results from previous investigations of stormwater-impacted waters, demonstrating their utility. The complexity of the microbiome in humans and animals suggests that no single organism is strictly specific to humans, and the use of multiple complementary markers in combination will provide the highest resolution and specificity for assessing fecal pollution sources.IMPORTANCE Traditional fecal indicator bacteria do not distinguish animal from human fecal pollution, which is necessary to evaluate health risks and mitigate pollution sources. Assessing water in urban areas is challenging, since the water can be impacted by sewage, which has a high likelihood of carrying human pathogens, as well as pet and urban wildlife waste. We demonstrate that the Lachno3 and Lachno12 markers are human associated and highly specific for the detection of human fecal pollution from urban sources, offering reliable identification of fecal pollution sources in urban waters.

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

AIMS

To validate host-specific Bacteroidales assays to identify faecal-source contamination of drinking water sources in the Kathmandu Valley, Nepal.

METHODS AND RESULTS

A total of 54 composite faecal-source samples were collected from human sewage, ruminants, pigs, dogs, chickens and ducks, which were analysed by quantitative polymerase chain reaction using human-specific (BacHum, HF183 SYBR, gyrB and HF183 TaqMan), ruminant-specific (BacCow and BacR), pig-specific (Pig2Bac and PF163) and dog-specific assays (BacCan SYBR). The BacHum, BacR and Pig2Bac assays were judged the best performing human-specific, ruminant-specific and pig-specific assays respectively. The BacCan SYBR assay highly cross-reacted with other species, resulting in poor performance. Furthermore, these validated assays were applied to microbial source tracking (MST) of 74 drinking water samples. Out of these, 20, 12 and 4% samples were judged contaminated by human, ruminant and pig faeces respectively. Detection ratios of human and ruminant faecal markers were relatively higher in built-up and agricultural areas respectively.

CONCLUSION

BacHum, BacR and Pig2Bac assays were found suitable for MST and both, human and animal faecal contaminations of drinking water sources were common in the valley.

SIGNIFICANCE AND IMPACT OF THE STUDY

MST could be an effective tool for preparing the faecal pollution strategies as these are site specific.

Microbial source tracking markers associated with domestic rainwater harvesting systems: Correlation to indicator organisms

Domestic rainwater harvesting (tank water) systems were screened for the presence of a panel of microbial source tracking (MST) markers and traditional indicator organisms. The indicator organisms were enumerated utilizing traditional culture-based methods, while the MST markers were quantified by quantitative PCR (qPCR). The indicators Escherichia coli (E. coli) and enterococci were also quantified using qPCR. Correlations and concurrence between these parameters were then investigated to determine which markers could be utilized to supplement traditional indicator analysis. Quantitative PCR analysis indicated that Bacteroides HF183, adenovirus, Lachnospiraceae and E. coli were detected and quantifiable in 100% of the tank water samples collected throughout the sampling period, while human mitochondrial DNA (mtDNA) was quantifiable in 90% of the tank water samples and Bifidobacterium adolescentis (B. adolescentis) and enterococci were quantifiable in 67% of the tank water samples, respectively. Significant positive correlations were recorded for Lachnospiraceae versus heterotrophic bacteria (p = 0.000), adenovirus versus E. coli (culturing) (p = 0.000) and heterotrophic bacteria (p = 0.024), the HF183 marker versus E. coli (qPCR) (p = 0.024) and B. adolescentis versus fecal coliforms (p = 0.037). In addition, 100% concurrence was observed for the HF183 marker, adenovirus and Lachnospiraceae versus E. coli (qPCR), enterococci (qPCR) and heterotrophic bacteria, amongst others. Based on the correlations and the concurrence analysis, the HF183 marker, Lachnospiraceae and adenovirus may be utilized to supplement indicator organism analysis for the monitoring of harvested rainwater quality.

Microbial source tracking in highly vulnerable karst drinking water resources

Water resources situated in areas with underlying karst geology are particularly vulnerable to fecal pollution. In such vulnerable systems, microbial source tracking (MST) methods are useful tools to elucidate the pathways of both animal and human fecal pollution, leading to more accurate water use risk assessments. Here, we describe the application of a MST toolbox using both culture-dependent bacteriophage and molecular-dependent 16S rRNA assays at spring and well sites in the karstic St Imier Valley, Switzerland. Culture-dependent and molecular-dependent marker performance varied significantly, with the 16S rRNA assays displaying greater sensitivity than their phage counterpart; HF183 was the best performing human wastewater-associated marker while Rum2Bac was the best performing ruminant marker. Differences were observed in pollution regimes between the well and spring sampling sites, with the spring water being more degraded than the well site. Our results inform the choice of marker selection for MST studies and highlight differences in microbial water quality between well and spring karst sites.

