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

Assessing the nucleic acid decay of human wastewater markers and enteric viruses in estuarine waters in Sydney, Australia

This research investigated the in-situ decay rates of four human wastewater-associated markers (Bacteroides HF183 (HF183), Lachnospiraceae Lachno3 (Lachno3), cross-assembling phage (crAssphage), pepper mild mottle virus (PMMoV) and three enteric viruses (human adenovirus 40/41 (HAdV 40/41), enterovirus (EV) and human norovirus GII (HNoV GII) in two estuarine water environments (Davidson Park (DP) and Hen and Chicken Bay (HCB) in temperate Sydney, NSW, Australia, employing qPCR and RT-qPCR assays. The study also aimed to compare decay rates observed in mesocosms with previously published laboratory microcosms, providing insights into the persistence of markers and viruses in estuarine environments. Results indicated varying decay rates between DP and HCB mesocosms, with HF183 exhibiting relatively faster decay rates compared to other markers and enteric viruses in sunlight and dark mesocosms. In DP mesocosms, HF183 decayed the fastest, contrasting with PMMoV, which exhibited the slowest. Sunlight induced higher decay rates for all markers and viruses in DP mesocosms. In HCB sunlight mesocosms, HF183 nucleic acid decayed most rapidly compared to other markers and enteric viruses. In dark mesocosms, crAssphage showed the fastest decay, while PMMoV decayed at the slowest rate in both sunlight and dark mesocosms. Comparisons with laboratory microcosms revealed faster decay of markers and enteric viruses in laboratory microcosms than the mesocosms, except for crAssphage and HAdV 40/41 in dark, and PMMoV in sunlight mesocosms. The study concludes that decay rates of markers and enteric viruses vary between estuarine mesocosms, emphasizing the impact of sunlight exposure, which was potentially influenced by the elevated turbidity at HCB estuarine waters. The generated decay rates contribute valuable insights for establishing site-specific risk-based thresholds of human wastewater-associated markers.

Assessing the defecation practices of unsheltered individuals and their contributions to microbial water quality in an arid, urban watershed

Outdoor defecation by people experiencing homelessness is frequently perceived as a potentially large source of human fecal pollution and a significant source of health risk in urban waterbodies with recreational contact. The goal of this study was to count the number of people experiencing homelessness and quantifies their sanitation habits in an urban river corridor setting, then use this information for estimating human fecal pollutant loading on a watershed scale. Two types of census counts were conducted including periodic point-in-time counts over six years and weekly counts of encampments. While the population census varied from count-to-count, the range of population estimates in the river corridor varied from 109 to 349 individuals during the six-year span, which mirrored the weekly counts of encampments. A face-to-face survey of people experiencing homelessness assessed the sanitation habits of the unsheltered population (N = 63), including outdoor defecation frequency and containment practices. Overall, 95 % of survey respondents reported defecating outdoors; 36 % practiced outdoor defecation between 4 and 7 days/week and 27 % practiced outdoor defecation <1 day/week. Of those that did practice outdoor defecation, 75 % contained their feces in a bucket or bag, thereby limiting fecal material contributions to the river; 6.7 % reported defecating on low ground near the river that could wash off when flood waters rise during a storm event. Only a single survey respondent reported defecating directly into the river. Based on literature values for average HF183 output for an adult human, and the average rainfall in the urban watershed, the total watershed contribution of HF183 averaged 1.2 × 1010 gene copies per storm event (95 % CI: 0.9 × 1010-1.6 × 1010) along the 41 km stretch of river in this study. This human fecal loading estimate is at least two orders of magnitude less than cumulative HF183 loading from all human sources measured at the bottom of the watershed.

Evaluation of crAssphages as a potential marker of human viral contamination in environmental water and fresh leafy greens

CrAssphages are human gut bacteriophages with potential use as an indicator of human fecal contamination in water and other environmental systems. We determined the prevalence and abundance of crAssphages in water, food, and fecal samples and compared these estimates with the prevalence of norovirus. Samples were tested using two crAssphage-specific qPCR assays (CPQ056 and TN201-203) and for norovirus using TaqMan realtime RT-PCR. CrAssphage was detected in 40% of human fecal specimens, 61% of irrigation water samples, 58.5% of stream water samples, and 68.5% of fresh leafy greens samples. Interestingly, across all sample categories, crAssphage concentrations were 2-3 log10 higher than norovirus concentrations. The correlation of detection of crAssphage and norovirus was significant for the irrigation water samples (r = 0.74, p = 7.4e-06). Sequences obtained from crAssphage positive samples from human fecal and stream water samples phylogenetically clustered with genotype I crAssphages, whereas sequences derived from irrigation water samples clustered differently from other genotypes. Our data show that crAssphages were prevalent in norovirus-positive water samples and in fresh leafy green samples, there was a strong correlation between the presence of crAssphage and norovirus. CrAssphage genomic copies were consistently higher than norovirus copies in all sample types. Overall, our findings suggest that crAssphages could be used as reliable indicators to monitor fecal-borne virus contamination within the food safety chain.

