Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers--is it feasible?

Village Settlements in Mountainous Tropical Areas, Hotspots of Fecal Contamination as Evidenced by Escherichia coli and Stanol Concentrations in Stormwater Pulses

Fecal bacteria in surface water may indicate threats to human health. Our hypothesis is that village settlements in tropical rural areas are major hotspots of fecal contamination because of the number of domestic animals usually roaming in the alleys and the lack of fecal matter treatment before entering the river network. By jointly monitoring the dynamics of Escherichia coli and of seven stanol compounds during four flood events (July-August 2016) at the outlet of a ditch draining sewage and surface runoff out of a village of Northern Lao PDR, our objectives were (1) to assess the range of E. coli concentration in the surface runoff washing off from a village settlement and (2) to identify the major contributory sources of fecal contamination using stanol compounds during flood events. E. coli pulses ranged from 4.7 × 104 to 3.2 × 106 most probable number (MPN) 100 mL-1, with particle-attached E. coli ranging from 83 to 100%. Major contributory feces sources were chickens and humans (about 66 and 29%, respectively), with the highest percentage switching from the human pole to the chicken pole during flood events. Concentrations indicate a severe fecal contamination of surface water during flood events and suggest that villages may be considered as major hotspots of fecal contamination pulses into the river network and thus as point sources in hydrological models.

Scenario-based assessment of fecal pathogen sources affecting bathing water quality: novel treatment options to reduce norovirus and Campylobacter infection risks

Wastewater discharge and runoff waters are significant sources of human and animal fecal microbes in surface waters. Human-derived fecal contamination of water is generally estimated to pose a greater risk to human health than animal fecal contamination, but animals may serve as reservoirs of zoonotic pathogens. In this study, quantitative microbial risk assessment (QMRA) tools were used to evaluate the hygienic impact of sewage effluents and runoff water from municipalities and animal farms on surface and bathing waters. The human-specific microbial source tracking (MST) marker HF183 was used to evaluate the dilution of fecal pathogens originating from the sewage effluent discharge to the downstream watershed. As novel risk management options, the efficiency of UV-LED disinfection and wetland treatment as well as biochar filtration was tested on-site for the contamination sources. According to the dilution pattern of the MST marker HF183, microbes from wastewater were diluted (2.3-3.7 log10) in the receiving waters. The scenario-based QMRA revealed, that the health risks posed by exposure to human-specific norovirus GII and zoonotic Campylobacter jejuni during the bathing events were evaluated. The risk for gastroenteritis was found to be elevated during wastewater contamination events, where especially norovirus GII infection risk increased (1-15 cases per day among 50 bathers) compared with the business as usual (BAU) situation (1 case per day). The noted C. jejuni infection risk was associated with animal farm contamination (1 case per day, versus 0.2-0.6 cases during BAU). Tertiary treatment of wastewater with wetland treatment and UV-LED disinfection effectively reduced the waterborne gastroenteritis risks associated with bathing. Based on the experiences from this study, a QMRA-based approach for health risk evaluations at bathing sites can be useful and is recommended for bathing site risk assessments in the future. In case of low pathogen numbers at the exposure sites, the MST marker HF183 could be used as a pathogen dilution coefficient for the watershed under evaluation. The full-scale implementation of novel tertiary treatment options at wastewater treatment plants (WWTPs) as well as on-site runoff water treatment options should be considered for infection risk management at locations where scenario-based QMRA implies elevated infection risks.

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.

Persistence of human- and cattle-associated Bacteroidales and mitochondrial DNA markers in freshwater mesocosms