Validation and application of quantitative PCR assays using host-specific Bacteroidales genetic markers for swine fecal pollution tracking

Genome fragment enrichment (GFE) method was applied to identify host-specific bacterial genetic markers that differ among different fecal metagenomes. To enrich for swine-specific DNA fragments, swine fecal DNA composite (n = 34) was challenged against a DNA composite consisting of cow, human, goat, sheep, chicken, duck and goose fecal DNA extracts (n = 83). Bioinformatic analyses of 384 non-redundant swine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode metabolism-associated, cellular processes and information storage and processing. After challenged against fecal DNA extracted from different animal sources, four sequences from the clone libraries targeting two Bacteroidales- (genes 1-38 and 3-53), a Clostridia- (gene 2-109) as well as a Bacilli-like sequence (gene 2-95), respectively, showed high specificity to swine feces based on PCR analysis. Host-specificity and host-sensitivity analysis confirmed that oligonucleotide primers and probes capable of annealing to select Bacteroidales-like sequences (1-38 and 3-53) exhibited high specificity (>90%) in quantitative PCR assays with 71 fecal DNAs from non-target animal sources. The two assays also demonstrated broad distributions of corresponding genetic markers (>94% positive) among 72 swine feces. After evaluation with environmental water samples from different areas, swine-targeted assays based on two Bacteroidales-like GFE sequences appear to be suitable quantitative tracing tools for swine fecal pollution.

Bacteriome genetic structures of urban deposits are indicative of their origin and impacted by chemical pollutants

Urban activities generate surface deposits over impervious surfaces that can represent ecological and health hazards. Bacteriome genetic structures of deposits washed off during rainfall events, over an urban industrial watershed, were inferred from 16 S rRNA gene (rrs) sequences generated by high throughput sequencing. Deposits were sampled over a 4 year-period from a detention basin (DB). Major shifts, matching key management practices, in the structure of these urban bacteriomes, were recorded. Correlation analyses of rrs similarities between samples and their respective concentrations in chemical pollutants, markers of human fecal contaminations (HF183) and antimicrobial resistances (integrons), were performed. Harsher environmental constraints building up in the older deposits led to an increase number of rrs reads from extremophiles such as Acidibacter and Haliangium. Deposits accumulating in the decantation pit of the DB showed an increase in rrs reads from warm blooded intestinal tract bacteria such as Bacteroides and Prevotella. This enrichment matched higher concentrations of Bacteroides HF183 genotypes normally restricted to humans. Bacteriomes of urban deposits appeared good indicators of human-driven environmental changes. Their composition was found representative of their origin. Soil particles and rain appeared to be major contributors of the inferred bacterial taxa recovered from recent deposits.

Tracking the downstream impacts of inadequate sanitation in central Appalachia

Poor sanitation in rural infrastructure is often associated with high levels of fecal contamination in adjacent surface waters, which presents a community health risk. Although microbial source tracking techniques have been widely applied to identify primary remediation needs in urban and/or recreational waters, use of human-specific markers has been more limited in rural watersheds. This study quantified the human source tracking marker Bacteroides-HF183, along with more general fecal indicators (i.e. culturable Escherichia coli and a molecular Enterococcus marker), in two Appalachian streams above and below known discharges of untreated household waste. Although E. coli and Enterococcus were consistently recovered in samples collected from both streams, Bacteroides-HF183 was only detected sporadically in one stream. Multiple linear regression analysis demonstrated a positive correlation between the concentration of E. coli and the proximity and number of known waste discharge points upstream; this correlation was not significant with respect to Bacteroides-HF183, likely due to the low number of quantifiable samples. These findings suggest that, while the application of more advanced source targeting strategies can be useful in confirming the influence of substandard sanitation on surface waters to justify infrastructure improvements, they may be of limited use without concurrent traditional monitoring targets and on-the-ground sanitation surveys.

