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

Hunting for a viral proxy in bioaerosols of swine buildings using molecular detection and metagenomics

There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine. The effectiveness of dust mitigation strategies such as oil sprinkling, to decrease risk of airborne virus transmission are unknown. Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents. Air particles were collected from swine buildings using high-volume air samplers. Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by high-throughput sequencing. Porcine astroviruses group 2 were common (from 102 to 105 genomic copies per cubic meter of air or gc/m3, 93% positivity) while no norovirus genogroup II was recovered from air samples. Porcine torque teno sus virus were detected by qPCR in low concentrations (from 101 to 102 gc/m3, 47% positivity). Among the identified viral families by metagenomics analysis, Herelleviridae, Microviridae, Myoviridae, Podoviridae, and Siphoviridae were dominant. The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m3 among the samples taken for the present study (97% positivity) and banked samples from 5- and 15-year old studies (89% positivity). According to the present study, both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.

Global metagenomic survey identifies sewage-derived hgcAB+ microorganisms as key contributors to riverine methylmercury production

Methylmercury (MeHg) in aquatic systems poses a serious public health risk through bioaccumulation in the aquatic food web. In recent years, MeHg has been observed to increase to concerning levels globally in rivers near cities; however, the causes of this increase are not well understood. Here, we demonstrate the significant role of sewage contamination by analyzing over 1,300 publicly available metagenomes in urban rivers worldwide, and conducting experiments with water samples across China. We find that sewage contamination significantly increases the abundance of mercury (Hg)-methylating microorganisms in urban rivers globally. This increase is primarily attributed to the high abundance of active Hg-methylating microorganisms in sewage, which migrate to rivers via direct discharge or combined sewer overflows (CSOs), becoming key contributors to elevated riverine MeHg levels. Our findings underscore the importance of effectively eliminating Hg-methylating microorganisms from sewage to mitigate the public health risks associated with MeHg in urban rivers.

CrAss-like phages are suitable indicators of antibiotic resistance genes found in abundance in fecally polluted samples

Antibiotic resistance genes (ARGs) have been extensively observed in bacterial DNA, and more recently, in phage particles from various water sources and food items. The pivotal role played by ARG transmission in the proliferation of antibiotic resistance and emergence of new resistant strains calls for a thorough understanding of the underlying mechanisms. The aim of this study was to assess the suitability of the prototypical p-crAssphage, a proposed indicator of human fecal contamination, and the recently isolated crAssBcn phages, both belonging to the Crassvirales group, as potential indicators of ARGs. These crAss-like phages were evaluated alongside specific ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, blaVIM, blaOXA-48, qnrA, qnrS, tetW and sul1) within the total DNA and phage DNA fractions in water and food samples containing different levels of fecal pollution. In samples with high fecal load (>103 CFU/g or ml of E. coli or somatic coliphages), such as wastewater and sludge, positive correlations were found between both types of crAss-like phages and ARGs in both DNA fractions. The strongest correlation was observed between sul1 and crAssBcn phages (rho = 0.90) in sludge samples, followed by blaCTX-M-9 and p-crAssphage (rho = 0.86) in sewage samples, both in the phage DNA fraction. The use of crAssphage and crAssBcn as indicators of ARGs, considered to be emerging environmental contaminants of anthropogenic origin, is supported by their close association with the human gut. Monitoring ARGs can help to mitigate their dissemination and prevent the emergence of new resistant bacterial strains, thus safeguarding public health.

Co-occurrence of adeno-associated virus 2 and human enteric adenovirus (group F) in wastewater after worldwide outbreaks of acute hepatitis of unknown etiology (AHUE)

In 2022, several cases of acute hepatitis of unknown etiology (AHUE) have been associated with Adeno-associated virus 2 (AAV-2) and the common childhood virus Adenovirus 41 (AdV-41). This outbreak has resulted in serious complications in patients which included 5 % of individuals requiring a liver transplant and 22 deaths. Before these AHUE cases, no previous information had been reported regarding the co-infections and co-occurrence of these two viruses in the human population. The present study utilized WBE tools to investigate the prevalence of AAV-2 and AdV-F (AdV-41 and AdV-40) in wastewater from two different waste-water treatment plants (WWTP) serving the city of Bloomington in Southern Indiana, USA. The concentrations of AAV-2 and AdV-F were quantified using digital PCR in weekly wastewater samples taken over the duration of 18 months. High levels of both viruses were observed in most of the samples where co-detection and correlation in the concentrations for AAV-2 and AdV-F were found to be significant (p < 0.01) throughout duration of the study. In addition, significant seasonal changes were observed in the viral concentrations of both viruses (P < 0.01), but these seasonal variations were different between WWTPs (p < 0.01). However, these seasonal variations in viral concentrations were similar for both viruses. The sequences of AdV-F and AAV were obtained from the wastewater samples and confirmed the detection of AAV-2, AdV-41, and AdV-40 in the samples analyzed. Even though our study was done after the 2022 outbreak of AHUE, our results demonstrated the persistence of infections with both viruses in the population. It also highlights the ongoing spread of both viruses in the population and the importance of WBE in surveillance of these viruses.

Persistence of sewage-associated genetic markers in advanced and conventional treated recycled water: implications for microbial source tracking in surface waters

Sewage contamination of environmental waters is increasingly assessed by measuring DNA from sewage-associated microorganisms in microbial source tracking (MST) approaches. However, DNA can persist through wastewater treatment and reach surface waters when treated sewage/recycled water is discharged, which may falsely indicate pollution from untreated sewage. Recycled water discharged from an advanced wastewater treatment (AWT) facility into a Florida stream elevated the sewage-associated HF183 marker 1,000-fold, with a minimal increase in cultured Escherichia coli. The persistence of sewage-associated microorganisms was compared by qPCR in untreated sewage and recycled water from conventional wastewater treatment (CWT) and AWT facilities. E. coli (EC23S857) and sewage-associated markers HF183, H8, and viral crAssphage CPQ_056 were always detected in untreated sewage (6.5-8.7 log10 GC/100 mL). Multivariate analysis found a significantly greater reduction of microbial variables via AWT vs CWT. Bacterial markers decayed ~4-5 log10 through CWT, but CPQ_056 was ~100-fold more persistent. In AWT facilities, the log10 reduction of all variables was ~5. In recycled water, bacterial marker concentrations were significantly correlated (P ≤ 0.0136; tau ≥ 0.44); however, CPQ_056 was not correlated with any marker, suggesting varying drivers of decay. Concentrations of cultured E. coli carrying the H8 marker (EcH8) in untreated sewage were 5.24-6.02 log10 CFU/100 mL, while no E. coli was isolated from recycled water. HF183 and culturable EcH8 were also correlated in contaminated surface waters (odds ratio β1 = 1.701). Culturable EcH8 has a strong potential to differentiate positive MST marker signals arising from treated (e.g., recycled water) and untreated sewage discharged into environmental waters.