Accurate identification of the origins of non-point source pollution is essential for the effective control of fecal pollution. Host-associated Bacteroidales and mitochondrial DNA (mtDNA) markers have been developed to identify the sources of human and cattle fecal pollution. However, the differences in persistence between these two types of markers under different environmental conditions are still poorly understood. Here, we conducted mesocosm experiments to investigate the influence of indigenous microbiota and nutrients on the decay of Bacteroidales and mtDNA markers associated with humans and cattle. Raw sewage or cattle feces were inoculated into mesocosms containing natural eutrophic water, sterile eutrophic water or artificial freshwater. The Bacteroidales markers HF183 (human) and CowM3 (cattle) and mtDNA markers HcytB (human) and QMIBo (cattle) were quantified using the quantitative polymerase chain reaction (qPCR) assays. All markers but HF183 decreased the fastest in the presence of indigenous microbiota. Nutrients caused a decrease in the persistence of HF183; however, no significant nutrient effects were observed for HcytB, CowM3, and QMIBo. The time to reach one log reduction (T90) for HF183 and HcytB was similar; CowM3 reached T90 earlier than QMIBo in all the treatments but eutrophic water. E. coli persisted longer than both Bacteroidales and mtDNA markers in the mesocosms regardless of inoculum type. Additionally, 16S rRNA gene amplicon sequencing was used to determine the changes in bacterial communities accompanying the marker decay. Analysis using the SourceTracker software showed that bacterial communities in the mesocosms became more dissimilar to those in the corresponding inoculants over time. Our results indicate that environmental factors are important determinants of genetic markers' persistence, but their impact can vary depending on the genetic markers. The cattle Bacteroidales markers may be more suitable for determining recent fecal contamination than cattle mtDNA.

Source-Associated Gastroenteritis Risk from Swimming Exposure to Aging Fecal Pathogens

Human contact with fecally contaminated waters often raises public health concern. The infection potential closely relates to the fecal source type and the aging persistence of waterborne pathogens. In this study, the health risk of contracting gastroenteritis from exposure to aging fecal contamination was predicted using source-associated markers. Microbial decay characteristics in typical summer seawater were incorporated into a pathogen dose estimation model for a constant fecal input. Results show that the median illness probability commensurate with the health benchmark of 36/1000 corresponded to the marker concentrations of ∼7.8, ∼6.6, ∼3.7, and ∼3.5 log₁₀ gene copies/100 mL for seagulls, cattle, raw sewage, and treated effluent, respectively. The error in risk estimates due to neglecting microbial decay was linearly correlated to the decay differences between markers and pathogens. Specifically, the health risk associated with nonhuman sources, which was primarily contributed by bacterial and parasitic pathogens, can be substantially overestimated, while that for virus-dominated human sources was insignificantly affected by the differential decay. Additionally, seagulls dominated the Enterococcus concentration in waters with a mixture of the above-mentioned sources, although they posed limited health risk. This study provides an approach to understanding the influence of fecal aging on health risk estimation.

Extended persistence of general and cattle-associated fecal indicators in marine and freshwater environment

Fecal contamination of recreational waters with cattle manure can pose a risk to public health due to the potential presence of various zoonotic pathogens. Fecal indicator bacteria (FIB) have a long history of use in the assessment of recreational water quality, but FIB quantification provides no information about pollution sources. Microbial source tracking (MST) markers have been developed in response to a need to identify pollution sources, yet factors that influence their decay in ambient waters are often poorly understood. We investigated the influence of water type (freshwater versus marine) and select environmental parameters (indigenous microbiota, ambient sunlight) on the decay of FIB and MST markers originating from cattle manure. Experiments were conducted in situ using a submersible aquatic mesocosm containing dialysis bags filled with a mixture of cattle manure and ambient water. Culturable FIB (E. coli, enterococci) were enumerated by membrane filtration and general fecal indicator bacteria (GenBac3, Entero1a, EC23S857) and MST markers (Rum2Bac, CowM2, CowM3) were estimated by qPCR. Water type was the most significant factor influencing decay (three-way ANOVA, p: 0.006 to <0.001), although the magnitude of the effect differed among microbial targets and over time. The presence of indigenous microbiota and exposure to sunlight were significantly correlated (three-way ANOVA, p: 0.044 to <0.001) with decay of enterococci and CowM2, while E. coli, EC23S857, Rum2Bac, and CowM3 (three-way ANOVA, p: 0.044 < 0.001) were significantly impacted by sunlight or indigenous microbiota. Results indicate extended persistence of both cultivated FIB and genetic markers in marine and freshwater water types. Findings suggest that multiple environmental stressors are important determinants of FIB and MST marker persistence, but their magnitude can vary across indicators. Selective exclusion of natural aquatic microbiota and/or sunlight typically resulted in extended survival, but the effect was minor and limited to select microbial targets.