Comparison of the Performance of Different Microbial Source Tracking Markers among European and North African Regions

Microbial source tracking (MST) has been extensively used to detect the sources of fecal pollution in water. The inclusion of MST in water management strategies improves the ecological status of the ecosystem and human and animal health under interdisciplinary analysis in all aspects of health care for humans, animals, and the environment (One Health approach). In this study, the performance of MST markers targeting host-specific Bacteroidales (HF183 and Rum-2-Bac) and species (HMBif and CWBif) were evaluated in raw sewage collected from human, ruminant, swine, and poultry sources in Tunisia, Cyprus, Ireland, and Spain. In addition, the ratio between somatic coliphages and bacteriophages infecting GA17 (SOMCPH/GA17PH) was measured in Tunisia and Spain. The obtained results showed variability of the bacterial markers between the four countries, suggesting that their usefulness could be affected by several conditions (dietary habits, agricultural practices, and climatic conditions) that differ between countries. The Rum-2-Bac marker stood out as a valid MST tool, particularly in Ireland, whereas CWBif was the best option in Tunisia, Spain, and Cyprus. The human-specific HMBif marker showed good sensitivity and specificity in Tunisia, Spain, and Ireland, whereas HF183 showed a low specificity. However, HF183 was suggested as a good human marker in Ireland and Cyprus because of its higher concentration than HMBif. Regarding viral markers, the ratio of SOMCPH/GA17PH showed a clear discrimination between human and nonhuman samples. The combined use of molecular bacterial markers and the ratio of SOMCPH/GA17PH may improve the success of MST.

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.

Variation of Bacterial Communities with Water Quality in an Urban Tropical Catchment

A major challenge for assessment of water quality in tropical environments is the natural occurrence and potential growth of Fecal Indicator Bacteria (FIB). To gain a better understanding of the relationship between measured levels of FIB and the distribution of sewage-associated bacteria, including potential pathogens, in the tropics this study compared the abundance of FIB (Total coliforms and E. coli) and the Bacteroidales (HF183 marker) with bacterial community structure determined by next-generation amplicon sequencing. Water was sampled twice over 6 months from 18 sites within a tropical urban catchment and reservoir, followed by extraction of DNA from microorganisms, and sequencing targeting the V3-V4 region of the 16S rRNA gene. Multivariate statistical analyses indicated that bacterial community composition (BCC) varied between reservoir and catchment, within catchment land-uses, and with E. coli concentration. Beta-regression indicated that the proportion of sequences from sewage-associated taxa (SAT) or pathogen-like sequences (PLS) were predicted most significantly by measured levels of E. coli(log MPN/100 mL) (χ² > 8.7; p < 0.003). In addition, SAT were significantly predicted by log HF183 levels (χ²=13.1; p = 0.0003) while PLS were not. Our study suggests that measurements of E. coli concentration could be useful in predicting samples enriched in sewage-associated and pathogen-like bacteria in tropical environments despite the potential for nonconservative behavior.

Change in the Structure of Escherichia coli Population and the Pattern of Virulence Genes along a Rural Aquatic Continuum

The aim of this study was to investigate the diversity of the Escherichia coli population, focusing on the occurrence of pathogenic E. coli, in surface water draining a rural catchment. Two sampling campaigns were carried out in similar hydrological conditions (wet period, low flow) along a river continuum, characterized by two opposite density gradients of animals (cattle and wild animals) and human populations. While the abundance of E. coli slightly increased along the river continuum, the abundance of both human and ruminant-associated Bacteroidales markers, as well as the number of E. coli multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites. A strong spatial modification of the structure of the E. coli population was observed. At the upstream site close to a forest, a higher abundance of the B2 phylogroup and Escherichia clade strains were observed. At the pasture upstream site, a greater proportion of both E and B1 phylogroups was detected, therefore suggesting a fecal contamination of mainly bovine origin. Conversely, in downstream urban sites, A, D, and F phylogroups were more abundant. To assess the occurrence of intestinal pathogenic strains, virulence factors [afaD, stx1, stx2, eltB (LT), estA (ST), ipaH, bfpA, eae, aaiC and aatA] were screened among 651 E. coli isolates. Intestinal pathogenic strains STEC O174:H21 (stx2) and EHEC O26:H11 (eae, stx1) were isolated in water and sediments close to the pasture site. In contrast, in the downstream urban site aEPEC/EAEC and DAEC of human origin, as well as extra-intestinal pathogenic E. coli belonging to clonal group A of D phylogroup, were sampled. Even if the estimated input of STEC (Shiga toxin-producing E. coli) - released in water at the upstream pasture site - at the downstream site was low, we show that STEC could persist in sediment. These results show that, the run-off of small cattle farms contributed, as much as the wastewater effluent, in the dissemination of pathogenic E. coli in both water and sediments, even if the microbiological quality of the water was good or to average quality according to the French water index.

