Phages of Bacteroides (GB-124): a novel tool for viral waterborne disease control?

Coliphages as viral indicators in municipal wastewater: A comparison between the ISO and the USEPA methods based on a systematic literature review

The use of traditional faecal indicator bacteria as surrogate organisms for pathogenic viruses in domestic wastewater has been noted as a problematic as concentrations and removal rates of bacteria and viruses do not seem to correlate. In this sense, bacteriophages (phages) emerge as potential viral indicators, as they are commonly found in wastewater in high levels, and can be quantified using simple, fast, low-cost methods. Somatic and F-specific coliphages comprise groups of phages commonly used as indicators of water quality. There are two internationally recognised methods to detect and enumerate coliphages in water samples, the International Standardization Organization (ISO) and the US Environmental Protection Agency (USEPA) methods. Both methods are based on the lysis of specific bacterial host strains infected by phages. Within this context, this systematic literature review aimed at gathering concentrations in raw and treated domestic wastewater (secondary, biological treatment systems and post-treatment systems), and removal efficiencies of somatic and F-specific coliphages obtained by ISO and USEPA methods, and then compare both methods. A total of 33 research papers were considered in this study. Results showed that the ISO method is more commonly applied than the USEPA method. Some discrepancies in terms of concentrations and removal efficiencies were observed between both methods. Higher removal rates were observed for both somatic and F-specific coliphages in activated sludge systems when using the USEPA method compared to the ISO method; in other secondary (biological) treatment systems, this was observed only for F-specific coliphages. The use of different standardised methods available might lead to difficulties in obtaining and comparing phage data in different conditions and locations. Future research comparing both ISO and USEPA methods as well as viral and bacterial pathogens and indicators in WWTP is recommended.

Microbial health risks associated with rotavirus and enteric bacteria in River Ala in Akure, Nigeria

AIM

This study was carried out to determine the microbial health risks associated with a surface water commonly used for bathing, drinking, domestic and irrigational activities in Akure, Nigeria.

METHODS AND RESULTS

Water samples were collected from the river from March to June, 2018. The load of enteric bacteria, somatic coliphages and rotavirus in the water samples were determined using culture-based methods and molecular technique. The physicochemical characteristics of the water samples were determined using standard methods. The risks of rotavirus, Salmonella and Shigella infections resulting from ingestion of the water from the river were estimated using dose-response model. Redundancy analysis revealed that the levels of E. coli and Salmonella were highly associated with salinity and turbidity. The risks of infection associated with rotavirus (3.3 × 10^-3 ) was higher than those associated with Salmonella (1.3 × 10^-4 ) and Shigella (1.3 × 10^-3 ), and were all above the WHO acceptable risk limit (10^-4 ).

CONCLUSION

Accidental or intentional ingestion of water from the river may pose potential risks of gastrointestinal illness to humans.

SIGNIFICANCE AND IMPACT OF STUDY

Quantitative microbial risk assessment is essential in establishing adequate water management practices that must be strictly followed in order to protect human health.

The occurrence and control of waterborne viruses in drinking water treatment: A review

As the coronavirus disease 2019 continues to spread globally, its culprit, the severe acute respiratory syndrome coronavirus 2 has been brought under scrutiny. In addition to inhalation transmission, the possible fecal-oral viral transmission via water/wastewater has also been brought under the spotlight, necessitating a timely global review on the current knowledge about waterborne viruses in drinking water treatment system - the very barrier that intercepts waterborne pathogens to terminal water users. In this article we reviewed the occurrence, concentration methods, and control strategies, also, treatment performance on waterborne viruses during drinking water treatment were summarized. Additionally, we emphasized the potential of applying the quantitative microbial risk assessment to guide drinking water treatment to mitigate the viral exposure risks, especially when the unregulated novel viral pathogens are of concern. This review paves road for better control of viruses at drinking water treatment plants to protect public health.