The Effects of Plants on Pollutant Removal, Clogging, and Bacterial Community Structure in Palm Mulch-Based Vertical Flow Constructed Wetlands

In this study, the effects of plants on the performance and bacterial community structure of palm mulch-based vertical flow constructed wetlands was studied. The wetlands were built in August 2013; one of them was planted with Canna indica and Xanthosoma sp., and the other one was not planted and used as a control. The experimental period started in September 2014 and finished in June 2015. The influent was domestic wastewater, and the average hydraulic surface loading was 208 L/m2d, and those of COD, BOD, and TSS were 77, 57, and 19 g/m2d, respectively. Although the bed without plants initially performed better, the first symptoms of clogging appeared in December 2014, and then, its performance started to fail. Afterwards, the wetland with plants provided better removals. The terminal restriction fragment length polymorphism (T-RFLP) analysis of Enterococci and Escherichia coli in the effluents suggests that a reduction in their biodiversity was caused by the presence of the plants. Thus, it can be concluded that the plants helped achieve better removals, delay clogging, and reduce Enterococci and E. coli biodiversity in the effluents.

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.

Quantitative microbial risk assessment of microbial source tracking markers in recreational water contaminated with fresh untreated and secondary treated sewage

Microbial source tracking (MST) methods have provided the means to identify sewage contamination in recreational waters, but the risk associated with elevated levels of MST targets such as sewage-associated Bacteroides HF183 and other markers is uncertain. Quantitative microbial risk assessment (QMRA) modeling allows interpretation of MST data in the context of the risk of gastrointestinal (GI) illness caused by exposure to pathogens. In this study, five sewage-associated, quantitative PCR (qPCR) MST markers [Bacteroides HF183 (HF183), Methanobrevibacter smithii nifH (nifH), human adenovirus (HAdV), human polyomavirus (HPyV) and pepper mild mottle virus (PMMoV)] were evaluated to determine at what concentration these nucleic acid markers reflected a significant health risk from exposure to fresh untreated or secondary treated sewage in beach water. The QMRA models were evaluated for a target probability of illness of 36 GI illnesses/1000 swimming events (i.e., risk benchmark 0.036) for the reference pathogens norovirus (NoV) and human adenovirus 40/41 (HAdV 40/41). Sewage markers at several dilutions exceeded the risk benchmark for reference pathogens NoV and HAdV 40/41. HF183 concentrations 3.22 × 10³ (for both NoV and HAdV 40/41) gene copies (GC)/100 mL of water contaminated with fresh untreated sewage represented risk >0.036. Similarly, HF183 concentrations 3.66 × 10³ (for NoV and HAdV 40/41) GC/100 mL of water contaminated with secondary treated sewage represented risk >0.036. HAdV concentration as low as 4.11 × 10¹ GC/100 mL of water represented risk >0.036 when water was contaminated with secondary treated sewage. Results of this study provide a valuable context for water quality managers to evaluate human health risks associated with contamination from fresh sewage. The approach described here may also be useful in the future for evaluating health risks from contamination with aged or treated sewage or feces from other animal sources as more data are made available.

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log₁₀ 7.2-8.0 marker equivalents (ME) 100 mL^-1) and biologically treated wastewater samples (median log₁₀ 4.6-6.0 ME 100 mL^-1) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

Toward Forensic Uses of Microbial Source Tracking

The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

Consideration of Natural Sources in a Bacteria TMDL-Lines of Evidence, Including Beach Microbial Source Tracking

Total Maximum Daily Load (TMDL) stipulations remained unmet at a southern California beach despite a suite of management actions carried out since 2001, prompting exploration of a Natural Sources Exclusion (NSE) provision within the TMDL. Quantitative Microbial Source Tracking (MST) was employed from 2012 to 2015 to inventory sources of natural and anthropogenic fecal indicator bacteria (FIB). Data suggested FIB exceedances could be traced to gulls based on gull marker prevalence and correlations with FIB concentrations in seawater, sand, and eelgrass. In contrast, human marker concentrations and a tracer dye test did not indicate prevalent human sources. Exponential decay of gull marker in sand amended with live Catellicoccus marimammalium suggested that measured marker reflected fecal inputs versus growth outside the host. Improved water quality was coincident with a 2013 bird exclusion structure, consistent with NSE. However, load allocation needed for TMDL reconsideration was hampered by variable ratios of FIB, MST markers, and pathogens measured in seawater and in gull, cat, and raccoon feces. Quantitative Microbial Risk Assessment is a suggested path forward because such models can incorporate distributions from a combination of FIB sources and communicate criteria in terms of human health risk.