IMPORTANCE

Genes in sewage-associated microorganisms are widely accepted indicators of sewage pollution in environmental waters. However, DNA persists through wastewater treatment and can reach surface waters when recycled water is discharged, potentially causing false-positive indications of sewage contamination. Previous studies have found that bacterial and viral sewage-associated genes persist through wastewater treatment; however, these studies did not compare different facilities or identify a solution to distinguish sewage from recycled water. In this study, we demonstrated the persistence of bacterial marker genes and the greater persistence of a viral marker gene (CPQ_056 of crAssphage) through varying wastewater treatment facilities. We also aim to provide a tool to confirm sewage contamination in surface waters with recycled water inputs. This work showed that the level of wastewater treatment affects the removal of microorganisms, particularly viruses, and expands our ability to identify sewage in surface waters.

CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker

CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.

Assessment of crAssphage as a human fecal source tracking marker in the lower Great Lakes

CrAssphage or crAss-like phage ranks as the most abundant phage in the human gut and is present in human feces-contaminated environments. Due to its high human specificity and sensitivity, crAssphage is a potentially robust source tracking indicator that can distinguish human fecal contamination from agricultural or wildlife sources. Its suitability in the Great Lakes area, one of the world's most important water systems, has not been well tested. In this study, we tested a qPCR-based quantification method using two crAssphage marker genes (ORF18-mod and CPQ_064) at Toronto recreational beaches along with their adjacent river mouths. Our results showed a 71.4 % (CPQ_064) and 100 % (ORF18-mod) human sensitivity for CPQ_064 and ORF18-mod, and a 100 % human specificity for both marker genes. CrAssphage was present in 57.7 % or 71.2 % of environmental water samples, with concentrations ranging from 1.45 to 5.14 log10 gene copies per 100 mL water. Though concentrations of the two marker genes were strongly correlated, ORF18-mod features a higher human sensitivity and higher positive detection rates in environmental samples. Quantifiable crAssphage was mostly present in samples collected in June and July 2021 associated with higher rainfall. In addition, rivers had more frequent crAssphage presence and higher concentrations than their associated beaches, indicating more frequent and greater human fecal contamination in the rivers. However, crAssphage was more correlated with E. coli and Enterococcus at the beaches than in the rivers, suggesting human fecal sources may be more predominant in driving the increases in E. coli and Enterococcus at the beaches when impacted by river plumes.

Traditional and new proposals for environmental microbial indicators-a review

The continuous increment in world population coupled with the greatest natural resource consumption and waste generation has an enormous impact on the environment. To date, using biological indicators (bioindicators) to evaluate the biological quality of natural environments is very common. Nonetheless, selecting those suitable for each ecosystem or contaminant is one of the most important issues for environmental sciences. Bacteria and helminths are mainly related to fecal contamination, while antibiotic-resistant bacteria, fungi, viruses, and microalgae are organisms used to determine deteriorated ecosystems by diverse contaminants. Nowadays, each bioindicator is used as a specific agent of different contaminant types, but detecting and quantifying these bioindicator microorganisms can be performed from simple microscopy and culture methods up to a complex procedure based on omic sciences. Developing new techniques based on the metabolism and physiological responses of traditional bioindicators is shown in a fast environmental sensitivity analysis. Therefore, the present review focuses on analyzing different bioindicators to facilitate developing suitable monitoring environmental systems according to different pollutant agents. The traditional and new methods proposed to detect and quantify different bioindicators are also discussed. Their vital role is considered in implementing efficient ecosystem bioprospection, restoration, and conservation strategies directed to natural resource management.

Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia

The most common DNA virus found in wastewaters globally is the cross-assembly phage (crAssphage). King Saud University wastewater treatment plant (KSU-WWTP); Manfoha wastewater treatment plant (MN-WWTP); and the Embassy wastewater treatment plant (EMB-WWTP) in Riyadh, Saudi Arabia were selected, and 36 untreated sewage water samples during the year 2022 were used in the current study. The meteorological impact on crAssphage prevalence was investigated. CrAssphage prevalence was recorded using PCR and Sanger sequencing. The molecular diversity of crAssphage sequences was studied for viral gene segments from the major capsid protein (MCP) and membrane protein containing the peptidoglycan-binding domain (MP-PBD). KSU-WWTP and EMB-WWTP showed a higher prevalence of crAssphage (83.3%) than MN-WWTP (75%). Phylogenetic analysis of MCP and MP-PBD segments depicted a close relationship to the Japanese isolates. The MCP gene from the current study's isolate WW/2M/SA/2022 depicted zero evolutionary divergence from 3057_98020, 2683_104905, and 4238_99953 isolates (d = 0.000) from Japan. A significant influence of temporal variations on the prevalence of crAssphage was detected in the three WWTPs. CrAssphage displayed the highest prevalence at high temperatures (33-44 °C), low relative humidity (6-14%), and moderate wind speed (16-21 Km/h). The findings provided pioneering insights into crAssphage prevalence and its genetic diversity in WWTPs in Riyadh, Saudi Arabia.

Inclusion of hydrodynamic properties of bathing waters is critical in selecting faecal indicators to assess public health impacts of faecal contamination

The EU Bathing Water Directive (BWD) requires member states to assess bathing water quality according to the levels of faecal indicator bacteria (FIB) in designated bathing areas. However, this criterion has two significant limitations given that the BWD does not; (i) account for differences in hydrodynamic properties of bathing waters and, (ii) assumes that all faecal pathogens decay equally in aquatic environments. This study simulated sewage discharge events in three hypothetical aquatic environments characterised by different advection and dispersion parameters in the solute transport equation. Temporal changes in the downstream concentration of six faecal indicators were determined in simulations that utilised measured decay rates of each faecal indicator from a programme of controlled microcosm experiments in fresh and seawater environments. The results showed that the decay rates of faecal indicators are not a critical parameter in advection dominant water bodies, such as in fast-flowing rivers. Therefore, faecal indicator selection is less important in such systems and for these, FIB remains the most cost-effective faecal indicator to monitor the public health impacts of faecal contamination. In contrast, consideration of faecal indicator decay is important when assessing dispersion and advection/dispersion dominant systems, which would pertain to transitional (estuarine) and coastal waterbodies. Results suggest that the inclusion of viral indicators, such as crAssphage and PMMoV, could improve the reliability of water quality modelling and minimise the risk of waterborne illnesses from faecal contamination.

Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens

Wastewater treatment plants (WWTPs) receive and treat large volumes of domestic, industrial, and urban wastewater containing pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances. WWTPs play an essential role in preserving human, animal, and environmental health by removing many of these toxic and infectious agents, particularly biological hazards. Wastewater contains complex consortiums of bacterial, viral, archaeal, and eukaryotic species, and while bacteria in WWTP have been extensively studied, the temporal and spatial distribution of nonbacterial microflora (viruses, archaea, and eukaryotes) is less understood. In this study, we analyzed the viral, archaeal, and eukaryotic microflora in wastewater throughout a treatment plant (raw influent, effluent, oxidation pond water, and oxidation pond sediment) in Aotearoa (New Zealand) using Illumina shotgun metagenomic sequencing. Our results suggest a similar trend across many taxa, with an increase in relative abundance in oxidation pond samples compared to influent and effluent samples, except for archaea, which had the opposite trend. Additionally, some microbial families, such as Podoviridae bacteriophages and Apicomplexa alveolates, appeared largely unaffected by the treatment process, with their relative abundance remaining stable throughout. Several groups encompassing pathogenic species, such as Leishmania, Plasmodium, Toxoplasma, Apicomplexa, Cryptococcus, Botrytis, and Ustilago, were identified. If present, these potentially pathogenic species could be a threat to human and animal health and agricultural productivity; therefore, further investigation is warranted. These nonbacterial pathogens should be considered when assessing the potential for vector transmission, distribution of biosolids to land, and discharge of treated wastewater to waterways or land. IMPORTANCE Nonbacterial microflora in wastewater remain understudied compared to their bacterial counterparts despite their importance in the wastewater treatment process. In this study, we report the temporal and spatial distributions of DNA viruses, archaea, protozoa, and fungi in raw wastewater influent, effluent, oxidation pond water, and oxidation pond sediments by using shotgun metagenomic sequencing. Our study indicated the presence of groups of nonbacterial taxa which encompass pathogenic species that may have potential to cause disease in humans, animals, and agricultural crops. We also observed higher alpha diversity in viruses, archaea, and fungi in effluent samples than in influent samples. This suggests that the resident microflora in the wastewater treatment plant may be making a greater contribution to the diversity of taxa observed in wastewater effluent than previously thought. This study provides important insights to better understand the potential human, animal, and environmental health impacts of discharged treated wastewater.

Applicability of crAssphage as a performance indicator for viral reduction during activated sludge wastewater treatment

A major threat to water quality is the discharge of human-derived wastewater, which can cause waterborne illnesses associated with enteric viruses. A poor association exists between fecal indicator bacteria and virus fate in the environment, especially during wastewater treatment. In the current study, the potential of using a novel human gut bacteriophage crAssphage as a wastewater treatment process indicator was evaluated. Using qPCR, influent and effluent wastewater samples of two wastewater treatment plants were analyzed for crAssphage and human viruses including human bocavirus (HBoV), human adenovirus (HAdV), and human polyomavirus (HPyV). All samples were positive for crAssphage. The annual crAssphage concentrations varied between 1.45E + 04 and 2.39E + 08 gc/l in influent samples and from 1.25E + 04 to 7.88E + 06 gc/l in effluent samples. Human viruses concentrations were some orders of magnitude lower than that of crAssphage. Data demonstrated a significant correlation between crAssphage, HAdV, and HPyV during the wastewater treatment process, suggesting that crAssphage and human viral pathogens have similar removal mechanisms. Ultimately, this work concludes that crAssphage could be a performance indicator for viral reduction in the wastewater treatment process.

CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water

Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota, and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. IMPORTANCE Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.

Spatial distribution of fecal pollution indicators in sewage sludge flocs and their removal and inactivation as revealed by qPCR/viability-qPCR during potassium ferrate treatment

Sludge reuse and utilization is one of important routines of disseminating fecal pollution to surface water and groundwater. However, it remains unclear the spatial distribution of fecal pollution indicators in sludge flocs and their reductions during sludge treatment processes. In this study, the abundances of fecal pollution indicators including cross-assembly phage (crAssphage), JC and BK polyomavirus (JCPyV, BKPyV), human adenovirus (HAdV), the human-specific HF183 Bacteroides (HF183) and Escherichia coli (EC) in soluble extracellular polymeric substances (S-EPS), loosely-bound EPS (LB-EPS), tightly-bound EPS (TB-EPS), and pellets of sludge flocs were determined, and the effect of potassium ferrate (PF) treatment on their removal and inactivation was investigated by using both qPCR and viability-qPCR. Results showed that all investigated indicators were detected in each fraction of sludge flocs. The PF treatment led to a great migration of indicators from sludge pellets to sludge EPS and some extent of their inactivation in each fraction of sludge flocs. The overall reductions of human fecal indicators in sludge determined by qPCR were 0-1.30 logs, which were 0-2 orders of magnitude lower than those of 0.69-2.39 logs detected by viability-qPCR, implying their inactivation by PF treatment to potentially alleviate the associated human health risks.

Unraveling the influence of human fecal pollution on antibiotic resistance gene levels in different receiving water bodies using crAssphage indicator gene

Discharged wastewater treatment plant (WWTP) effluents can contaminate receiving water bodies with human feces and alter the abundance of antibiotic resistance genes (ARGs). In this study, we examined the co-occurrence of ARGs, human fecal pollution indicator crAssphage, and antibiotics in human feces and a series of connected receiving water bodies affected by human feces, including water from different treatment units of a WWTP, river, lake, and tap waters. Results showed that crAssphage was detected in 68.2 % of the studied water bodies, confirming widespread human fecal contamination. Both ARG and crAssphage abundances exhibited a distance-decay effect from the emission source to the receiving environment. Interestingly, the detected ARG abundance in the water bodies was significantly correlated with crAssphage abundance but not with the residual antibiotic concentration, demonstrating that the presence of ARG could largely be explained by the extent of fecal pollution, with no clear signs of antibiotic selection. In addition, 14 ARGs co-shared by human feces and water bodies were significantly correlated with crAssphage. Furthermore, a close evolutionary relationship was observed between the bla_TEM-1 gene from human feces and aquatic environments. These results imply a potential ARG exchange between human feces and receiving water bodies. Overall, this study provides important insights into the distribution and sources of ARGs in water bodies affected by human fecal contamination.

Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

The One Health framework recognizes that human, animal, and environmental health are linked and highly interdependent. Fecal contamination of water, soil, foodstuff, and air may impact many aspects of One Health, and culture, PCR-based, and sequencing methods are utilized in the detection of fecal contamination to determine source, load, and risk to inform targeted mitigation strategies. Viruses, particularly, have been considered as fecal contamination indicators given the narrow host range many exhibit and their association with other biological contaminants. Culture- and molecular-based methods are considered the gold-standards for virus detection and for determining specific sources of fecal contamination via viral indicators. However, viral metagenomics is also being considered as a tool for tracking sources of fecal contamination. In the present review, studies tracking potential sources of fecal contamination in freshwaters, marine waters, foodstuff, soil, and air using viral metagenomics are discussed to highlight the potential of viral metagenomics for optimizing fecal source tracking. Limitations of the use of viral metagenomics to track fecal contamination sources, including sample processing, nucleic acid recovery, sequencing depth, and bioinformatics are also discussed. Finally, the present review discusses the potential of viral metagenomics as part of the toolbox of methods in a One Health approach.

Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters

Antibiotic resistance is a global threat to human health. Many surface water resources are environmental hotspots of antibiotic resistant gene (ARG) transfer, with agricultural runoff and human waste highlighted as common sources of ARGs to aquatic systems. Here we quantified fecal marker genes and ARGs in 992 stream water samples collected seasonally during a 5-year period from 115 sites across the Upper Oconee watershed (Georgia, USA), an area characterized by gradients of agricultural and urban development. Widespread fecal contamination was found from humans (48% of samples), ruminants (55%), and poultry (19%), and 73% of samples tested positive for at least one of the six targeted ARGs (ermB, tet(B), bla_CTX-M-1, bla_KPC, bla_SHV, and qnrS). While ARGs were strongly correlated with human fecal markers, many highly contaminated samples were not associated with sewage outfalls, an expected source of fecal and ARG pollution. To determine sources of contamination, we synthesized ARG and fecal marker data with geospatial data on land use/land cover and wastewater infrastructure across the watershed. This novel analysis found strong correlations between ARGs and measures of sewer density, sewer length, and septic system age within sample watersheds, indicating non-point sources of fecal contamination from aging wastewater infrastructure can be critical disseminators of anthropogenic ARGs in the environment.

CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment

Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.

Effectiveness of two wastewater disinfection strategies for the removal of fecal indicator bacteria, bacteriophage, and enteric viral pathogens concentrated using dead-end hollow fiber ultrafiltration (D-HFUF)

Primary influent and final effluent samples were collected from wastewater treatment plants using either chlorination or ultraviolet (UV) disinfection biweekly for one year. Paired measurements were determined for fecal indicator bacteria (Escherichia coli and enterococci), cultivated bacteriophages (somatic, F+, and CB-390 coliphage and GB-124 Bacteroides phage), human-associated viral markers (human polyomavirus [HPyV] and crAssphage), enteric pathogens (adenovirus, noroviruses genogroups I and II) as well as total infectious enteric virus. To increase the probability of detecting low concentration targets, both primary (10L) and final effluent wastewater samples (40-100 L) were concentrated using a dead-end hollow-fiber ultrafilter (D-HFUF). Despite seasonal temperature fluctuations, concentration shifts of FIB, bacteriophages, human-associated viruses, and viral pathogens measured in primary influent samples were minimal, while levels of infectious enteric virus were significantly higher in the spring and fall (P range: 0.0003-0.0409). FIB levels measured in primary influents were 1-2 log₁₀ higher than bacteriophage, human-associated viral markers (except crAssphage) and viral pathogens measured. FIB displayed the greatest sensitivity to chlorine disinfection, while crAssphage, adenoviruses and infectious enteric viruses were significantly less sensitive (P ≤ 0.0096). During UV treatment, bacteriophages F+ and GB-124 were the most resistant of the culturable viruses measured (P ≤ 0.001), while crAssphage were the most resistant (P ≤ 0.0124) overall. When UV lamps were inactive, infectious enteric viruses were significantly more resilient to upstream treatment processes than all other targets measured (P ≤ 0.0257). Similar to infectious enteric viruses and adenoviruses; GB-124, F+, and crAssphages displayed the highest resistance to UV irradiation, signaling a potential applicability as pathogen surrogates in these systems. The use of D-HFUF enhanced the ability to estimate removal of viruses through wastewater treatment, with the expectation that future applications of this method will be used to better elucidate viral behavior within these systems.

Sources, fates and treatment strategies of typical viruses in urban sewage collection/treatment systems: A review

The ongoing coronavirus pandemic (COVID-19) throughout the world has severely threatened the global economy and public health. Due to receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a wide variety of sources (e.g., households, hospitals, slaughterhouses), urban sewage treatment systems are regarded as an important path for the transmission of waterborne viruses. This review presents a quantitative profile of the concentration distribution of typical viruses within wastewater collection systems and evaluates the influence of different characteristics of sewer systems on virus species and concentration. Then, the efficiencies and mechanisms of virus removal in the units of wastewater treatment plants (WWTPs) are summarized and compared, among which the inactivation efficiencies of typical viruses by typical disinfection approaches under varied operational conditions are elucidated. Subsequently, the occurrence and removal of viruses in treated effluent reuse and desalination, as well as that in sewage sludge treatment, are discussed. Potential dissemination of viruses is emphasized by occurrence via aerosolization from toilets, the collection system and WWTP aeration, which might have a vital role in the transmission and spread of viruses. Finally, the frequency and concentration of viruses in reclaimed water, the probability of infection are also reviewed for discussing the potential health risks.

Occurrence of bacterial and viral fecal markers in municipal sewage sludge and their removal during sludge conditioning processes

Fecal contamination in wastewater treatment system may pose severe threats to human health, but the detailed contamination of fecal bacterial and viral pathogens in municipal sewage sludge remains unclear. In addition, it is also unclear how sludge conditioning treatments would impact the distribution of fecal markers in conditioned sewage sludge. Before addressing these two issues, the possible polymerase chain reaction (PCR) inhibition effect when determining the abundances of fecal markers in both sludge solids and sludge supernatants should be solved, and methods of effectively concentrating fecal markers from sludge supernatant should also be developed. In the present study, we found that the serial tenfold dilution effectively reduced the PCR inhibition effect when determining the abundances of fecal markers including cross-assembly phages (CrAssphage), JC polyomavirus (JCPyV), human-specific HF183 bacteroides (HF183), human BK polyomavirus (BKPyV), human adenovirus (HAdV) and Escherichia coli (EC), while the utilization of negatively charged HA membrane was effective to recover fecal markers from sludge supernatant. The results of a six-month monitoring revealed that gene markers of CrAssphage, JCPyV, HF183, BKPyV, HAdV, and EC can be detected in municipal sewage sludge collected from a local wastewater treatment plant. Among the investigated four chemical conditioning methods, i.e., chemical conditioning with polyacrylamide (PAM), Fe[III]/CaO, or Fenton's reagent, and chemical acidification conditioning, chemical conditioning with Fenton's reagent was much more effective than the other three conditioning methods to reduce the abundances of fecal markers in the supernatant and solid of conditioned sewage sludge. Furthermore, the investigated fecal markers in the conditioned sewage sludge can be simultaneously attenuated by employing suitable conditioning methods, consequently reducing the associated environmental risks.