Microbial source tracking of fecal pollution to coral reef lagoons of Norfolk Island, Australia

Fecal pollution contributes to global degradation of water quality and requires identification of the source(s) for predicting human health risk, tracking disease, and developing management strategies. While fecal indicator bacteria are commonly used to detect fecal pollution, they cannot identify sources. Novel approaches, such as microbial source tracking (MST), can be applied to evaluate the origin of fecal pollution. This study examined fecal pollution in the coral reef lagoons of Norfolk Island, Australia where reef health decline has been related to nutrient input. The primary objective of this study was to evaluate the host sensitivity and specificity of two human wastewater-associated marker genes (Bacteroides HF183 (HF183) and cross-assembly phage (crAssphage)) and four animal feces associated marker genes targeting avian, ruminant, dog, and pig (Helicobacter-associated GFD (GFD), Bacteroides BacR (BacR), Bacteroides DogBact (DogBact), and Bacteroides Pig-2-Bac (Pig-2-Bac)) in wastewater and animal fecal samples collected from Norfolk Island. The prevalence and concentrations of these marker genes along with enterococci genetic marker (ENT 23S rRNA) of general fecal pollution and human adenovirus (HAdV), which is considered predominantly a pathogen but also a human-wastewater associated marker gene, were determined in surface, ground, and marine water resources. A secondary objective of this study was to assess the sources and pathways of fecal pollution to a sensitive marine environment under rainfall events. HF183, crAssphage, HAdV, and BacR demonstrated absolute host sensitivity values of 1.00, while GFD and Pig-2-Bac had host sensitivity values of 0.60, and 0.20, respectively. Host specificity values were > 0.94 for all marker genes. Human and animal (avian, ruminant, dog) fecal sources were present in the coral reef lagoons and surface water whereas groundwater was polluted by human wastewater markers. This study provides understanding of fecal pollution in water resources on Norfolk Island, Australia after precipitation events. The results may aid in effective water quality management, mitigating potential adverse effects on both human and environmental health.

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.

Meta-analysis of microbial source tracking for the identification of fecal contamination in aquatic environments based on data-mining

Microbial source tracking (MST) technology represents an innovative approach employed to trace fecal contamination in environmental water systems. The performance of primers may be affected by amplification techniques, target primer categories, and regional differences. To investigate the influence of these factors on primer recognition performance, a meta-analysis was conducted on the application of MST in water environments using three databases: Web of Science, Scopus, and PubMed (n = 2291). After data screening, 46 studies were included in the final analysis. The investigation encompassed Polymerase Chain Reaction (PCR)/quantitative PCR (qPCR) methodologies, dye-based (SYBR)/probe-based (TaqMan) techniques, and geographical differences of a human host-specific (HF183) primer and other 21 additional primers. The results indicated that the primers analyzed were capable of differentiating host specificity to a certain degree. Nonetheless, by comparing sensitivity and specificity outcomes, it was observed that virus-based primers exhibited superior specificity and recognition capacity, as well as a stronger correlation with human pathogenicity in water environments compared to bacteria-based primers. This finding highlights an important direction for future advancements. Moreover, within the same category, qPCR did not demonstrate significant benefits over conventional PCR amplification methods. In comparing dye-based and probe-based techniques, it was revealed that the probe-based method's advantage lay primarily in specificity, which may be associated with the increased propensity of dye-based methods to produce false positives. Furthermore, the heterogeneity of the HF183 primer was not detected in China, Canada, and Singapore respectively, indicating a low likelihood of regional differences. The variation among the 21 other primers may be attributable to regional differences, sample sources, detection techniques, or alternative factors. Finally, we identified that economic factors, climatic conditions, and geographical distribution significantly influence primer performance.

High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers

Contamination of water with bacterial, viral, and protozoan pathogens can cause human diseases. Both humans and nonhumans can release these pathogens through their feces. To identify the sources of fecal contamination in the water environment, microbial source tracking (MST) approaches have been developed; however, the relationship between MST markers and pathogens is still not well understood most likely due to the lack of comprehensive datasets of pathogens and MST marker concentrations. In this study, we developed a novel microfluidic quantitative PCR (MFQPCR) platform for the simultaneous quantification of 37 previously validated MST markers, two fecal indicator bacteria (FIB), 22 bacterial, 11 viral, and five protozoan pathogens, and three internal amplification/process controls in many samples. The MFQPCR chip was applied to analyze pathogen removal rates during the wastewater treatment processes. In addition, multiple host-specific MST markers, FIB, and pathogens were successfully quantified in human and avian-impacted surface waters. While the genes for pathogens were relatively infrequently detected, positive correlations were observed between some potential pathogens such as Clostridium perfringens and Mycobacterium spp., and human MST markers. The MFQPCR chips developed in this study, therefore, can provide useful information to monitor and improve water quality.

Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study

With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.

Widespread human waste pollution in surface waters observed throughout the urbanized, coastal communities of Lee County, Florida, USA

The coastal communities of Lee County, Florida, USA have grown rapidly since the 1970s. In this county, drainage ditches, canals, creeks, and the Caloosahatchee River Estuary often have high concentrations of nutrients and bacteria limiting their designated uses. Septic systems have previously been identified as a major pollution source in some areas of Lee County; therefore, this study sought to identify the extent of this issue throughout the county. To accomplish this, surface water samples were collected at 25 ditch, creek, or canal sites suspected of human waste contamination from septic systems in various drainage basins throughout Lee County during January 2020-January 2021. Water samples were analyzed for nutrients, dual stable nitrate isotopes (δ¹⁵N-NO₃^-, δ¹⁸O-NO₃^-), fecal indicator bacteria (enterococci, Escherichia coli), a molecular tracer of human waste (HF183), and chemical tracers of human waste (the artificial sweetener sucralose, pharmaceuticals). Particulate organic matter (POM) and macrophytes were also collected and analyzed for stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopes, as well as elemental composition (C:N:P). To broaden the assessment of stable isotope values and C:N:P, archived macrophyte samples from 2019 were also included in analyses. Ammonium concentrations were high (> 4.3 μM) in 55 % of samples. Fecal bacteria were high in 66 % of samples. HF183 was detected in 50 % of samples and positively correlated with enterococci (r = 0.32). Sucralose concentrations were high (> 380 ng/L) in 54 % of samples, while carbamazepine was detected in 40 % of samples. Human waste N sources were indicated by δ¹⁵N > 3.00 ‰ at 44 % of sites by δ¹⁵N-NO₃^-, 68 % of sites by POM, and at 100 % of sites where macrophyte samples were collected. This large-scale study provides evidence of widespread human waste pollution throughout Lee County and can help guide infrastructure improvements to promote sustainable development. These findings should be applicable to urbanized regions globally that are experiencing declines in water quality and harmful algal blooms due to development with inadequate infrastructure.