Elucidation of fecal inputs into the River Tagus catchment (Portugal) using source-specific mitochondrial DNA, HAdV, and phage markers

Determining the source of fecal contamination in a water body is important for the application of appropriate remediation measures. However, it has been suggested in the extant literature that this can best be achieved using a 'toolbox' of molecular- and culture-based methods. In response, this study deployed three indicators (Escherichia coli (EC), intestinal enterococci (IE) and somatic coliphages (SC)), one culture-dependent human marker (Bacteroides (GB-124) bacteriophage) and five culture-independent markers (human adenovirus (HAdV), human (HMMit), cattle (CWMit), pig (PGMit) and poultry (PLMit) mitochondrial DNA markers (mtDNA)) within the River Tagus catchment (n = 105). Water samples were collected monthly over a 13-month sampling campaign at four sites (impacted by significant specific human and non-human inputs and influenced by differing degrees of marine and freshwater mixing) to determine the dominant fecal inputs and assess geographical, temporal, and meteorological (precipitation, UV, temperature) fluctuations. Our results revealed that all sampling sites were not only highly impacted by fecal contamination but that this contamination originated from human and from a range of agricultural animal sources. HMMit was present in a higher percentage (83%) and concentration (4.20 log GC/100 mL) than HAdV (32%, 2.23 log GC/100 mL) and GB-124 bacteriophage with the latter being detected once. Animal mtDNA markers were detected, with CWMit found in 73% of samples with mean concentration of 3.74 log GC/100 mL. Correlation was found between concentrations of fecal indicators (EC, IE and SC), CWMit and season. Levels of CWMit were found to be related to physico-chemical parameters, such as temperature and UV radiation, possibly as a result of the increasing presence of livestock outside in warmer months. This study provides the first evaluation of such a source-associated 'toolbox' for monitoring surface water in Portugal, and the conclusions may inform future implementation of surveillance and remediation strategies for improving water quality.

Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.

Evaluation of Low-Cost Phage-Based Microbial Source Tracking Tools for Elucidating Human Fecal Contamination Pathways in Kolkata, India

Phages, such as those infecting Bacteroides spp., have been proven to be reliable indicators of human fecal contamination in microbial source tracking (MST) studies, and the efficacy of these MST markers found to vary geographically. This study reports the application and evaluation of candidate MST methods (phages infecting previously isolated B. fragilis strain GB-124, newly isolated Bacteroides strains (K10, K29, and K33) and recently isolated Kluyvera intermedia strain ASH-08), along with non-source specific somatic coliphages (SOMCPH infecting strain WG-5) and indicator bacteria (Escherichia coli) for identifying fecal contamination pathways in Kolkata, India. Source specificity of the phage-based methods was first tested using 60 known non-human fecal samples from common animals, before being evaluated with 56 known human samples (municipal sewage) collected during both the rainy and dry season. SOMCPH were present in 40-90% of samples from different animal species and in 100% of sewage samples. Phages infecting Bacteroides strain GB-124 were not detected from the majority (95%) of animal samples (except in three porcine samples) and were present in 93 and 71% of the sewage samples in the rainy and dry season (Mean = 1.42 and 1.83 log10PFU/100mL, respectively), though at lower levels than SOMCPH (Mean = 3.27 and 3.02 log10PFU/100mL, respectively). Phages infecting strain ASH-08 were detected in 89 and 96% of the sewage samples in the rainy and dry season, respectively, but were also present in all animal samples tested (except goats). Strains K10, K29, and K30 were not found to be useful MST markers due to low levels of phages and/or co-presence in non-human sources. GB-124 and SOMCPH were subsequently deployed within two low-income neighborhoods to determine the levels and origin of fecal contamination in 110 environmental samples. E. coli, SOMCPH, and phages of GB-124 were detected in 68, 42, and 28% of the samples, respectively. Analyses of 166 wastewater samples from shared community toilets and 21 samples from sewage pumping stations from the same districts showed that SOMCPH were present in 100% and GB-124 phages in 31% of shared toilet samples (Median = 5.59 and <1 log10 PFU/100 mL, respectively), and both SOMCPH and GB-124 phages were detected in 95% of pumping station samples (Median = 5.82 and 4.04 log10 PFU/100 mL, respectively). Our findings suggest that GB-124 and SOMCPH have utility as low-cost fecal indicator tools which can facilitate environmental surveillance of enteric organisms, elucidate human and non-human fecal exposure pathways, and inform interventions to mitigate exposure to fecal contamination in the residential environment of Kolkata, India.