Monitoring Human Viral Pathogens Reveals Potential Hazard for Treated Wastewater Discharge or Reuse

Wastewater discharge to the environment or its reuse after sanitization poses a concern for public health given the risk of transmission of human viral diseases. However, estimating the viral infectivity along the wastewater cycle presents technical challenges and still remains underexplored. Recently, human-associated crAssphage has been investigated to serve as viral pathogen indicator to monitor fecal impacted water bodies, even though its assessment as biomarker for infectious enteric viruses has not been explored yet. To this end, the occurrence of potentially infectious norovirus genogroup I (GI), norovirus GII, hepatitis A virus (HAV), rotavirus A (RV), and human astrovirus (HAstV) along with crAssphage was investigated in influent and effluent water sampled in four wastewater treatment plants (WWTPs) over 1 year by a PMAxx-based capsid integrity RT-qPCR assay. Moreover, influent and effluent samples of a selected WWTP were additionally assayed by an in situ capture RT-qPCR assay (ISC-RT-qPCR) as estimate for viral infectivity in alternative to PMAxx-RT-qPCR. Overall, our results showed lower viral occurrence and concentration assessed by ISC-RT-qPCR than PMAxx-RT-qPCR. Occurrence of potentially infectious enteric virus was estimated by PMAxx-RT-qPCR as 88–94% in influent and 46–67% in effluent wastewaters with mean titers ranging from 4.77 to 5.89, and from 3.86 to 4.97 log₁₀ GC/L, with the exception of HAV that was sporadically detected. All samples tested positive for crAssphage at concentration ranging from 7.41 to 9.99 log₁₀ GC/L in influent and from 4.56 to 6.96 log₁₀ GC/L in effluent wastewater, showing higher mean concentration than targeted enteric viruses. Data obtained by PMAxx-RT-qPCR showed that crAssphage strongly correlated with norovirus GII (ρ = 0.67, p < 0.05) and weakly with HAstV and RV (ρ = 0.25–0.30, p < 0.05) in influent samples. In effluent wastewater, weak (ρ = 0.27–0.38, p < 0.05) to moderate (ρ = 0.47–0.48, p < 0.05) correlations between crAssphage and targeted viruses were observed. Overall, these results corroborate crAssphage as an indicator for fecal contamination in wastewater but a poor marker for either viral occurrence and viral integrity/infectivity. Despite the viral load reductions detected in effluent compared to influent wastewaters, the estimates of viral infectivity based on viability molecular methods might pose a concern for (re)-using of treated water.

Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse

Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.

Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes

We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used confidently as complementary viral indicators of human fecal pollution.

Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments

We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a 10 month time period that overlapped with October 2020 and winter/spring 2021 COVID-19 outbreaks in each municipality. We fit lagged regression models to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Lags of 0 to 1 days resulted in the greatest predictive power for the model. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. The close relationship between case rates and SARS-CoV-2 concentrations demonstrates the utility of using primary sludge samples for monitoring COVID-19 outbreak dynamics. Estimating case rates from wastewater data can be useful in locations with limited testing availability, testing disparities, or delays in individual COVID-19 testing programs.

Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review

Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.

Co-occurrence of crAssphage and antibiotic resistance genes in agricultural soils of the Yangtze River Delta, China

Agricultural soil is highly susceptible to manure contamination and thus is a potential source for the spread of pathogens and antibiotic resistance genes (ARGs). Routine monitoring fecal contamination in agricultural soil can reduce the manure-derived ARG contaminations. This study investigated the distribution of crAssphage, a highly human-specific indicator of fecal pollution, in agricultural soils in the Yangtze River Delta (YRD) of China, and its potential in serving as an indicator of soil ARGs. CrAssphage was indeed strongly correlated with the abundance of soil ARGs, and particularly tetracycline resistance gene tetW (rho = 0.55, p < 0.01). Meanwhile, with the increasing of crAssphage abundance, the frequency of multiple abundant ARGs is also increased. When the relative abundance of crAssphage in soil samples exceeded 4.94 × 10^-4 copies per copy of the 16S rRNA gene, there would be more than three types of co-existing ARGs. Regional differences in crAssphage and ARGs abundances were observed for samples collected from Zhejiang, Shanghai, Jiangsu, and Anhui in the YRD, indicating different levels of fecal pollution therein. High sewage treatment capacity could contribute to the reduce of fecal pollution and the control ARG transmission in agricultural soils.

crAssphage as a human molecular marker to evaluate temporal and spatial variability in faecal contamination of urban marine bathing waters

Bathing water quality may be negatively impacted by diffuse pollution arising from urban and agricultural activities and wildlife, it is therefore important to be able to differentiate between biological and geographical sources of faecal pollution. crAssphage was recently described as a novel human-associated microbial source tracking marker. This study aimed to evaluate the performance of the crAssphage marker in designated bathing waters. The sensitivity and specificity of the crAss_2 marker was evaluated using faecal samples from herring gulls, dogs, sewage and a stream impacted by human pollution (n = 80), which showed that all human impacted samples tested positive for the marker while none of the animal samples did. The crAss_2 marker was field tested in an urban marine bathing water close to the discharge point of human impacted streams. In addition, the bathing water is affected by dog and gull fouling. Analysis of water samples taken at the compliance point every 30 min during a tidal cycle following a rain event showed that the crAss_2 and HF183 markers performed equally well (Spearman correlation ρ = 0.84). The levels of these marker and faecal indicators (Escherichia coli, intestinal enterococci, somatic coliphages) varied by up to 2.5 log₁₀ during the day. Analysis of a high-tide transect perpendicular to the shoreline revealed high levels of localised faecal contamination 1 km offshore, with a concomitant spike in the gull marker. In contrast, both the crAss_2 and HF183 markers remained at a constant level, showing that human faecal contamination is homogenously distributed, while gull pollution is localised. Performance of the crAss_2 and HF183 assay was further evaluated in bimonthly compliance point samples over an 18-month period. The co-occurrence between the crAss_2 and HF183 markers in compliance sampling was 76%. A combination of both markers should be applied in low pollution impacted environments to obtain a high confidence level.