Soil Ingestion is Associated with Child Diarrhea in an Urban Slum of Nairobi, Kenya

Diarrhea is a leading cause of mortality in children under 5 years of age. We conducted a cross-sectional study of 54 children aged 3 months to 5 years old in Kibera, an urban slum in Nairobi, Kenya, to assess the relationship between caregiver-reported soil ingestion and child diarrhea. Diarrhea was significantly associated with soil ingestion (adjusted odds ratio = 9.9, 95% confidence interval = 2.1-47.5). Soil samples from locations near each household were also collected and analyzed for Escherichia coli and a human-associated Bacteroides fecal marker (HF183). Escherichia coli was detected in 100% of soil samples (mean 5.5 log colony forming units E. coli per gram of dry soil) and the Bacteroides fecal marker HF183 was detected in 93% of soil samples. These findings suggest that soil ingestion may be an important transmission pathway for diarrheal disease in urban slum settings.

Legacy of contaminant N sources to the NO3- signature in rivers: a combined isotopic (δ15N-NO3-, δ18O-NO3-, δ11B) and microbiological investigation

Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (δ¹⁵N and δ¹⁸O of nitrate and δ¹¹B) and fecal indicators to trace nitrate sources and pathways to the stream. We tested this approach on two rivers in an agricultural region of SW France. Boron isotopic ratios evidenced inflow from anthropogenic waters, microbiological markers revealed organic contaminations from both human and animal wastes. Nitrate δ^15N and δ¹⁸O traced inputs from the surface leaching during high flow events and from the subsurface drainage in base flow regime. They also showed that denitrification occurred within the soils before reaching the rivers. Furthermore, this study highlighted the determinant role of the soil compartment in nitrate formation and recycling with important spatial heterogeneity and temporal variability.

Water quality at points-of-use in the Galapagos Islands

Piped drinking water is often considered a gold standard for protecting public health but research is needed to explicitly evaluate the effect of centralized treatment systems on water quality in developing world settings. This study examined the effect of a new drinking water treatment plant (DWTP) on microbial drinking water quality at the point-of-use on San Cristobal Island, Galapagos using fecal indicator bacteria total coliforms and Escherichia coli. Samples were collected during six collection periods before and after operation of the DWTP began from the freshwater sources (n=4), the finished water (n=6), and 50 sites throughout the distribution system (n=287). This study found that there was a significant decrease in contamination by total coliforms (two orders of magnitude) and E. coli (one order of magnitude) after DWTP operation began (p<0.001). However, during at least one post-construction collection cycle, total coliforms and E. coli were still found at 66% and 28% of points-of-use (n=50), respectively. During the final collection period, conventional methods were augmented with human-specific Bacteroides assays - validated herein - with the goal of elucidating possible microbial contamination sources. Results show that E. coli contamination was not predictive of contamination by human wastes and suggests that observed indicator bacteria contamination may have environmental origins. Together these findings highlight the necessity of a holistic approach to drinking water infrastructure improvements in order to deliver high quality water through to the point-of-use.

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments. OTU patterns were found impacted by combined sewer overflows (CSO) through an observed increase in diversity from the sewer to the hyporheic sediments. These changes appeared driven by direct transfers of bacterial contaminants from wastewaters but also by organic inputs favoring previously undetectable bacterial groups among sediments. These NGS datasets appeared more sensitive at tracking community changes than MST markers. The human-specific MST marker HF183 was strictly detected among CSO-impacted surface waters and not river bed sediments. The ruminant-specific DNA marker was more broadly distributed but intense bovine pollution was required to detect transfers from surface water to benthic and hyporheic sediments. Some OTU showed distribution patterns in line with these MST datasets such as those allocated to the Aeromonas, Acinetobacter, and Pseudomonas. Fecal indicators (Escherichia coli and total thermotolerant coliforms) were detected all over the river course but their concentrations were not correlated with MST ones. Overall, MST and NGS datasets suggested a poor colonization of river sediments by bovine and sewer bacterial contaminants. No environmental outbreak of these bacterial contaminants was detected.