Microbial source tracking of untreated human wastewater and animal scats in urbanized estuarine waters

The study assessed the performance characteristics of host sensitivity, host specificity and concentration for seven human wastewater- and six animal scat-associated marker genes by analysing human wastewater and animal scat samples from urban catchments of the mega-coastal city of Sydney, Australia. Absolute host sensitivity was exhibited across three criteria used to assess seven human wastewater-associated marker genes of cross-assembly phage (CrAssphage), human adenovirus (HAdV), Bacteroides HF183 (HF183), human polyomavirus (HPyV), Lachnospiraceae (Lachno3), Methnobrevibacter smithii nifH (nifH) and pepper mild mottle virus (PMMoV). In contrast, only the horse scat-associated marker gene Bacteroides HoF597 (HoF597) exhibited absolute host sensitivity. The absolute host specificity value of 1.0 was returned for the wastewater-associated marker genes of HAdV, HPyV, nifH and PMMoV for each of the three applied host specificity calculation criteria, while values of >0.9 were returned for CrAssphage and Lachno3. Ruminants and cow scat-associated marker genes of BacR and CowM2, respectively exhibited the absolute host specificity value of 1.0. Concentrations of Lachno3 were greater in most human wastewater samples followed by CrAssphage, HF183, nifH, HPyV, PMMoV and HAdV. Human wastewater marker genes were detected in several scat samples from cats and dogs, and this suggests concordant sampling of animal scat-associated marker genes and at least two human wastewater-associated marker genes will be required to assist in interpretation of fecal sources in environmental waters. A greater prevalence, together with several samples with greater concentrations of human wastewater-associated marker genes PMMoV and CrAssphage warrant consideration by water quality managers for the detection of diluted human fecal pollution in estuarine waters.

Microbial source tracking using molecular and cultivable methods in a tropical mixed-use drinking water source to support water safety plans

Microbial contamination deteriorates source water quality, posing a severe problem for drinking water suppliers worldwide and addressed by the Water Safety Plan framework to ensure high-quality and reliable drinking water. Microbial source tracking (MST) is used to examine different microbial pollution sources via host-specific intestinal markers for humans and different types of animals. However, the application of MST in tropical surface water catchments that provide raw water for drinking water supplies is limited. We analyzed a set of MST markers, namely, three cultivable bacteriophages and four molecular PCR and qPCR assays, together with 17 microbial and physicochemical parameters, to identify fecal pollution from general, human-, swine-, and cattle-specific sources. Seventy-two river water samples at six sampling sites were collected over 12 sampling events during wet and dry seasons. We found persistent fecal contamination via the general fecal marker GenBac3 (100 % detection; 2.10-5.42 log₁₀ copies/100 mL), with humans (crAssphage; 74 % detection; 1.62-3.81 log₁₀ copies/100 mL) and swine (Pig-2-Bac; 25 % detection; 1.92-2.91 log₁₀ copies/100 mL). Higher contamination levels were observed during the wet season (p < 0.05). The conventional PCR screening used for the general and human markers showed 94.4 % and 69.8 % agreement with the respective qPCR results. Specifically, in the studied watershed, coliphage could be a screening parameter for the crAssphage marker (90.6 % and 73.7 % positive and negative predictive values; Spearman's rank correlation coefficient = 0.66; p < 0.001). The likelihood of detecting the crAssphage marker significantly increased when total and fecal coliforms exceeded 20,000 and 4000 MPN/100 mL, respectively, as Thailand Surface Water Quality Standards, with odds ratios and 95 % confidence intervals of 15.75 (4.43-55.98) and 5.65 (1.39-23.05). Our study confirms the potential benefits of incorporating MST monitoring into water safety plans, supporting the use of this approach to ensure high-quality drinking water supplies worldwide.

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments

The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.

Improvement of crAssphage detection/quantification method and its extensive application for food safety

Water-borne diseases are usually caused by the fecal-oral transmission of human fecal pathogens. Traditionally, coliforms and enterococci are widely used as indicator bacteria, but they do not allow to differentiate between human and animal fecal contamination. Owing to its presence only in the human gut environment, crAssphage has been suggested as an alternative indicator of human fecal contamination to overcome the above challenges. In this study, 139 human and 89 animal fecal samples (e.g., chicken, cow, dog, pig, pigeon, and mouse) were collected. For the rapid detection of human crAssphage in fecal samples, quantitative real-time PCR (qPCR) was performed using five different oligonucleotide primer/probe combinations. These included three previously reported oligonucleotide primer/probe combinations (RQ, CPQ056, and CrAssBP) and two newly developed combinations (ORF00018-targeting CrAssPFL1 and ORF00044-targeting CrAssPFL2). The detection rate (crAssphage-positive rate) in human fecal samples were 23.0, 30.2, 28.8, 20.1, and 30.9%, respectively, suggesting CrAssPFL2 showed the highest detection rate. Furthermore, the lowest copy numbers (436.16 copy numbers) could be detected using the CrAssPFL2 combination. Interestingly, no difference in crAssphage detection rates was found between healthy people and intestinal inflammatory patients. As expected, no crAssphage was detected in any animal fecal samples, indicating its human specificity. Furthermore, qPCR analysis of sewage samples collected from five different sewage treatment plants revealed that they were all contaminated with 10^5.71 copy numbers/mL of crAssphage on average. The simulation test of crAssphage-contaminated food samples also confirmed that the detection limit was from 10^7.55 copy numbers of crAssphage in foods. Therefore, the newly developed and optimized qPCR would be useful for the sensitive detection of crAssphage while identifying the source of human fecal contamination.