Integrative Survey of 68 Non-overlapping Upstate New York Watersheds Reveals Stream Features Associated With Aquatic Fecal Contamination

Aquatic fecal contamination poses human health risks by introducing pathogens in water that may be used for recreation, consumption, or agriculture. Identifying fecal contaminant sources, as well as the factors that affect their transport, storage, and decay, is essential for protecting human health. However, identifying these factors is often difficult when using fecal indicator bacteria (FIB) because FIB levels in surface water are often the product of multiple contaminant sources. In contrast, microbial source-tracking (MST) techniques allow not only the identification of predominant contaminant sources but also the quantification of factors affecting the transport, storage, and decay of fecal contaminants from specific hosts. We visited 68 streams in the Finger Lakes region of Upstate New York, United States, between April and October 2018 and collected water quality data (i.e., Escherichia coli, MST markers, and physical–chemical parameters) and weather and land-use data, as well as data on other stream features (e.g., stream bed composition), to identify factors that were associated with fecal contamination at a regional scale. We then applied both generalized linear mixed models and conditional inference trees to identify factors and combinations of factors that were significantly associated with human and ruminant fecal contamination. We found that human contaminants were more likely to be identified when the developed area within the 60 m stream buffer exceeded 3.4%, the total developed area in the watershed exceeded 41%, or if stormwater outfalls were present immediately upstream of the sampling site. When these features were not present, human MST markers were more likely to be found when rainfall during the preceding day exceeded 1.5 cm. The presence of upstream campgrounds was also significantly associated with human MST marker detection. In addition to rainfall and water quality parameters associated with rainfall (e.g., turbidity), the minimum distance to upstream cattle operations, the proportion of the 60 m buffer used for cropland, and the presence of submerged aquatic vegetation at the sampling site were all associated based on univariable regression with elevated levels of ruminant markers. The identification of specific features associated with host-specific fecal contaminants may support the development of broader recommendations or policies aimed at reducing levels of aquatic fecal contamination.

Application of crAssphage, F-RNA phage and pepper mild mottle virus as indicators of human faecal and norovirus contamination in shellfish

Shellfish growing waters contaminated with inadequately treated human wastewater is a major source of norovirus in shellfish and poses a significant human health risk to consumers. Microbial source tracking (MST) markers have been widely used to identify the source (s) of faecal contamination in water but data are limited on their use for shellfish safety. This study evaluated the source specificity, sensitivity, occurrence and concentration of three viral MST markers i.e. cross-assembly phage (crAssphage), F-specific RNA bacteriophage genogroup II (F-RNA phage GII) and pepper mild mottle virus (PMMoV) using animal faeces (n = 119; 16 animal groups), influent wastewater (n = 12), effluent wastewater (n = 16) and shellfish (n = 33). CrAssphage, F-RNA phage GII and PMMoV had source specific values of 0.97, 0.99 and 0.91, respectively. The sensitivity of MST markers was confirmed by their 100% detection frequency in influent wastewaters. The frequency of detection in effluent wastewater ranged from 81.3% (F-RNA phage GII) to 100% (PMMoV). Concentration of F-RNA phage GII was one log₁₀ (influent wastewater) and 2-3 log₁₀ (effluent wastewater) lower than crAssphage and PMMoV, respectively. Despite lower prevalence of F-RNA phage GII in oysters and mussels compared to crAssphage and PMMoV, concentrations of the three MST markers were similar in mussels. As an indicator of norovirus contamination in shellfish, crAssphage and PMMoV had greater predictive sensitivity (100%; [95% CI; 81.5%-100%)]) and F-RNA phage GII had greater predictive specificity (93.3%; [95% CI; 68.1%-99.8%]). In contrast, crAssphage and F-RNA phage GII have similar accuracy for predicting norovirus in shellfish, however, PMMoV significantly overestimated its presence. Therefore, a combination of crAssphage and F-RNA phage GII analysis of shellfish could provide a robust estimation of the presence of human faecal and norovirus contamination.

Occurrence and Accumulation of Human Enteric Viruses and Phages in Process Water from the Fresh Produce Industry

The virological quality of process water (PW) used by the produce industry has received limited attention. As a first step to overcoming technical limitations in monitoring viruses in PW, the analytical performance of ultrafiltration was assessed to concentrate viral particles from 20 L of spiked PW. The selected method used for sample concentration of PW was carefully validated, thus enabling the accurate quantification and estimation of viral titers of human enteric viruses and phages. PW from the produce industry was collected periodically from the washing tanks of commercial facilities. The analysis of coliphages was performed by plaque assay, while the occurrence of enteric viruses and crAssphage was determined by molecular techniques. Significant differences in the physicochemical composition of PW, mostly due to the different nature of fresh produce types and differences in the sanitizer used in commercial operation, were observed. Accumulation of crAssphage and coliphages was observed in PW, but correlation with human enteric viruses was not possible due to the low prevalence of these pathogens in the PW analyzed. The obtained results showed that depending on the type of product washed, the product/water ratio and the residual concentrations of the sanitizers, the prevalence and concentration of bacteriophages changed significantly.

Bacterial and Bacteriophage Antibiotic Resistance in Marine Bathing Waters in Relation to Rivers and Urban Streams

Fecal pollution of surface water may introduce bacteria and bacteriophages harboring antibiotic resistance genes (ARGs) into the aquatic environment. Watercourses discharging into the marine environment, especially close to designated bathing waters, may expose recreational users to fecal pollution and therefore may increase the likelihood that they will be exposed to ARGs. This study compares the bacterial and bacteriophage ARG profiles of two rivers (River Tolka and Liffey) and two small urban streams (Elm Park and Trimleston Streams) that discharge close to two marine bathing waters in Dublin Bay. Despite the potential differences in pollution pressures experienced by these waterways, microbial source tracking analysis showed that the main source of pollution in both rivers and streams in the urban environment is human contamination. All ARGs included in this study, bla_TEM, bla_SHV, qnrS, and sul1, were present in all four waterways in both the bacterial and bacteriophage fractions, displaying a similar ARG profile. We show that nearshore marine bathing waters are strongly influenced by urban rivers and streams discharging into these, since they shared a similar ARG profile. In comparison to rivers and streams, the levels of bacterial ARGs were significantly reduced in the marine environment. In contrast, the bacteriophage ARG levels in freshwater and the marine were not significantly different. Nearshore marine bathing waters could therefore be a potential reservoir of bacteriophages carrying ARGs. In addition to being considered potential additional fecal indicators organism, bacteriophages may also be viewed as indicators of the spread of antimicrobial resistance.