Environmental Escherichia coli: ecology and public health implications-a review

Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae. The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through faeces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent faecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extraintestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a faecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics revealed the diversity and complexity of E. coli strains in various environments, which are affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments with regard to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia. The impact of environmental E. coli on water quality and public health is also discussed.

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.

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling

Urban estuaries around the world are experiencing contamination from diffuse and point sources, which increases risks to public health. To mitigate and manage risks posed by elevated levels of contamination in urban waterways, it is critical to identify the primary water sources of contamination within catchments. Source tracking using microbial community fingerprints is one tool that can be used to identify sources. However, results derived from this approach have not yet been evaluated using independent datasets. As such, the key objectives of this investigation were: (1) to identify the major sources of water responsible for bacterial loadings within an urban estuary using microbial source tracking (MST) using microbial communities; and (2) to evaluate this method using a 3-dimensional hydrodynamic model. The Yarra River estuary, which flows through the city of Melbourne in South-East Australia was the focus of this study. We found that the water sources contributing to the bacterial community in the Yarra River estuary varied temporally depending on the estuary's hydrodynamic conditions. The water source apportionment determined using microbial community MST correlated to those determined using a 3-dimensional hydrodynamic model of the transport and mixing of a tracer in the estuary. While there were some discrepancies between the two methods, this investigation demonstrated that MST using bacterial community fingerprints can identify the primary water sources of microorganisms in an estuarine environment. As such, with further optimization and improvements, microbial community MST has the potential to become a powerful tool that could be practically applied in the mitigation of contaminated aquatic systems.

Decay of sewage-sourced microbial source tracking markers and fecal indicator bacteria in marine waters

The decay of sewage-sourced enterococci, Escherichia coli, three human-associated microbial source tracking (MST) markers, Salmonella, Campylobacter, and norovirus GII was measured in situ in coastal, marine waters. Experiments examined the effects of sunlight intensity and season on decay. Seawater was seeded with untreated sewage, placed into permeable dialysis bags, and deployed in the coastal ocean near the water surface, and at 18 cm, and 99 cm depths, to vary solar intensity, during winter and summer seasons. Microbial decay was modeled using a log-linear or shoulder log-linear decay model. Pathogen levels were too low in sewage to obtain kinetic parameters. Human-associated MST markers all decayed with approximately the same rate constant (k ∼ 1.5 d^-1) in all experimental treatments, suggesting markers could be detectable up to ∼6 days after a raw sewage spill. E. coli and enterococci (culturable and molecular marker) k significantly varied with season and depth; enterococci decayed faster at shallow depths and during the summer, while E. coli decayed faster at shallow depths and during the winter. Rate constants for MST markers and culturable FIB diverged except at the deepest depth in the water column potentially complicating the use of MST marker concentrations to allocate sources of FIB contamination.

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL⁻¹. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.

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.

Differential decomposition of bacterial and viral fecal indicators in common human pollution types

Understanding the decomposition of microorganisms associated with different human fecal pollution types is necessary for proper implementation of many water quality management practices, as well as predicting associated public health risks. Here, the decomposition of select cultivated and molecular indicators of fecal pollution originating from fresh human feces, septage, and primary effluent sewage in a subtropical marine environment was assessed over a six day period with an emphasis on the influence of ambient sunlight and indigenous microbiota. Ambient water mixed with each fecal pollution type was placed in dialysis bags and incubated in situ in a submersible aquatic mesocosm. Genetic and cultivated fecal indicators including fecal indicator bacteria (enterococci, E. coli, and Bacteroidales), coliphage (somatic and F+), Bacteroides fragilis phage (GB-124), and human-associated genetic indicators (HF183/BacR287 and HumM2) were measured in each sample. Simple linear regression assessing treatment trends in each pollution type over time showed significant decay (p ≤ 0.05) in most treatments for feces and sewage (27/28 and 32/40, respectively), compared to septage (6/26). A two-way analysis of variance of log10 reduction values for sewage and feces experiments indicated that treatments differentially impact survival of cultivated bacteria, cultivated phage, and genetic indicators. Findings suggest that sunlight is critical for phage decay, and indigenous microbiota play a lesser role. For bacterial cultivated and genetic indicators, the influence of indigenous microbiota varied by pollution type. This study offers new insights on the decomposition of common human fecal pollution types in a subtropical marine environment with important implications for water quality management applications.