Isolating the impact of septic systems on fecal pollution in streams of suburban watersheds in Georgia, United States

The presence of multiple sources of fecal pollution at the watershed level presents challenges to efforts aimed at identifying the influence of septic systems. In this study multiple approaches including targeted sampling and monitoring of host-specific Bacteroidales markers were used to identify the impact of septic systems on microbial water quality. Twenty four watersheds with septic density ranging from 8 to 373 septic units/km² were monitored for water quality under baseflow conditions over a 3-year period. The levels of the human-associated HF183 marker, as well as total and ruminant Bacteroidales, were quantified using quantitative polymerase chain reaction. Human-associated Bacteroidales yield was significantly higher in high density watersheds compared to low density areas and was negatively correlated (r = -0.64) with the average distance of septic systems to streams in the spring season. The human marker was also positively correlated with the total Bacteroidales marker, suggesting that the human source input was a significant contributor to total fecal pollution in the study area. Multivariable regression analysis indicates that septic systems, along with forest cover, impervious area and specific conductance could explain up to 74% of the variation in human fecal pollution in the spring season. The results suggest septic system impact through contributions to groundwater recharge during baseflow or failing septic system input, especially in areas with >87 septic units/km². This study supports the use of microbial source tracking approaches along with traditional fecal indicator bacteria monitoring and land use characterization in a tiered approach to isolate the influence of septic systems on water quality in mixed-use watersheds.

A tool box strategy using Bacteroides genetic markers to differentiate human from non-human sources of fecal contamination in natural water

Bacteroides genetic markers have been widely used to identify fecal pollution of water originating from human and animal sources. Many of the assays currently used for detecting human-specific Bacteroides produce false positive results. The focus of this study was to develop a microbial source tracking (MST) tool box strategy for differentiating Bacteroides from human and animal sources. Bacteroides 16S rRNA gene sequences from fish and selected animals were aligned against human fecal Bacteroides isolates to compare and characterize the variable regions within the 16S rRNA gene sequence. Conserved sequences between 4 variable regions were deleted and the truncated sequences were combined to develop a hyper-variable genomic segment (HVGS). The cladogram created from truncated sequences show a clear separation of Bacteroides from human feces and those from animal sources. The proposed strategy was field tested by collecting water samples from central Arizona source waters and three different recreational ponds. PCR using HF134 and HF183 primer sets was performed and sequences from positive reactions were aligned against human Bacteroides sequences to identify the source of contamination. Based on PCR results, the source of fecal contamination was presumptively identified as either human or from another source. For samples testing positive using the HF183 primer set (8/13), fecal contamination was presumed to be from human sources, but to confirm the results, PCR products were sequenced and aligned against the four variable regions and then incorporated within the truncated cladogram. As expected, the sequences from water samples with human fecal contamination grouped in a separate clade. A variability matrix, developed after exclusion of conserved sequences among the four regions, was utilized to establish discrete groupings for sequences within the truncated cladogram, generally differentiating Bacteroides isolates from varying host animals, but most importantly, separating Bacteroides from human feces from Bacteroides from other animals. The proposed strategy offers a new tool box method for MST and a step-wise methodology essential for identifying human sources of fecal pollution.

Tracking the relative concentration between Bacteroidales DNA markers and culturable Escherichia coli in fecally polluted subtropical seawater: potential use in differentiating fresh and aged pollution

Routine water quality monitoring practices based on the enumeration of culturable Escherichia coli provides no information about the source or age of fecal pollution. An emerging strategy is to use culturable E. coli and the DNA markers of Bacteroidales complementarily for microbial source tracking. In this study, we consistently observed in seawater microcosms of 3 different conditions that culturable E. coli decayed faster (T₉₉ = 1.14 - 4.29 days) than Bacteroidales DNA markers did (T₉₉ = 1.81 - 200.23 days). Concomitantly, the relative concentration between Bacteroidales DNA markers and culturable E. coli increased over time in all treatments. Particularly, the increase during the early stage of the experiments (before T₉₉ of E. coli was reached) was faster than during the later stage (after T₉₉ of E. coli was attained). We propose that the tracking of the relative concentration between Bacteroidales DNA markers and culturable E. coli provides an opportunity to differentiate a pollution that is relatively fresh from one that has aged. This method, upon further investigation and validation, could be useful in episodic pollution events where the surge of E. coli concentration causes noncompliance to the single sample maximum criterion that mandates high frequency follow-up monitoring.