Pathogen infection risk to recreational water users, associated with surface waters impacted by de facto and indirect potable reuse activities

Water deficit, exacerbated by global population increases and climate change, necessitates the investigation of alternative non-traditional water sources to augment existing supplies. Indirect potable reuse (IPR) represents a promising alternative water source in water-stressed regions. Of high concern is the presence of pathogenic microorganisms in wastewater, such as enteric viruses, protozoa and bacteria. Therefore, a greater understanding of the potential impact to human health is required. The aim of this research was to use a quantitative microbial risk assessment (QMRA) approach to calculate the probability of potential pathogen infection risk to the public in surface waters used for a range of recreational activities under scenarios: 1) existing de facto wastewater reuse conditions; 2) after augmentation with conventionally treated wastewater; and 3) after augmentation with reclaimed wastewater from proposed IPR schemes. Forty-four 31 l samples were collected from river sites and a coastal wastewater treatment works from July 2016-May 2017. Concentrations of faecal indicator organisms (enterococci, faecal coliforms, somatic coliphages and Bacteroides phages) determined using culture-based approaches and selected pathogens (adenovirus, Salmonella and Cryptosporidium) determined using molecular approaches (qPCR) were used to inform QMRA. The mean probability of infection from adenovirus under de facto conditions was high (>0.90) for all recreational activities, per single event. The risk of adenovirus and Cryptosporidium infection increased under augmentation scenario (2) (mean probability 0.95-1.00 and 0.01-0.06 per single event, respectively). Adenovirus and Cryptosporidium infection risk decreased under reclaimed water augmentation scenario (3) (mean probability <0.79, excluding swimming, which remained 1.00 and <0.01 per single event, respectively). Pathogen reduction after reclaimed water augmentation in surface waters impacted by de facto reuse, provides important evidence for alternative water supply option selection. As such, this evidence may inform water managers and the public of the potential benefits of IPR and improve acceptance of such practices in the future.

Viral and Bacterial Fecal Indicators in Untreated Wastewater across the Contiguous United States Exhibit Geospatial Trends

Cultivated fecal indicator bacteria such as Escherichia coli and enterococci are typically used to assess the sanitary quality of recreational waters. However, these indicators suffer from several limitations, such as the length of time needed to obtain results and the fact that they are commensal inhabitants of the gastrointestinal tract of many animals and have fate and transport characteristics dissimilar to pathogenic viruses. Numerous emerging technologies that offer same-day water quality results or pollution source information or that more closely mimic persistence patterns of disease-causing pathogens that may improve water quality management are now available, but data detailing geospatial trends in wastewater across the United States are sparse. We report geospatial trends of cultivated bacteriophage (somatic, F⁺, and total coliphages and GB-124 phage), as well as genetic markers targeting polyomavirus, enterococci, E. coli, Bacteroidetes, and human-associated Bacteroides spp. (HF183/BacR287 and HumM2) in 49 primary influent sewage samples collected from facilities across the contiguous United States. Samples were selected from rural and urban facilities spanning broad latitude, longitude, elevation, and air temperature gradients by using a geographic information system stratified random site selection procedure. Most indicators in sewage demonstrated a remarkable similarity in concentration regardless of location. However, some exhibited predictable shifts in concentration based on either facility elevation or local air temperature. Geospatial patterns identified in this study, or the absence of such patterns, may have several impacts on the direction of future water quality management research, as well as the selection of alternative metrics to estimate sewage pollution on a national scale.IMPORTANCE This study provides multiple insights to consider for the application of bacterial and viral indicators in sewage to surface water quality monitoring across the contiguous United States, ranging from method selection considerations to future research directions. Systematic testing of a large collection of sewage samples confirmed that crAssphage genetic markers occur at a higher average concentration than key human-associated Bacteroides spp. on a national scale. Geospatial testing also suggested that some methods may be more suitable than others for widespread implementation. Nationwide characterization of indicator geospatial trends in untreated sewage represents an important step toward the validation of these newer methods for future water quality monitoring applications. In addition, the large paired-measurement data set reported here affords the opportunity to conduct a range of secondary analyses, such as the generation of new or updated quantitative microbial risk assessment models used to estimate public health risk.