Host-Associated Bacteroides 16S rDNA-Based Markers for Source Tracking of Fecal Pollution in Laguna Lake, Philippines

Sources of fecal contamination in Laguna Lake, Philippines, were identified using a library-independent microbial source tracking method targeting host-associated Bacteroides 16S rDNA-based markers. Water samples from nine lake stations were assessed for the presence of the fecal markers HF183 (human), BoBac (cattle), Pig-2-Bac (swine), and DuckBac (duck) from August 2019 to January 2020. HF183 (average concentration = 1.91 log₁₀ copies/mL) was the most frequently detected, while Pig-2-Bac (average concentration = 2.47 log₁₀ copies/mL) was the most abundant. The detected marker concentrations in different stations corresponded to the land use patterns around the lake. Generally, all marker concentrations were higher during the wet season (August-October), suggesting the effect of rainfall-associated factors on the movement and retention of markers from sources. There was a significant association (ρ = 0.45; p < 0.001) between phosphate and the concentration of HF183, suggesting domestic sewage-derived pollution. The markers had acceptable sensitivity and specificity, i.e., HF183 (S = 0.88; R = 0.99), Pig-2-Bac (S = 1.00; R = 1.00), and DuckBac (S = 0.94; R = 1.00), and therefore may be used for the continuous monitoring of fecal pollution in the lake and in designing interventions to improve the quality of the lake water.

Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates

Escherichia coli has been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identify E. coli microbial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewater E. coli genomes sequenced by us (n = 50) and RefSeq animal E. coli genomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewater E. coli genomes and 3318 RefSeq animal E. coli genomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associated E. coli isolates. These two markers showed higher performance than the previously developed human wastewater-associated E. coli markers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9 % and sensitivity of 25.7 %. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detecting E. coli isolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.

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.

Distribution and correlation between antibiotic resistance genes and host-associated markers before and after swine fever in the longjiang watershed

Antibiotic resistance genes (ARGs) are abundantly shed in feces. Thus, it is crucial to identify their host sources so that ARG pollution can be effectively mitigated and aquatic ecosystems can be properly conserved. Here, spatiotemporal variations and sources of ARGs in the Longjiang watershed of South China were investigated by linking them with microbial source tracker (MST) indicators. The most frequently detected ARGs (>90%) were sulI, sulII, bla_TEM, tetW, ermF, and the mobile element intI1. Spatial distribution analyses showed that tributaries contributed significantly more sulI, sulII, and ermF contamination to the Longjiang watershed than the main channel. MST indicator analysis revealed that the Longjiang watershed was contaminated mainly by human fecal pollution. Livestock- and poultry-associated fecal pollution significantly declined after the swine fever outbreak. The occurrence of most ARGs is largely explained by human fecal pollution. In contrast, pig fecal pollution might account for the prevalence of tetO. Moreover, combined human-pig fecal pollution contributed to the observed bla_NDM-1 distribution in the Longjiang watershed. Subsequent analysis of the characteristics of MST markers disclosed that the relatively lower specificities of BacHum and Rum-2-Bac may lead to inaccurate results of tracking ARG pollution source. The present study determined spatiotemporal variations and ARG origins in the Longjiang watershed by combining MST markers. It also underscored the necessity of using multiple MST markers simultaneously to identify and characterize ARG pollution sources accurately.

Distribution of human fecal marker genes and their association with pathogenic viruses in untreated wastewater determined using quantitative PCR

Quantitative microbial risk assessment (QMRA) of human health risks using human fecal marker genes (HFMGs) is an useful water quality management tool. To inform accurate QMRA analysis, generation of probability distribution functions for HFMGs, and reference pathogenic viruses can be improved by input of correlation and ratios based upon measurement of HFMGs and gene copies (GC) of pathogenic viruses in untreated wastewater. The concentrations of four HFMGs (Bacteroides HF183, Lachnospiraceae Lachno3, CrAssphage and pepper mild mottle virus (PMMoV)), and GC of three reference pathogenic viruses human adenovirus 40/41 (HAdV 40/41), human norovirus GI + GII HNoV GI + GII and enterovirus (EV) were measured in untreated wastewater samples collected over a period of 12 months from two wastewater treatment plants in Sydney, Australia using quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR). Over the course of the study, the GC of potential pathogenic viruses were 3-5 orders of magnitude lower than HFMGs in untreated wastewater. The GC of pathogenic viruses were highly variable over the course of the study, which contrasted with the concentrations of HFMGs that were quite stable with little variation observed within and between WWTPs. Among the HFMGs, HF183, CrAssphage and PMMoV correlated well with pathogenic virus GC, whereas weak or negative correlations were observed between Lachno3 and pathogenic virus GC. While the two assessed WWTPs had dissimilar population service sizes, the ratios between log₁₀ transformed pathogenic virus GC and HFMGs demonstrated similar central tendency and variability for the same combinations between WWTP A and WWTP B with no difference between the WWTPs. This suggests the widespread presence of these HFMGs in both populations serviced by these two WWTPs. The observed correlation and ratios of HFMGs and GC of reference pathogenic viruses can contribute to improved QMRA of human health risks in environmental waters subject to fresh sewer overflows.