Bayesian meta-analysis to synthesize decay rate constant estimates for common fecal indicator bacteria

For decades, fecal indicator bacteria have been used as proxies to quantitatively estimate fecal loading into water bodies. Widely used cultured indicators (e.g. Escherichia coli and Enterococcus spp.) and more recently developed genetic markers are well studied, but their decay in the environment is still poorly understood. We used Hierarchical Bayesian Linear Modeling to conduct a series of meta-analyses using published decay rate constant estimates, to synthesize findings into pooled estimates and identify gaps in the data preventing reliable estimates. In addition to the meta-analysis assuming all estimates come from the same population, meta-regressions including covariates believed to contribute to decay were fit and used to provided synthesized estimates for specific combinations of significant variables. Additionally, statements regarding the significance of variables across studies were made using the 95% confidence interval for meta-regression coefficients. These models were used to construct a mean decay rate constant estimate as well as credible intervals for the mean and the distribution of all likely data points. While synthesized estimates for each targeted indicator bacteria were developed, the amount of data available varied widely for each target, as did the predictive power of the models as determined by testing with additional data not included in the modeling. Temperature was found to be significant for all selected indicators, while light was found to be significant only for culturable indicators. Results from the models must be interpreted with caution, as they are based only on the data available, which may not be representative of decay in other scenarios.

A controlled, before-and-after trial of an urban sanitation intervention to reduce enteric infections in children: research protocol for the Maputo Sanitation (MapSan) study, Mozambique

INTRODUCTION

Access to safe sanitation in low-income, informal settlements of Sub-Saharan Africa has not significantly improved since 1990. The combination of a high faecal-related disease burden and inadequate infrastructure suggests that investment in expanding sanitation access in densely populated urban slums can yield important public health gains. No rigorous, controlled intervention studies have evaluated the health effects of decentralised (non-sewerage) sanitation in an informal urban setting, despite the role that such technologies will likely play in scaling up access.

METHODS AND ANALYSIS

We have designed a controlled, before-and-after (CBA) trial to estimate the health impacts of an urban sanitation intervention in informal neighbourhoods of Maputo, Mozambique, including an assessment of whether exposures and health outcomes vary by localised population density. The intervention consists of private pour-flush latrines (to septic tank) shared by multiple households in compounds or household clusters. We will measure objective health outcomes in approximately 760 children (380 children with household access to interventions, 380 matched controls using existing shared private latrines in poor sanitary conditions), at 2 time points: immediately before the intervention and at follow-up after 12 months. The primary outcome is combined prevalence of selected enteric infections among children under 5 years of age. Secondary outcome measures include soil-transmitted helminth (STH) reinfection in children following baseline deworming and prevalence of reported diarrhoeal disease. We will use exposure assessment, faecal source tracking, and microbial transmission modelling to examine whether and how routes of exposure for diarrhoeagenic pathogens and STHs change following introduction of effective sanitation.

ETHICS

Study protocols have been reviewed and approved by human subjects review boards at the London School of Hygiene and Tropical Medicine, the Georgia Institute of Technology, the University of North Carolina at Chapel Hill, and the Ministry of Health, Republic of Mozambique.

TRIAL REGISTRATION NUMBER

NCT02362932.

Spatial and hydrologic variation of Bacteroidales, adenovirus and enterovirus in a semi-arid, wastewater effluent-impacted watershed

Bacteroidales and viruses were contemporaneously measured during dry and wet weather conditions at a watershed-scale in a semi-arid watershed impacted by a mixture of agricultural runoff, municipal wastewater effluent and municipal runoff. The results highlight the presence of municipal wastewater effluent as a confounding factor for microbial source tracking (MST) studies, and thus data were segregated into groups based on whether they were impacted by wastewater effluent. In semi-arid environments such as the Calleguas Creek watershed, located in southern California, the relative contribution of municipal wastewater effluent is dependent on hydrology as storm events lead to conditions where agricultural and municipal stormwater dominate receiving waters (rather than municipal wastewater, which is the case during dry weather). As such, the approach to data segregation was dependent on hydrology/storm conditions. Storm events led to significant increases in ruminant- and dog-associated Bacteroidales concentrations, indicating that overland transport connects strong non-human fecal sources with surface waters. Because the dataset had a large number of non-detect samples, data handling included the Kaplan-Meir estimator and data were presented graphically in a manner that reflects the potential effect of detection limits. In surface water samples with virus detections, Escherichia coli concentrations were often below (in compliance with) the recreational water quality criteria. In fact, sites downstream of direct inputs of municipal wastewater effluent exhibited the lowest concentrations of E. coli, but the highest concentrations of human-associated Bacteroidales and highest detection rates of human viruses. The toolkit, comprised of the four Bacteroidales assays and human virus assays used, can be successfully applied to inform watershed managers seeking to comply with recreational water quality criteria. However, care should be taken when analyzing data to account for the effect of non-detect samples, sources with differing microbial viability, and diverging hydrologic conditions.