Bacteriophages as Fecal Pollution Indicators

Bacteriophages are promising tools for the detection of fecal pollution in different environments, and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages mimic the fate and transport of enteric viruses. Enteric bacteriophages, especially phages infecting Escherichia coli (coliphages), have been proposed as alternatives or complements to fecal indicator bacteria. Here, we provide a general overview of the potential use of enteric bacteriophages as fecal and viral indicators in different environments, as well as the available methods for their detection and enumeration, and the regulations for their application.

Human Fecal Pollution Monitoring and Microbial Risk Assessment for Water Reuse Potential in a Coastal Industrial-Residential Mixed-Use Watershed

Rapid economic development has caused industrial expansion into residential communities, leading to higher fecal pollution loads that could be discharged into aquatic environments. However, little is known regarding the potential microbial impact on human health. This study investigated microbial contamination from coastal industrial–residential community areas in nine sampling sites in waterways during three dry events. A general microbial source tracking (MST) marker, GenBac3, was detected in all samples from all three events, indicating continuing fecal pollution in the area, mostly from human sewage contamination. This was shown by the human-specific genetic marker crAssphage (88.9%) and human polyomavirus (HPyVs; 92.6%) detection. Enteric human adenovirus (HAdV40/41) showed three positive results only from residential sites in the first event. No spatial difference was observed for MST markers and traditional fecal indicators (total coliforms and Escherichia coli) in each event. Still, a significantly lower abundance of GenBac3, HPyVs, and total coliforms in the first sampling event was detected. Spearman’s rho analysis indicated a strong correlation among certain pairs of microbial parameters. Multivariate analysis revealed two clusters of samples separated by land use type (industrial vs. residential). According to factor analysis of mixed data, the land use parameter was more associated with physicochemical parameters (i.e., salinity, conductivity, water temperature, and dissolved oxygen). A Quantitative Microbial Risk Assessment (QMRA) was then conducted to estimate the annual infection risks of HAdV40/41 for non-potable water reuse purposes using predicted concentrations from crAssphage and HPyVs. The highest risks (95th percentiles) were ranked by food crop irrigation, aquaculture, and toilet flushing, at 10^–1, 10^–2, and 10^–3 per person per year (pppy). Required treatment levels to achieve a 10^–4 pppy annual infection risk were estimated. QMRA-based water treatment scenarios were suggested, including chlorination for toilet flushing reuse and depth filtration prior to chlorination for aquaculture and food crop irrigation. Microbial monitoring combined with a QMRA could provide better insights into fecal pollution patterns and the associated risks, facilitating effective water quality management and appropriate prior treatments for water reuse.

Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand

Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log₁₀ copies/100 mL), crAssphage (5.28-7.38 log₁₀ copies/100 mL), and HPyVs (3.66-6.53 log₁₀ copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log₁₀ copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log₁₀ copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log₁₀ copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log₁₀ copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.

Does over a century of aerobic phage work provide a solid framework for the study of phages in the gut?

Bacterial viruses (bacteriophages, phages) of the gut have increasingly become a focus in microbiome studies, with an understanding that they are likely key players in health and disease. However, characterization of the virome remains largely based on bioinformatic approaches, with the impact of these viromes inferred based on a century of knowledge from aerobic phage work. Studying the phages infecting anaerobes is difficult, as they are often technically demanding to isolate and propagate. In this review, we primarily discuss the phages infecting three well-studied anaerobes in the gut: Bifidobacterium, Clostridia and Bacteroides, with a particular focus on the challenges in isolating and characterizing these phages. We contrast the lessons learned from these to other anaerobic work on phages infecting facultative anaerobes of the gut: Enterococcus and Lactobacillus. Phages from the gut do appear to adhere to the lessons learned from aerobic work, but the additional challenges of working on them has required ingenious new approaches to enable their study. This, in turn, has uncovered remarkable biology likely underpinning phage-host relationships in many stable environments.

Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments

We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a 10 month time period that overlapped with October 2020 and winter/spring 2021 COVID-19 outbreaks in each municipality. We fit lagged regression models to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Lags of 0 to 1 days resulted in the greatest predictive power for the model. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. The close relationship between case rates and SARS-CoV-2 concentrations demonstrates the utility of using primary sludge samples for monitoring COVID-19 outbreak dynamics. Estimating case rates from wastewater data can be useful in locations with limited testing availability, testing disparities, or delays in individual COVID-19 testing programs.

Bacteriophages in water pollution control: Advantages and limitations

Wastewater is a breeding ground for many pathogens, which may pose a threat to human health through various water transmission pathways. Therefore, a simple and effective method is urgently required to monitor and treat wastewater. As bacterial viruses, bacteriophages (phages) are the most widely distributed and abundant organisms in the biosphere. Owing to their capacity to specifically infect bacterial hosts, they have recently been used as novel tools in water pollution control. The purpose of this review is to summarize and evaluate the roles of phages in monitoring pathogens, tracking pollution sources, treating pathogenic bacteria, infecting bloom-forming cyanobacteria, and controlling bulking sludge and biofilm pollution in wastewater treatment systems. We also discuss the limitations of phage usage in water pollution control, including phage-mediated horizontal gene transfer, the evolution of bacterial resistance, and phage concentration decrease. This review provides an integrated outlook on the use of phages in water pollution control.

CrAssphage for fecal source tracking in Chile: Covariation with norovirus, HF183, and bacterial indicators

Anthropogenic fecal pollution in urban waterbodies can promote the spread of waterborne disease. The objective of this study was to test crAssphage, a novel viral human fecal marker not previously applied for fecal source tracking in Latin America, as a fecal pollution marker in an urban river in Chile. Human fecal markers crAssphage CPQ_064 and Bacteroides HF183, the human pathogen norovirus GII, and culturable fecal indicator bacteria (FIB) were quantified at six locations spanning reaches of the Mapocho River from upstream to downstream of Santiago, as well as in repeated sub-daily frequency samples at two urban locations. Norovirus showed positive correlation trends with crAssphage (τ = 0.57, p = 0.06) and HF183 (τ = 0.64, p = 0.03) in river water, but not with E. coli or enterococci. CrAssphage and HF183 concentrations were strongly linearly related (slope = 0.97, p < 0.001). Chlorinated wastewater effluent was an important source of norovirus GII genes to the Mapocho. Precipitation showed non-significant positive relationships with human and general fecal indicators. Concentrations of crAssphage and HF183 in untreated sewage were 8.35 and 8.07 log₁₀ copy/100 ml, respectively. Preliminary specificity testing did not detect crAssphage or HF183 in bird or dog feces, which are predominant non-human fecal sources in the urban Mapocho watershed. This study is the first to test crAssphage for microbial source tracking in Latin America, provides insight into fecal pollution dynamics in a highly engineered natural system, and indicates river reaches where exposure to human fecal pollution may pose a public health risk.