Developing a novel Bifidobacterium phage quantitative polymerase chain reaction-based assay for tracking untreated wastewater

Microbial source tracking (MST) tools provide insights on fecal pollution levels in aquatic environments using predominantly quantitative PCR (qPCR) assays that target host-associated molecular marker genes. Existing wastewater-associated marker genes have shown limited or significant cross-reactions with non-human fecal samples. In this study, we mined the current Gut Phage Database (GPD) and designed a novel untreated wastewater-specific Bifidobacterium phage qPCR assay (i.e., Bifi assay). The sensitivity and specificity of the Bifi marker genes were assessed by collectively analyzing untreated (n = 33) and treated (n = 15) wastewater and non-human fecal samples (i.e., Rabbit, mouse, cow, horse, pig, chicken, sheep, dog, deer, kangaroos; n = 113) in Shenzhen, Guangdong Province, China and Brisbane, Australia. Bifi assay revealed 100% host-specificity against non-human fecal samples collected from Shenzhen and Brisbane. Furthermore, this marker gene was also detected in all untreated and treated wastewater samples, whose concentrations ranged from 5.54 to 6.83 log₁₀ GC/L. In Shenzhen, the concentrations of Bifi marker gene were approximately two orders of magnitude lower than Bacteroides (HF183/BacR287 assay) and CrAssphage (CPQ_56 assay). The concentration of Bifi marker gene in untreated wastewater from Brisbane was 1.35 log₁₀ greater than those in Shenzhen. Our results suggest that Bifi marker gene has the potential to detect and quantify the levels of human fecal pollution in Shenzhen and Brisbane. If additional detection sensitivity is required for environmental studies, Bifi marker gene should be paired with either CrAssphage or HF183/BacR287 marker genes.

Microbial source tracking of fecal contamination in stormwater runoff

Concerns over fecal contamination in stormwater canals have promoted the need for pollution control strategies, including the use of microbial source tracking, to identify fecal contamination in the Greater New Orleans Area. Surface water samples were collected over a 12-month period at five canal locations within Jefferson Parish, Louisiana. Quantitative polymerase chain reaction and the IDEXX method were used to assess the concentrations of coliforms, Escherichia coli (E. coli) and human fecal 183 bacteroides (HF183) in stormwater samples. A 100% positive detection rate of total coliforms and E. coli was observed across all tested sites. Despite the closeness of the five sites, when averaged across all sampling time points, Kruskal-Wallis tests indicated that E. coli was present at significantly different concentrations in these locations (χ²(5) = 19.8, p = 0.0005). HF183 was detected in 62% of the water samples collected during the stormwater sampling. Without further testing for HF183 markers, the conclusion from this study would have been that fecal contamination from an unknown source was always present at varying levels during the study period. Analysis of HF183 markers therefore adds another layer of conclusions to the results deductible from E. coli concentrations. A 100% E. coli detection rate, high E. coli concentrations coupled with low rates of HF183 detection particularly at the Esplanade, Poplar Street, and Bonnabel Boat Launch sites, the sites closest to the lake outlet, throughout the study period, indicate that fecal contamination at these stormwater canal sites comes primarily from non-human sources. However, the Metairie Road and Napoleon Avenue sites, which have the highest HF183 detection rates, on top of chronic pollution by other non-human sources, are also influenced by human fecal pollution, possibly because of human development and faulty infrastructure. This study highlights the advantages of the use of microbial source-tracking methods to complement traditional indicator bacteria.

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.

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

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

Microbial Source Tracking as a Method of Determination of Beach Sand Contamination

Beach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring.

Evaluation of crAssphage as a human-specific microbial source-tracking marker in the Republic of Korea

CrAssphage is a novel and by far the most abundant bacteriophage in the human gut and has been proposed as a human-specific microbial source tracking (MST) marker. However, its global use as a human-specific MST marker requires validation in more extensive regions. The purpose of this study was to evaluate the specificity and abundance of the human-specific MST marker crAssphage with PCR and RT-PCR assays in human and animal feces in Korea. The prevalence of crAssphage was confirmed in 94 human feces samples (subjects: 19 to 45 years old) and 56 animal feces samples (from birds, raccoons, squirrels, weasels, deer, wild boars, hares, cats, and dogs). CrAssphage showed sensitivity of 0.39 and specificity of 1.00 in Korea, with a sequencing analysis showing that genotype II was dominant at 71.9%. The quantitative analysis showed that crAssphage is sufficiently abundant in human feces given the high concentration range of 4.26 to 8.25 log gene copies (GC)/ng in human feces. In conclusion, this study confirmed the crAssphage as a specific and abundant MST marker with which to identify human fecal contamination in Korea.

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.

Human Fecal Contamination Corresponds to Changes in the Freshwater Bacterial Communities of a Large River Basin

Microbial water quality is generally monitored by culturable fecal indicator bacteria (FIB), which are intended to signal human health risk due to fecal pollution. However, FIB have limited utility in most urbanized watersheds as they do not discriminate among fecal pollution sources, tend to make up a small fraction of the total microbial community, and do not inform on pollution impacts on the native ecosystem. To move beyond these limitations, we assessed entire bacterial communities and investigated how bacterial diversity relates to traditional ecological and human health-relevant water quality indicators throughout the Milwaukee River Basin. Samples were collected from 16 sites on 5 days during the summer, including both wet and dry weather events, and were processed by 16S rRNA gene amplicon sequencing. Historical water quality at each sampling location, as opposed to upstream land use, was associated significantly with bacterial community alpha diversity. Source partitioning the sequence data was important for determining water quality relationships. Sewage-associated bacterial sequences were detected in all samples, and the relative abundance of sewage sequences was strongly associated with the human Bacteroides fecal marker. From this relationship, we developed a preliminary threshold for human sewage pollution when using bacterial community sequence data. Certain abundant freshwater bacterial sequences were also associated with human fecal pollution, suggesting their possible utility in water quality monitoring. This study sheds light on how bacterial community analysis can be used to supplement current water quality monitoring techniques to better understand interactions between ecological water quality and human health indicators. IMPORTANCE Surface waters in highly developed mixed-use watersheds are frequently impacted by a wide variety of pollutants, leading to a range of impairments that must be monitored and remediated. With advancing technologies, microbial community sequencing may soon become a feasible method for routine evaluation of the ecological quality and human health risk of a water body. In this study, we partnered with a local citizen science organization to evaluate the utility of microbial community sequencing for identifying pollution sources and ecological impairments in a large mixed-use watershed. We show that changes in microbial community diversity and composition are indicative of both long-term ecological impairments and short-term fecal pollution impacts. By source partitioning the sequence data, we also estimate a threshold target for human sewage pollution, which may be useful as a starting point for future development of sequencing-based water quality monitoring techniques.