Droplet digital PCR for simultaneous quantification of general and human-associated fecal indicators for water quality assessment

Despite wide application to beach water monitoring and microbial source identification, results produced by quantitative PCR (qPCR) methods are subject to bias introduced by reliance on quantitative standards. Digital PCR technology provides direct, standards-free quantification and may potentially alleviate or greatly reduce other qPCR limitations such as difficulty in multiplexing and susceptibility to PCR inhibition. This study examined the efficacy of employing a duplex droplet digital PCR (ddPCR) assay that simultaneously quantifies Enterococcus spp. and the human fecal-associated HF183 marker for water quality assessment. Duplex ddPCR performance was evaluated side-by-side with qPCR and simplex ddPCR using reference material and 131 fecal and water samples. Results for fecal and water samples were highly correlated between ddPCR and simplex qPCR (coefficients > 0.93, p < 0.001). Duplexing Enterococcus and HF183 in qPCR led to competition and resulted in non-detection or underestimation of the target with low concentration relative to the other, while results produced by simplex and duplex ddPCR were consistent and often indistinguishable from one another. ddPCR showed greater tolerance for inhibition, with no discernable effect on quantification at inhibitor concentrations one to two orders of magnitude higher than that tolerated by qPCR. Overall, ddPCR also exhibited improved precision, higher run-to-run repeatability, similar diagnostic sensitivity and specificity on the HF183 marker, but a lower upper limit of quantification than qPCR. Digital PCR has the potential to become a reliable and economical alternative to qPCR for recreational water monitoring and fecal source identification. Findings from this study may also be of interest to other aspects of water research such as detection of pathogens and antibiotic resistance genes.

Temporal stability of the microbial community in sewage-polluted seawater exposed to natural sunlight cycles and marine microbiota

Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources.

Human health risk implications of multiple sources of faecal indicator bacteria in a recreational waterbody

We simulate the influence of multiple sources of enterococci (ENT) as faecal indicator bacteria (FIB) in recreational water bodies on potential human health risk by considering waters impacted by human and animal sources, human and non-pathogenic sources, and animal and non-pathogenic sources. We illustrate that risks vary with the proportion of culturable ENT in water bodies derived from these sources and estimate corresponding ENT densities that yield the same level of health protection that the recreational water quality criteria in the United States seeks (benchmark risk). The benchmark risk is based on epidemiological studies conducted in water bodies predominantly impacted by human faecal sources. The key result is that the risks from mixed sources are driven predominantly by the proportion of the contamination source with the greatest ability to cause human infection (potency), not necessarily the greatest source(s) of FIB. Predicted risks from exposures to mixtures comprised of approximately 30% ENT from human sources were up to 50% lower than the risks expected from purely human sources when contamination is recent and ENT levels are at the current water quality criteria levels (35 CFU 100 mL(-1)). For human/non-pathogenic, human/gull, human/pig, and human/chicken faecal mixtures with relatively low human contribution, the predicted culturable enterococci densities that correspond to the benchmark risk are substantially greater than the current water quality criteria values. These findings are important because they highlight the potential applicability of site specific water quality criteria for waters that are predominantly un-impacted by human sources.

Recommendations following a multi-laboratory comparison of microbial source tracking methods

Microbial source tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero Ct values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution source that was being targeted, i.e., the samples were true positives. Given these results, and the fact that MST often requires detection of targets present in low concentrations, we propose that such samples be reported and identified in a unique category to facilitate data analysis and method comparisons. Important data can be lost when such samples are simply reported as positive or negative. Actionable thresholds were not derived in the SIPP study due to limitations that included geographic scope, age of samples, and difficulties interpreting low concentrations of target in environmental samples. Nevertheless, the results of the study support the use of MST for water management, especially to prioritize impaired waters in need of remediation. Future integration of MST data into quantitative microbial risk assessments and other models could allow managers to more efficiently protect public health based on site conditions.