Naphthoquinone glycosides for bioelectroanalytical enumeration of the faecal indicator Escherichia coli

Microbial water quality monitoring for the presence of faecal indicator bacteria (FIB) is a mandatory activity in many countries and is key in public health protection. Despite technological advances and a need for methodological improvements, chromogenic and fluorogenic enzymatic techniques remain the mainstays of water quality monitoring for both public health agencies and regulated utilities. We demonstrated that bioelectroanalytical approaches to FIB enumeration are possible and can be achieved using commercially available enzyme-specific resorufin glycosides, although these are expensive, not widely available or designed for purpose. Following this, we designed two naphthoquinone glycosides which performed better, achieving Escherichia coli detection in the range 5.0 × 102 to 5.0 × 105 CFU ml-1 22-54% quicker than commercially available resorufin glycosides. The molecular design of the naphthoquinone glycosides requires fewer synthetic steps allowing them to be produced for as little as US$50 per kg. Tests with environmental samples demonstrated the low tendency for abiotic interference and that, despite specificity being maintained between β-glucuronidase and β-galactosidase, accurate enumeration of E. coli in environmental samples necessitates development of a selective medium. In comparison to a commercially available detection method, which has U.S. Environmental Protection Agency (EPA) approval, our approach performed better at high organism concentrations, detecting 500 organisms in 9 h compared with 13.5 h for the commercial method. Bioelectroanalytical detection is comparable to current approved methods and with further development could result in improved detection times. A recent trend for low-cost open-source hardware means that automated, potentiostatically controlled E. coli detection systems could be constructed for less than US$100 per channel.

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii.

IMPORTANCE

This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers.

Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples

The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat- and environment-associated samples and provides a tool for quantification of fungal DNA useful for research and monitoring purposes. However, precise quantification of nucleic acid from P. destructans is dependent on effective and standardized methods for extracting nucleic acid from various relevant sample types. We describe optimized methodologies for extracting fungal nucleic acids from sediment, guano, and swab-based samples using commercial kits together with a combination of chemical, enzymatic, and mechanical modifications. Additionally, we define modifications to a previously published intergenic spacer-based qPCR test for P. destructans to refine quantification capabilities of this assay.

Evaluation of Faecalibacterium 16S rDNA genetic markers for accurate identification of swine faecal waste by quantitative PCR

A genetic marker within the 16S rRNA gene of Faecalibacterium was identified for use in a quantitative PCR (qPCR) assay to detect swine faecal contamination in water. A total of 146,038 bacterial sequences were obtained using 454 pyrosequencing. By comparative bioinformatics analysis of Faecalibacterium sequences with those of numerous swine and other animal species, swine-specific Faecalibacterium 16S rRNA gene sequences were identified and Polymerase Chain Okabe (PCR) primer sets designed and tested against faecal DNA samples from swine and non-swine sources. Two PCR primer sets, PFB-1 and PFB-2, showed the highest specificity to swine faecal waste and had no cross-reaction with other animal samples. PFB-1 and PFB-2 amplified 16S rRNA gene sequences from 50 samples of swine with positive ratios of 86 and 90%, respectively. We compared swine-specific Faecalibacterium qPCR assays for the purpose of quantifying the newly identified markers. The quantification limits (LOQs) of PFB-1 and PFB-2 markers in environmental water were 6.5 and 2.9 copies per 100 ml, respectively. Of the swine-associated assays tested, PFB-2 was more sensitive in detecting the swine faecal waste and quantifying the microbial load. Furthermore, the microbial abundance and diversity of the microbiomes of swine and other animal faeces were estimated using operational taxonomic units (OTUs). The species specificity was demonstrated for the microbial populations present in various animal faeces.