Cryptosporidium genotyping and land use mapping for hazard identification and source tracking in a small mixed rural-urban watershed in Southeastern Brazil

Cryptosporidium, faecal indicator organisms and physical and chemical water quality variables were monitored in a small mixed rural–urban watershed in southeastern Brazil. Cryptosporidium was present in 43% of 117 water samples analysed by microscopy. Concentrations varied from non-detects to 14 oocysts L−1. All samples were further analysed by nested-PCR, and Cryptosporidium spp. were detected in 24% (28) of them. Sequencing at the 18S rRNA locus gave high quality sequences in eight samples, revealing the presence of Cryptosporidium parvum. Cryptosporidium was not correlated with faecal indicator organisms (total coliforms, Escherichia coli, Enterococcus and coliphages), nor with physical and chemical water quality variables (e.g. turbidity, electrical conductivity and chemical oxygen demand), but it was with farm animal density (number of animals per ha). Land use mapping reinforced the suggestions from Cryptosporidium genotyping that both animals (livestock) and humans are potential sources to environmental contamination with oocysts within the watershed.

A bioassay-based protocol for chemical neutralization of human faecal wastes treated by physico-chemical disinfection processes: A case study on benzalkonium chloride

In situ physico-chemical disinfection of high risk faecal waste is both effective and widely used as a sanitation management strategy for infection prevention and control. Systematic tests where the performance of alternative physico-chemical disinfection methods is systematically compared and optimized must be based on reliable protocols. These protocol are currently not adequately addressing the neutralization related issues: the neutralization of the tested disinfectant after specified conditions of concentration and contact time (CT) is necessary to prevent continued disinfection after the intended contact time; moreover such neutralization is often necessary in practice and on a large scale to prevent adverse health and ecological impacts from remaining disinfectant after the target CT is achieved. Few studies adequately assess the extent of neutralization of the chemical disinfectant and are intended to optimize on-site disinfection practices for waste matrices posing high microbial risks. Hence, there is a need for effective and reproducible neutralization protocols in chemical disinfection trials and practice. Furthermore, for most of chemical disinfectants used in healthcare settings there is no practical methodology to reliably and conveniently measure the residual disinfectant concentration after its neutralization and also determine the optimum concentration of the neutralizer. Because some neutralizing compounds can themselves be toxic to the test microorganisms, it is necessary to optimize neutralization procedures in disinfection experiments for the development of infection control practices using accepted positive control microbes. In the presented work, a stepwise bioassay-based protocol using representative faecal indicator microbes is described for optimizing chemical disinfection and subsequent disinfectant neutralization of any infectious faecal waste matrix. The example described is for the quaternary ammonium compound benzalkonium chloride and its recommended chemical neutralizer in a high strength human faecal waste matrix.