Integrated analyses of fecal indicator bacteria, microbial source tracking markers, and pathogens for Southeast Asian beach water quality assessment

The degradation of coastal water quality from fecal pollution poses a health risk to visitors at recreational beaches. Fecal indicator bacteria (FIB) are a proxy for fecal pollution; however the accuracy of their representation of fecal pollution health risks at recreational beaches impacted by non-point sources is disputed due to non-human derivation. This study aimed to investigate the relationship between FIB and a range of culturable and molecular-based microbial source tracking (MST) markers and pathogenic bacteria, and physicochemical parameters and rainfall. Forty-two marine water samples were collected from seven sampling stations during six events at two tourist beaches in Thailand. Both beaches were contaminated with fecal pollution as evident from the GenBac3 marker at 88%-100% detection and up to 8.71 log₁₀ copies/100 mL. The human-specific MST marker human polyomaviruses JC and BK (HPyVs) at up to 4.33 log₁₀ copies/100 mL with 92%-94% positive detection indicated that human sewage was likely the main contamination source. CrAssphage showed lower frequencies and concentrations; its correlations with the FIB group (i.e., total coliforms, fecal coliforms, and enterococci) and GenBac3 diminished its use as a human-specific MST marker for coastal water. Human-specific culturable AIM06 and SR14 bacteriophages and general fecal indicator coliphages also showed less sensitivity than the human-specific molecular assays. The applicability of the GenBac3 endpoint PCR assay as a lower-cost prescreening step prior to the GenBac3 qPCR assay was supported by its 100% positive predictive value, but its limited negative predictive values required subsequent qPCR confirmation. Human enteric adenovirus and Vibrio cholerae were not found in any of the samples. The HPyVs related to Vibrio parahaemolyticus, Vibrio vulnificus, and 5-d rainfall records, all of which were more prevalent and concentrated during the wet season. More monitoring is therefore recommended during wet periods. Temporal differences but no spatial differences were observed, suggesting the need for a sentinel site at each beach for routine monitoring. The exceedance of FIB water quality standards did not indicate increased prevalence or concentrations of the HPyVs or Vibrio spp. pathogen group, so the utility of FIB as an indicator of health risks at tropical beaches maybe challenged. Accurate assessment of fecal pollution by incorporating MST markers could lead to developing a more effective water quality monitoring plan to better protect human health risks in tropical recreational beaches.

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.

Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow

Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except bla_VIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.

Occurrence and distributions of human-associated markers in an impacted urban watershed

Numerous genetic markers for microbial source tracking (MST) have been evaluated by testing a panel of target and nontarget faecal samples. However, the performance of MST markers may vary between faecal and water samples, thereby resulting in inaccurate water quality assessment. In this study, a 30-day sampling study was conducted in an urban river impacted by human- and sewage-associated pollution to evaluate the performance of different human-associated markers in environmental water. Additionally, marker decay was assessed via a microcosms approach. Overall, Bacteroidales 16sRNA and crAssphage markers exhibited higher prevalence in the study area, and their detection frequencies exceeded 90%. In contrast, Bacteroidales protein markers exhibited poor detection frequencies compared to other markers, with the prevalence of Hum2 and Hum163 reaching only 63% and 84%, respectively. Regarding marker abundance, there was no significant difference in the detection concentrations between Bacteroidales 16sRNA and crAssphage markers (p > 0.05); however, the concentrations of Bacteroidales protein markers were nearly 1 order of magnitude lower than those of other MST markers. The microcosm experiments indicated that the decay rate of crAssphage markers was significantly lower than that of other bacterial target markers, which may improve their detectability when the pollution source is located far from the sampling site. Due to the observed differences in performance and decay patterns among Bacteroidales 16sRNA, crAssphage, and Bacteroidales protein markers, we recommend the simultaneous use of multiple markers from different target microorganisms to obtain a more comprehensive understanding of the pollution sources. This approach would also provide an accurate assessment of pollution levels and health risks.

A weight-of-evidence approach for identifying potential sources of untreated sewage inputs into a complex urbanized catchment

The Hawkesbury-Nepean River (HNR) is the largest catchment in the Sydney region and is undergoing unprecedented population growth. The HNR system receives a mix of anthropogenic inputs such as treated sewage, stormwater and agricultural runoff. Combined, these can diminish the ecological system health and pose potential concerns to human health. Of particular concern are inputs of untreated sewage, that can occur due to a range of different reasons including illegal point source discharges, failure of the sewerage network, and overloading of wastewater treatment plants during storm events. Here, we present findings of an intensive assessment across the HNR catchment where we used a weight-of-evidence (WOE) approach to identify untreated sewage contamination in surface waters against the background of treated effluent and diffuse inputs during post high flow conditions. Total nitrogen and phosphorus concentrations were used to assess treated effluent and diffuse inputs, and microbial analysis, including both culture-based traditional methods for E. coli and enterococci and qPCR analysis of Bacteroides and Lachnospiraceae, were used to assess raw sewage contamination. Despite a background of diffuse inputs from recent high flow events and the influence of treated wastewater, we found no gradient of faecal contamination along the HNR system or its tributaries. We observed two sites with evidence of untreated sewage contamination, where the human markers Bacteroides and Lachnospiraceae qPCR copy numbers were high. The biological and chemical approaches suggested these latter two hotspots originate from an industrial runoff source and possibly from a dry weather sewage leak. Our findings demonstrate the potential of a WOE approach in the assessment of human faecal signal in an urban river that can also pinpoint small sources of contamination as a strategy that can reshape the way monitoring is performed and the chemical end-points chosen to provide pertinent information on the potential risks to aquatic system health.