Frontier review on the propensity and repercussion of SARS-CoV-2 migration to aquatic environment

Increased concern has recently emerged pertaining to the occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in aquatic environment during the current coronavirus disease 2019 (COVID-19) pandemic. While infectious SARS-CoV-2 has yet to be identified in the aquatic environment, the virus potentially enters the wastewater stream from patient excretions and a precautionary approach dictates evaluating transmission pathways to ensure public health and safety. Although enveloped viruses have presumed low persistence in water and are generally susceptible to inactivation by environmental stressors, previously identified enveloped viruses persist in the aqueous environment from days to several weeks. Our analysis suggests that not only the surface water, but also groundwater, represent SARS-CoV-2 control points through possible leaching and infiltrations of effluents from health care facilities, sewage, and drainage water. Most fecally transmitted viruses are highly persistent in the aquatic environment, and therefore, the persistence of SARS-CoV-2 in water is essential to inform its fate in water, wastewater and groundwater and subsequent human exposure.

Seasonal influences on the use of genetic markers as performance indicators for small wastewater treatment plants

The development of microbial source tracking methods has resulted in an array of genetic faecal markers for assessing human health risks posed from surface water pollution. However, their use as performance metrics at wastewater treatment plants (WWTPs) has not been explored extensively. Here we compared three Bacteroides (HF183, HumM2, AllBac) and two E. coli (H8, RodA) genetic markers for summer and winter performance monitoring at twelve small rural (<250 PE) and three larger WWTPs in NE England. Small WWTPs are of interest because they are poorly understood and their impact on surface water quality may be underestimated. Overall, genetic marker data showed significant differences in treatment performance at smaller versus larger WWTPs. For example, effluent abundances of HF183 and HumM2 were significantly higher in smaller systems (p = 0.003 for HumM2; p = 0.02 for HF183). Genetic markers also showed significant differences in performance between seasons (p < 0.01, n = 120), with human-specific markers (i.e., HF183, HumM2, H8) being generally better for summer WWTP monitoring. In contrast, Bacteroides markers were much more suitable for winter monitoring, possibly because the E. coli markers are less sensitive to differences in temperature and sunlight conditions. Overall, Bacteroides markers best described WWTP treatment performance across all samples, although seasonal differences suggest caution is needed when markers are used for performance monitoring. Genetic markers definitely provide rapid and new information about WWTP performance, but more spatially diverse studies are needed to refine their use for routine WWTP monitoring.

CrAssphage abundance and correlation with molecular viral markers in Italian wastewater

Current fecal indicators for environmental health monitoring are primarily based on fecal indicator bacteria (FIB) which do not accurately represent viral pathogens. There is a need for highly abundant, human-associated viral fecal indicators to represent viral pathogens in sewage-contaminated water. In the present study, we evaluate the abundance of the emerging viral fecal indicator crAssphage in 156 Italian wastewater samples collected between 2014 and 2018. Samples were collected using two separate viral concentration methods, glycine-CF and PEG-dextran and qPCR assays were run for crAssphage (CPQ56) and Human Polyomavirus (HPyV) and endpoint PCR assays were run for Human Bocavirus (HBoc) and Hepatitis E Virus (HepE). CrAssphage was detected in 96% of samples and no statistically significant difference was observed in crAssphage abundance between concentration methods (p = 0.39). CrAssphage concentrations also did not correlate with location (latitude) or size (load and capacity) of the wastewater treatment plant. HPyV detection rates with the glycine-CF and PEG-dextran methods were 64% and 100%, respectively, and the concentrations of HPyV were statistically significantly influenced by the concentration method (p < 0.0001). CrAssphage was measured at significantly higher concentrations than HPyV for both concentration methods (p < 0.0001). The observed concentration ranges were 3.84-7.29 log₁₀GC/100 mL for crAssphage and 3.45-5.17 log₁₀GC/100 mL for HPyV. There was a strong positive correlation between crAssphage and HPyV abundance for both concentration methods; however, the slope of the correlation depended on the concentration method. CrAssphage presence correlated with the presence of HBoc in samples concentrated with glycine-CF, but did not correlate with the presence of HBoc concentrated with the PEG-dextran method or with the presence of HepE. Overall, these results demonstrate that crAssphage is an abundant viral fecal indicator in wastewater with statistically significant correlation with human viral pathogens (e.g., HPyV) and viral concentration methods influence the interpretation of fecal viral indicator detection.

Potential indicators of virus transport and removal during soil aquifer treatment of treated wastewater effluent

Increased water demands have led to a notable interest in the use of treated wastewater for reuse. Typically, this results from the implementation of advanced treatment of final effluent from wastewater treatment plants prior to reuse for potable or non-potable purposes. Soil aquifer treatment (SAT) is a natural treatment process in which water from sources of varying quality is infiltrated into the soil to further improve its quality. The goal of this study was to determine the log₁₀ reduction values (LRVs) of viruses naturally present in treated effluent and evaluate two potential indicators of virus removal and transport, pepper mild mottle virus (PMMoV) and crAssphage, during SAT of treated effluent. Groundwater was sampled at three wells with different attributes within the Sweetwater Recharge Facility (SWRF) in Tucson, AZ. These sites vary greatly in operational parameters such as effluent infiltration rates and wetting/drying cycles, which may influence virus removal efficiency. Detection of adenovirus, enterovirus, PMMoV, and crAssphage were determined by qPCR/RT-qPCR and log₁₀ reduction values (LRVs) were determined. PMMoV and crAssphage were detected in groundwater associated with a set of recharge basins that exhibited shorter wetting/drying cycles and faster infiltration rates. LRVs for crAssphage and PMMoV at this site ranged from 3.9 to 5.8, respectively. Moreover, PMMoV was detected downflow of the SAT sites, indicating the potential degradation of microbial groundwater quality in the region surrounding managed aquifer recharge facilities. Overall, PMMoV and crAssphage showed potential as conservative process indicators of virus removal during SAT, particularly for attribution of LRV credits. Moreover, the detection of these viruses indicated the potential influence of wetting/drying cycles on virus removal by SAT, a parameter that has not yet been studied with respect to biological contaminants.