Distribution of human fecal marker GB-124 bacteriophages in urban sewage and reclaimed water of São Paulo city, Brazil

Bacteriophages infecting Bacteroides fragilis GB-124 have been described as potential markers of human fecal contamination in water sources. The aim of this study was to evaluate the occurrence of GB-124 phages in raw sewage, secondary effluents and reclaimed water of the São Paulo city using a low-cost microbial source tracking method. Samples were collected monthly from April 2015 to March 2016 in four municipal wastewater treatment plants that operate with activated sludge processes followed by different tertiary treatments (sand-anthracite filtration, membrane bioreactor/reverse osmosis) and final chlorination. GB-124 phages were detected in 100% of the raw sewage samples, with viral loads varying from 7.5 × 10³ to 1.32 × 10⁶ PFU/L. Virus removal efficiency in activated sludge processes ranged from 1.89 to 2.31 log₁₀. Frequencies of phage detection were lower in reclaimed water samples (0-22.2%). The results indicated that GB-124 phage could be a complementary low-cost viral marker for the detection of human fecal pollution in waters impacted with urban sewage in this region. However, the datasets of tertiary effluents resulted in several samples with concentrations below the detection limit (DL ≤1 PFU/mL) suggesting the need to obtain analytical methods with lower DL for greater accuracy of negative results.

The application of bacteriophages as novel indicators of viral pathogens in wastewater treatment systems

Many wastewater treatment technologies have been shown to remove bacterial pathogens more effectively than viral pathogens and, in aquatic environments, levels of traditional faecal indicator bacteria (FIB) do not appear to correlate consistently with levels of human viral pathogens. There is, therefore, a need for novel viral indicators of faecal pollution and surrogates of viral pathogens, especially given the increasing importance of indirect and direct wastewater reuse. Potential candidates include bacteriophages (phages) and the study described here sought to elucidate the relationship between three groups of phages (somatic coliphages (SOMPH), F-RNA coliphages (F-RNAPH) and human-specific phages infecting B. fragilis (Bf124PH) - enumeration using double layer agar technique) and viral pathogens (human adenovirus (HuAdV) and norovirus (NoV) - enumeration using molecular methods) through full-scale municipal wastewater treatment processes. FIB (faecal coliforms (FC) and intestinal enterococci (ENT) - enumeration using membrane filtration) were also monitored. Samples were collected every fortnight, during a twelve-month period, at each stage of four full-scale wastewater treatment plants (WWTP) in southern England (two activated sludge (AS) and two trickling filter (TF) plants) (n = 360 samples). FIB and SOMPH were consistently found in all samples tested, whereas F-RNAPH, Bf124PH and HuAdV were less frequently detected, especially following AS treatment. The detection rate of NoV was low and consequently discussion of this group of viruses is limited. Concentrations of SOMPH and FIB were statistically higher (p value < 0.05) than concentrations of F-RNAPH, Bf124PH and HuAdV in raw wastewater. FIB were more effectively removed than phages in both systems. Removal rates of HuAdV were similar to those of phages at the secondary treatment stage of both systems. In TF systems, HuAdV were removed at the same rate as F-RNAPH, but at lower rates than SOMPH and Bf124PH. The findings suggest that phages (in particular SOMPH) are better indicators of the fate of viral pathogens in WWTP than existing FIB and that these organisms may have a useful role to play in future sanitation safety planning.

Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement

Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal-indicator bacteria are used; however, they cannot distinguish human fecal waste from other animal pollution sources. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based on initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against an animal fecal reference library, and crAssphage genetic markers were highly abundant in raw sewage and sewage-impacted water samples. In addition, CPQ_056 and CPQ_064 performance was compared to HF183/BacR287 and HumM2 assays in paired experiments. Findings confirm that viral crAssphage qPCR assays perform at a similar level to well-established bacterial human-associated fecal-source-identification approaches. These new viral-based assays could become important water quality management and research tools.

Bacteriophages as indicators of faecal pollution and enteric virus removal

Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal.