Presence of microbial and chemical source tracking markers in roof-harvested rainwater and catchment systems for the detection of fecal contamination

Microbial source tracking (MST) and chemical source tracking (CST) markers were utilized to identify fecal contamination in harvested rainwater and gutter debris samples. Throughout the sampling period, Bacteroides HF183 was detected in 57.5 % of the tank water samples and 95 % of the gutter debris samples, while adenovirus was detected in 42.5 and 52.5 % of the tank water and gutter debris samples, respectively. Human adenovirus was then detected at levels ranging from below the detection limit to 316 and 1253 genome copies/μL in the tank water and debris samples, respectively. Results for the CST markers showed that salicylic acid (average 4.62 μg/L) was the most prevalent marker (100 %) in the gutter debris samples, caffeine (average 18.0 μg/L) was the most prevalent in the tank water samples (100 %) and acetaminophen was detected sporadically throughout the study period. Bacteroides HF183 and salicylic acid (95 %) and Bacteroides HF183 and caffeine (80 %) yielded high concurrence frequencies in the gutter debris samples. In addition, the highest concurrence frequency in the tank water samples was observed for Bacteroides HF183 and caffeine (60 %). The current study thus indicates that Bacteroides HF183, salicylic acid and caffeine may potentially be applied as source tracking markers in rainwater catchment systems in order to supplement fecal indicator analyses.

Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR

The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at which 95% of positive samples are detected) for the entire process of waterborne pathogen detection. We began by spiking the lowest concentration that was consistently positive at the qPCR step (based on its standard curve) into each procedural step working backwards (i.e., extraction, secondary concentration, primary concentration), which established a concentration that was detectable following losses of the pathogen from processing. Using the fraction of positive replicates (n = 10) at this concentration, we selected and analyzed a second, and then third, concentration. If the fraction of positive replicates equaled 1 or 0 for two concentrations, we selected another. We calculated the LOD using probit analysis. To demonstrate our approach we determined the 95% LOD for Salmonella enterica serovar Typhimurium, adenovirus 41, and vaccine-derived poliovirus Sabin 3, which were 11, 12, and 6 genomic copies (gc) per reaction (rxn), respectively (equivalent to 1.3, 1.5, and 4.0 gc L(-1) assuming the 1500 L tap-water sample volume prescribed in EPA Method 1615). This approach limited the number of analyses required and was amenable to testing multiple genetic targets simultaneously (i.e., spiking a single sample with multiple microorganisms). An LOD determined this way can facilitate study design, guide the number of required technical replicates, aid method evaluation, and inform data interpretation.

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water

Bacteroides spp. have been proposed as indicators of fecal contamination in microbial source tracking (MST) methodologies. The aim of this study was to develop new qPCR assays that target host‐specific Bacteroidal 16S ribosomal RNA genes, to determine the source of fecal contamination in water. Denaturing gradient gel electrophoresis (DGGE) was used to select for host‐specific bands of Bacteroides associated with a fecal pollution source and later to design four qPCR host‐specific assays. A set of common primers for Bacteroides spp., four different Bacteroides spp. host‐associated hydrolysis probes (human, cattle, pig, and poultry), and one hydrolysis probe for the Bacteroides genus were designed. This set of qPCR assays together with other previously developed Bacteroidetes MST targets were used to analyze water samples with fecal contamination from the four sources studied. The host‐specific Bacteroides qPCRs designed for human (HMprobeBac), pig (PGprobeBac), and poultry (PLprobeBac) were highly specific for its sources (1.0, 0.97, and 1.0, respectively) although its sensitivity was lower (0.45, 0.50, and 0.73, respectively). The cattle‐specific qPCR was totally unspecific and was discarded for future experiments. When compared to previously designed assays, the human and pig qPCRs showed better accuracies (0.86 and 0.84) than their counterparts HF183 and Pig‐2‐Bac (0.38 and 0.65). Thus, the newly designed human, pig, and poultry qPCR assays outperform other methods developed until date and may be useful for source tracking purposes.

Detection of human-derived fecal contamination in Puerto Rico using carbamazepine, HF183 Bacteroides, and fecal indicator bacteria

The level of fecal pollution in 17 sites in Puerto Rico was determined by Escherichia coli (E.coli) enumeration using an enzyme substrate medium and Quanti-Tray®/2000. Human fecal pollution was identified using an enzyme-linked immunosorbent assay for the detection of carbamazepine (CBZ) and quantitative polymerase chain reaction (qPCR) detection of the human Bacteroides marker, HF183. Carbamazepine was detected in 16 out of 17 sites, including Condado Lagoon, a popular recreational area. Elevated E.coli levels (>410 CFU 100 mL(-1)) were detected in 13 sites. Average CBZ concentrations ranged from 0.005 μg L(-1) to 0.482 μg L(-1) and 7 sites were positive for HF183. Higher CBZ concentrations were associated with the detection of HF183 (Mann-Whitney test; U=42.0; df=7; 1-tailed P value=0.013). This was the second study to determine surface water concentrations of CBZ in the Caribbean and the first in Puerto Rico.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 10(6) gene copies per ml), followed by those of HF183 (8.0 × 10(5) gene copies per ml) and Enterococcus spp. (3.6 × 10(5) gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters.