The roles of bacteriophages in membrane-based water and wastewater treatment processes: A review

Membrane filtration processes have been widely applied in water and wastewater treatment for many decades. Concerns related to membrane treatment effectiveness, membrane lifespan, and membrane fouling control have been paid great attention. To achieve sustainable membrane operation with regards to low energy and maintenance cost, monitoring membrane performance and applying suitable membrane control strategies are required. As the most abundant species in water and wastewater, bacteriophages have shown great potential to be employed in membrane processes as (1) indicators to assess membrane performance considering their similar properties to human pathogenic waterborne viruses; (2) surrogate particles to monitor membrane integrity due to their nano-sized nature; and (3) biological agents to alleviate membrane fouling because of their antimicrobial properties. This study aims to provide a comprehensive review on the roles of bacteriophages in membrane-based water and wastewater treatment processes, with focuses on their uses for membrane performance examination, membrane integrity monitoring, and membrane biofouling control. The advantages, limitations, and influencing factors for bacteriophage-based applications are reported. Finally, the challenges and prospects of bacteriophage-based applications in membrane processes for water treatment are highlighted.

Removal of phages and viral pathogens in a full-scale MBR: Implications for wastewater reuse and potable water

The aim of this study was to demonstrate how seasonal variability in the removal efficacy of enteric viral pathogens from an MBR-based water recycling system might affect risks to human health if the treated product were to be used for the augmentation of potable water supplies. Samples were taken over a twelve month period (March 2014-February 2015), from nine locations throughout a water recycling plant situated in East London and tested for faecal indicator bacteria (thermotolerant coliforms, intestinal enterococci n = 108), phages (somatic coliphage, F-specific RNA phage and Bacteroides phage (GB-124) n = 108), pathogenic viruses (adenovirus, hepatitis A, norovirus GI/GII n = 48) and a range of physico-chemical parameters (suspended solids, DO, BOD, COD). Thermotolerant coliforms and intestinal enterococci were removed effectively by the water recycling plant throughout the study period. Significant mean log reductions of 3.9-5.6 were also observed for all three phage groups monitored. Concentrations of bacteria and phages did not vary significantly according to season (P < 0.05; Kruskal-Wallis), though recorded levels of norovirus (GI) were significantly higher during autumn/winter months (P = 0.027; Kruskal-Wallis). Log reduction values for norovirus and adenovirus following MBR treatment were 2.3 and 4.4, respectively. However, both adenovirus and norovirus were detected at low levels (2000 and 3240 gene copies/L, respectively) post chlorination in single samples. Whilst phage concentrations did correlate with viral pathogens, the results of this study suggest that phages may not be suitable surrogates, as viral pathogen concentrations varied to a greater degree seasonally than did the phage indicators and were detected on a number of occasions on which phages were not detected (false negative sample results).

The application of phage-based faecal pollution markers to predict the concentration of adenoviruses in mussels (Mytilus edulis) and their overlying waters

AIM

This study set out to determine whether phage-based indicators may provide a 'low-tech' alternative to existing approaches that might help maintain the microbial safety of shellfish and their overlying waters.

METHODS AND RESULTS

Mussels and their overlying waters were collected biweekly from an estuary in southeast England over a 2-year period (May 2013-April 2015) (n = 48). Levels of bacterial indicators were determined using membrane filtration and most probable number methods and those of bacteriophages were determined by direct plaque assay. The detection of adenovirus was determined using real-time polymerase chain reaction. The results revealed that somatic coliphages demonstrated the most significant correlations with AdV F and G in mussels (ρ = 0·55) and overlying waters (ρ = 0·66), followed by GB124 phages (ρ = 0·43) while Escherichia coli showed no correlation with AdV F and G in mussels.

CONCLUSION

This study demonstrates that the use of somatic coliphages and GB124 phages may provide a better indication of the risk of adenovirus contamination of mussels and their overlying waters than existing bacterial indicators.

SIGNIFICANCE AND IMPACT OF THE STUDY

Phage-based detection may be particularly advantageous in low-resource settings where viral infectious disease presents a significant burden to human health.

Thermal Inactivation of Enteric Viruses and Bioaccumulation of Enteric Foodborne Viruses in Live Oysters (Crassostrea virginica)

Human enteric viruses are among the main causative agents of shellfish-associated outbreaks. In this study, the kinetics of viral bioaccumulation in live oysters and the heat stabilities of the predominant enteric viruses were determined both in tissue culture and in oyster tissues. A human norovirus (HuNoV) GII.4 strain, HuNoV surrogates (murine norovirus [MNV-1], Tulane virus [TV]), hepatitis A virus (HAV), and human rotavirus (RV) bioaccumulated to high titers within oyster tissues, with different patterns of bioaccumulation for the different viruses. We tested the thermal stability of each virus at 62, 72, and 80°C in culture medium. The viruses can be ranked from the most heat resistant to the least stable as follows: HAV, RV, TV, MNV-1. In addition, we found that oyster tissues provided protection to the viruses during heat treatment. To decipher the mechanism underlying viral inactivation by heat, purified TV was treated at 80°C for increasing time intervals. It was found that the integrity of the viral capsid was disrupted, whereas viral genomic RNA remained intact. Interestingly, heat treatment leading to complete loss of TV infectivity was not sufficient to completely disrupt the receptor binding activity of TV, as determined by the porcine gastric mucin-magnetic bead binding assay. Similarly, HuNoV virus-like particles (VLPs) and a HuNoV GII.4 strain retained some receptor binding ability following heat treatment. Although foodborne viruses have variable heat stability, 80°C for >6 min was sufficient to completely inactivate enteric viruses in oysters, with the exception of HAV.

U.S. Recreational Water Quality Criteria: A Vision for the Future

This manuscript evaluates the U.S. Recreational Water Quality Criteria (RWQC) of 2012, based upon discussions during a conference held 11-13 March 2013, in Honolulu, Hawaii. The RWQC of 2012 did not meet expectations among the research community because key recommended studies were not completed, new data to assess risks to bathers exposed to non-point sources of fecal indicator bacteria (FIB) were not developed, and the 2012 RWQC did not show marked improvements in strategies for assessing health risks for bathers using all types of recreational waters. The development of the 2012 RWQC was limited in scope because the epidemiologic studies at beach sites were restricted to beaches with point sources of pollution and water samples were monitored for only enterococci. The vision for the future is development of effective RWQC guidelines based on epidemiologic and quantitative microbial risk assessment (QMRA) studies for sewage specific markers, as well as human enteric pathogens so that health risks for bathers at all recreational waters can be determined. The 2012 RWQC introduced a program for states and tribes to develop site-specific water quality criteria, and in theory this approach can be used to address the limitations associated with the measurements of the traditional FIB.

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.

Bacteriophage removal in a full-scale membrane bioreactor (MBR) - Implications for wastewater reuse

The aim of this study was to assess the potential removal efficacy of viruses in a full-scale membrane bioreactor (MBR) wastewater reuse system, using a range of indigenous and 'spiked' bacteriophages (phages) of known size and morphology. Samples were taken each week for three months from nine locations at each treatment stage of the water recycling plant (WRP) and tested for a range of microbiological parameters (n = 135). Mean levels of faecal coliforms were reduced to 0.3 CFU/100 ml in the MBR product and were undetected in samples taken after the chlorination stage. A relatively large reduction (5.3 log) in somatic coliphages was also observed following MBR treatment. However, F-specific and human-specific (GB124) phages were less abundant at all stages, and demonstrated log reductions post-MBR of 3.5 and 3.8, respectively. In 'spiking' experiments, suspended 'spiked' phages (MS2 and B-14) displayed post-MBR log reductions of 2.25 and 2.30, respectively. The removal of these suspended phages, which are smaller than the membrane pore size (0.04 μm), also highlights the possible role of the membrane biofilm as an effective additional barrier to virus transmission. The findings from this study of a full-scale MBR system demonstrate that the enumeration of several phage groups may offer a practical and conservative way of assessing the ability of MBR to remove enteric viruses of human health significance. They also suggest that phage removal in MBR systems may be highly variable and may be closely related on the one hand to both the size and morphology of the viruses and, on the other, to whether or not they are attached to solids.