Persistence of mitochondrial DNA markers as fecal indicators in water environments

Mitochondrial DNA (mtDNA) polymerase chain reaction (PCR) technology has recently been developed to identify sources of fecal contamination, but information regarding environmental fate of mtDNA is limited. In this study, quantitative real-time PCR was used to determine the persistence of three species-specific mtDNA markers (human, pig and chicken) in river microcosms under different laboratory conditions and in dialysis tubes incubated in river environments during different seasons. Human feces had a higher abundance of mtDNA marker than pig and chicken feces. A biphasic decay pattern was observed for the mtDNA markers in microcosms incubated in darkness, and T90 (time needed for 90% reduction) ranged from 2.03 to 13.83 d. Each species-specific mtDNA marker persisted for relatively longer time at lower temperatures, and light exposure and predation increased the decay rates. Field experiments showed that the mtDNA markers could survive for longer time in winter (T90: 1.79-4.37 d) than in summer (T90: 0.60-0.75 d). Field application of mtDNA technology indicated that the markers were mainly distributed on the sites near animal breeding plants and had lower abundance in downstream water of the receiving river. This study expands our knowledge of the environmental fate of mtDNA markers and the results may be useful for practical application of the technology in fecal source tracking.

Storm loads of culturable and molecular fecal indicators in an inland urban stream

Elevated concentrations of fecal indicator bacteria in receiving waters during wet-weather flows are a considerable public health concern that is likely to be exacerbated by future climate change and urbanization. Knowledge of factors driving the fate and transport of fecal indicator bacteria in stormwater is limited, and even less is known about molecular fecal indicators, which may eventually supplant traditional culturable indicators. In this study, concentrations and loading rates of both culturable and molecular fecal indicators were quantified throughout six storm events in an instrumented inland urban stream. While both concentrations and loading rates of each fecal indicator increased rapidly during the rising limb of the storm hydrographs, it is the loading rates rather than instantaneous concentrations that provide a better estimate of transport through the stream during the entire storm. Concentrations of general fecal indicators (both culturable and molecular) correlated most highly with each other during storm events but not with the human-associated HF183 Bacteroides marker. Event loads of general fecal indicators most strongly correlated with total runoff volume, maximum discharge, and maximum turbidity, while event loads of HF183 most strongly correlated with the time to peak flow in a hydrograph. These observations suggest that collection of multiple samples during a storm event is critical for accurate predictions of fecal indicator loading rates and total loads during wet-weather flows, which are required for effective watershed management. In addition, existing predictive models based on general fecal indicators may not be sufficient to predict source-specific genetic markers of fecal contamination.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways.

Evaluation of molecular- and culture-dependent MST markers to detect fecal contamination and indicate viral presence in good quality groundwater

Microbial contamination of groundwater represents a significant health risk to resource users. Culture-dependent Bacteroides phage and molecular-dependent Bacteroidales 16S rRNA assays are employed in microbial source tracking (MST) studies globally, however little is known regarding how these important groups relate to each other in the environment and which is more suitable to indicate the presence of waterborne fecal pollution and human enteric viruses. This study addresses this knowledge gap by examining 64 groundwater samples from sites with varying hydrogeological properties using a MST toolbox containing two bacteriophage groups (phage infecting GB-124 and ARABA-84), and two Bacteroidales 16S rRNA markers (Hf183 and BacR); those were compared to fecal indicator bacteria, somatic coliphage, Bacteroidales 16S rRNA marker AllBac, four human enteric viruses (norovirus GI and II, enterovirus and group A rotavirus) and supplementary hydrogeological/chemical data. Bacteroidales 16S rRNA indicators offered a more sensitive assessment of both human-specific and general fecal contamination than phage indicators, but may overestimate the risk from enteric viral pathogens. Comparison with hydrogeological and land use site characteristics as well as auxiliary microbiological and chemical data proved the plausibility of the MST findings. Sites representing karst aquifers were of significantly worse microbial quality than those with unconsolidated or fissured aquifers, highlighting the vulnerability of these hydrogeological settings.