The application of removal coefficients for viruses in different wastewater treatment processes calculated using stochastic modelling

This study proposes that calculating and interpreting removal coefficients (K20) for bacteriophages in activated sludge (AS) and trickling filter (TF) systems using stochastic modelling may provide important information that may be used to estimate the removal of phages in such systems using simplified models. In order to achieve this, 14 samples of settled wastewater and post-secondary sedimentation wastewater were collected every 2 weeks, over a 6-month period (May to November), from two AS and two TF systems situated in southern England. Initial results have demonstrated that the removal of somatic coliphages in both AS and TF systems is considerably higher than that of F-RNA coliphages, and that AS more effectively removes both phage groups than TF. The results have also demonstrated that K20 values for phages in AS are higher than in TF, which could be justified by the higher removal rates observed in AS and the models assumed for both systems. The research provides a suggested framework for calculating and predicting removal rates of pathogens and indicator organisms in wastewater treatment systems using simplified models in order to support integrated water and sanitation safety planning approaches to human health risk management.

Bacteriophages infecting Bacteroides as a marker for microbial source tracking

Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination.

Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States

Phages infecting human-associated Bacteroides fragilis (GB-124 phages) have been employed in the European Union (EU) to identify human faecal pollution, but their utility for the United States was unclear. Primary sewage samples were collected seasonally from seven wastewater treatment plants (WWTP) across the continental United States, and more time-intensive sampling was conducted at local WWTPs. All samples were assayed for plaque-forming units (PFU) of GB-124 phages, somatic and FRNA-specific coliphages, as well as adenoviruses (by quantitative PCR [qPCR]). Animal faecal samples (>250) from 14 different species were tested for the presence of the three phage groups. GB-124 phages were consistently detected in sewage (10-10(2) PFU ml(-1) ), but not in animal faeces. While density estimates of both coliphages in sewage were approximately one order of magnitude higher than GB-124 phages, they were both randomly detected in animal faecal samples (10(2) -10(5) g(-1) dry weight). Stability of all three phages was inversely proportional to temperature; persistence was greatest at 5°C compared to 20 and 35°C, where no phages were detectable after a week. In summary, GB-124 phages appear to be a feasible alternative indicator organism and benefit from being sewage associated, while providing an inexpensive detection technique for infectious virions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteroides fragilis GB-124 phages appear to be restricted to human sewage sources in the United States, being absent from 264 animal faecal samples from 14 different species and present in approx. 90% (34/38) of primary sewage effluent samples collected across the country. Although somatic and F-specific coliphages were present in sewage samples at higher densities, unlike GB-124 phages, both coliphage types were also detected in animal faecal samples. Hence, GB-124 phages may prove to be a useful novel indicator group for human faecal pollution in the continental United States.

Correlative assessment of fecal indicators using human mitochondrial DNA as a direct marker

Identifying the source of surface water fecal contamination is paramount to mitigating pollution and risk to human health. Fecal bacteria such as E. coli have been staple indicator organisms for over a century, however there remains uncertainty with E. coli-based metrics since these bacteria are abundant in the environment. The relationships between the presence of direct indicator of human waste (human mitochondrial DNA), human-specific Bacteroidales, and E. coli were studied for water samples taken from an urban creek system (Duck Creek Watershed, Cincinnati, OH) impacted by combined sewer overflows. Logistic regression analysis shows that human-specific Bacteroidales correlates much more closely to human mitochondrial DNA (R = 0.62) relative to E. coli (R = 0.33). We also examine the speciation of Bacteroidales within the Duck Creek Watershed using next-generation sequencing technology (Ion Torrent) and show the most numerous populations to be associated with sewage. Here we demonstrate that human-specific Bacteroidales closely follow the dynamics of human mitochondrial DNA concentration changes, indicating that these obligate anaerobes are more accurate than E. coli for fecal source tracking, lending further support to risk overestimation using coliforms, especially fecal coliforms and E. coli.