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.

Intraday variability of indicator and pathogenic viruses in 1-h and 24-h composite wastewater samples: Implications for wastewater-based epidemiology

We monitored the concentration of indicator viruses crAssphage and pepper mild mottle virus (PMMoV) and human pathogen adenovirus (HAdV) in influent from a wastewater treatment plant in Brisbane, Australia in 1-h and 24-h composite samples. Over three days of sampling, the mean concentration of crAssphage gene copies (GC)/mL in 24-h composite samples did not differ significantly (p = 0.72-0.92), while for PMMoV GC/mL (p value range: 0.0002-0.0321) and HAdV GC/mL (p value range: 0.0028-0.0068) significant differences in concentrations were observed on one day of sampling compared to the other two. For all three viruses, the variation observed in 1-h composite samples was greater than the variation observed in 24-h composite samples. For crAssphage, in 54.1% of 1-h composite samples, the concentration was less than that observed in 24-h composite samples; whereas for PMMoV and HAdV the concentration was less in 79.2 and 70.9% of 1-h composite samples, respectively, compared to the relevant 24-h composite samples. Similarly, the concentration of crAssphage in 1-h compared to 24-h composite samples did not differ (p = 0.1082) while the concentrations of PMMoV (p < 0.0001) and HAdV (p < 0.0001) in 1-h composite samples were significantly different from 24-h composite samples. These results suggest that 24-h composite samples offer increased analytical sensitivity and decreased variability compared to 1-h composite samples when monitoring wastewater, especially for pathogenic viruses with low infection rates within a community. Thus, for wastewater-based epidemiology applications, 24-h composite samples are less likely to produce false negative results and erroneous public health information.

CrAssphage and its bacterial host in cat feces

CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages' cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat's feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.

Assessing the faecal source sensitivity and specificity of ruminant and human genetic microbial source tracking markers in the central Ethiopian highlands

This study tested genetic microbial source tracking (MST) methods for identifying ruminant‐ (BacR) and human‐associated (HF183/BacR287, BacHum) bacterial faecal contaminants in Ethiopia in a newly created regional faecal sample bank (n = 173). BacR performed well, and its marker abundance was high (100% sensitivity (Sens), 95% specificity (Spec), median log₁₀ 8·1 marker equivalents (ME) g⁻¹ ruminant faeces). Human‐associated markers tested were less abundant in individual human samples (median: log₁₀ 5·4 and 4·2 (ME + 1) g⁻¹) and were not continuously detected (81% Sens, 91% Spec for BacHum; 77% Sens, 91% Spec for HF183/BacR287). Furthermore, the pig‐associated Pig2Bac assay was included and performed excellent (100% Sens, 100% Spec). To evaluate the presence of MST targets in the soil microbiome, representative soil samples were tested during a whole seasonal cycle (n = 60). Only BacR could be detected, but was limited to the dry season and to sites of higher anthropogenic influence (log₁₀ 3·0 to 4·9 (ME + 1) g⁻¹ soil). In conclusion, the large differences in marker abundances between target and non‐target faecal samples (median distances between distributions ≥log₁₀ 3 to ≥log₁₀ 7) and their absence in pristine soil indicate that all tested assays are suitable candidates for diverse MST applications in the Ethiopian area.

Interlaboratory accuracy and precision among results of three sewage-associated marker genes in urban environmental estuarine waters and freshwater streams

The application of quantitative polymerase chain reaction (qPCR) based microbial source tracking (MST) marker genes are increasingly being used to identify contaminating sources and inform management decisions. In this study, we assessed interlaboratory agreement on duplicate environmental water samples collected from estuarine and freshwater locations, by comparing results of qPCR based testing for Bacteroides HF183, crAssphage CPQ_056, and pepper mild mottle virus (PMMoV). The overall agreements (co-detection and non-co-detection) between CSIRO Land and Water (CLW) laboratory and Sydney Water (SW) laboratory for the HF183, crAssphage CPQ_056 and PMMoV marker genes for duplicate water samples were 74, 75 and 74%, respectively. Cohene's kappa (k) revealed fair to moderate agreements and acceptable relative percent difference (RPD) values of <15% for duplicate samples. The pooled mean abundances of HF183, CPQ_056, and PMMoV in measurable samples at the CLW laboratory were 5.19 ± 0.93, 5.12 ± 0.82, and 4.42 ± 0.65 log₁₀ copies/L, respectively. However, the pooled mean abundances were significantly lower at the SW laboratory, HF183 (4.58 ± 0.84 log₁₀ copies/L), crAssphage CPQ_056 (4.20 ± 0.63 log₁₀ copies/L), and PMMoV (3.89 ± 0.41 log₁₀ copies/L). At individual sample level, most of the paired samples had <1 log₁₀ difference. Significant positive Spearman rank correlations were obtained between two laboratories for the HF183 (R_s = 0.65; p < 0.05), CPQ_056 (R_s = 0.79; p < 0.05), and PMMoV (R_s = 0.54; p < 0.05) marker genes. Several factors such as standards, qPCR platforms, PCR inhibitors, nucleic acid extraction efficiency and low levels of targets in some samples may have contributed to the observed discrepancies. Results presented in this study highlight the importance of standardized protocol, laboratory equipment (such as digital PCR), sample processing strategies and appropriate quality controls that may need implementation to further improve accuracy and precision of results between laboratories.

Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group

Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.

Prevalence and abundance of traditional and host-associated fecal indicators in urban estuarine sediments: Potential implications for estuarine water quality monitoring

This study aimed to determine the prevalence and abundance of sewage and animal fecal contamination of sediment at seven estuarine locations in Sydney, NSW, Australia. Sediment samples were tested for the occurrence of microbial targets including molecular marker genes of enterococci (ENT), Bacteroides HF183 (HF183), Methanobrevibacter smithii (nifH), human adenovirus (HAdV) and emerging sewage-associated marker genes crAssphage (CPQ_056) and Lachnospiraceae (Lachno3) and animal feces-associated marker genes, including avian feces-associated Helicobacter spp. (GFD), canine-feces associated Bacteroides (DogBact), cattle-feces associated (cowM2) and horse feces-associated Bacteroides (HoF597). Results from this study showed that urban estuarine sediment can act as a reservoir of fecal indicator bacteria (FIB) and several microbial source tracking (MST) marker genes, including previously unreported Lachno3. The sewage-associated marker gene CPQ_056 was most prevalent, in 63.8% of sediment samples, while the avian associated marker gene GFD had the highest mean abundance. The GFD marker gene was highly abundant and widely detected in sediment samples from all seven locations compared to the other animal feces-associated marker genes. In all, 31 (44.9%) sediment samples were positive for at least two sewage-associated marker genes. However, the non-quantifiable detection of the HAdV marker gene did not always align with the detection of two or more sewage-associated marker genes. In addition, the most frequent wet weather overflow exposure occurred at locations that did not have a consistent pattern of detection of the sewage-associated marker genes, suggesting sediments may not be a suitable measure of recent sewage contamination. To assist water quality and public health managers better understand past microbial contamination of estuarine sediment, further studies seem justified to explore the role of decay of MST marker genes in sediment. Further work is also needed on the role of resuspension of MST marker genes from sediment during storm events to the water column as a source of contamination for both the GFD and sewage-associated marker genes.

Relationship between Rainfall, Fecal Pollution, Antimicrobial Resistance, and Microbial Diversity in an Urbanized Subtropical Bay

The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.

Urbanized bays are vulnerable to fecal bacterial pollution, and the extent of this pollution, in marine recreational waters, is commonly assessed by quantifying enterococcus concentrations. Recent reports have questioned the utility of enterococci as an indicator of fecal bacterial pollution in subtropical bays impaired by non-point source pollution, and enterococcus data alone cannot identify fecal bacterial sources (i.e., hosts). The purpose of this study was to assess relationships between rainfall, fecal bacterial pollution, antimicrobial resistance, and microbial diversity in an urbanized subtropical bay. Thus, a comprehensive bacterial source tracking (BST) study was conducted using a combination of traditional and modern BST methods. Findings show that rainfall was directly correlated with elevated enterococcus concentrations, including the increased prevalence of Enterococcus faecium, although it was not correlated with an increase in the prevalence of antimicrobial-resistant strains. Rainfall was also correlated with decreased microbial diversity. In contrast, neither rainfall nor enterococcus concentrations were directly correlated with the concentrations of three omnipresent host-associated fecal markers (i.e., human, canine, and gull). Notably, the human fecal marker (HF183) was inversely correlated with enterococcus concentrations, signifying that traditional enterococcus data alone are not an accurate proxy for human fecal waste in urbanized subtropical bays.

IMPORTANCE The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

PURPOSE OF REVIEW

Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination.

RECENT FINDINGS

This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.

Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution

The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log₁₀ copies/g and 0.41 log₁₀ copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log₁₀ copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.

Identification of reliable marker genes for the detection of canine fecal contamination in sub-tropical Australia

Animal fecal contamination in aquatic environments is a major source of zoonotic diseases in humans. While concerns are focused on livestock, companion animals such as dogs can also be a source of a wide range of zoonotic pathogens. Therefore, detection of dog or canine fecal contamination in aquatic environments is important for mitigating risks. In this study, host-sensitivity and specificity of four canine fecal-associated marker genes were evaluated by analyzing 30 canine and 240 non-canine fecal samples. The application of these markers was also tested in water from an urban river under dry weather conditions. The host sensitivity values of the Bacteroides BacCan-UCD, DogBact, DF113 and DF418 were 1.00, 0.90, 0.83, and 0.90, respectively. The host specificity value of the BacCan-UCD, DogBact, DF113 and DF418 were 0.87, 0.98, 0.83, and 0.41, respectively. The mean concentrations of DF418 were highest (7.82 ± 1.13 log₁₀ gene copies (GC)/g of feces) followed by BacCan-UCD (7.61 ± 1.06 log₁₀ GC/g) and DogBact (7.15 ± 0.92 log₁₀ GC/g). The mean concentration of DF113 (5.80 ± 1.25 log₁₀ GC/g) was 1.5 to 2.5 orders of magnitude lower than the other marker genes. The DogBact marker gene was not detected in any other animal feces other than a small number of untreated sewage samples. The BacCan-UCD marker gene cross-reacted with cat, chicken, and pig fecal samples, while the DF113 marker gene cross-reacted with cat, chicken, cattle fecal and untreated sewage samples. The DF418 marker gene was detected in all sewage and animal feces and deemed not suitable for canine fecal contamination tracking in sub-tropical Australia. Canine fecal contamination was infrequently detected in environmental water samples. Based on the results obtained in this study, we recommend that at least two canine feces-associated marker genes should be used in field studies.

Performance of host-associated genetic markers for microbial source tracking in China

Numerous genetic markers have been developed to establish microbial source tracking (MST) assays in the last decade. However, the selection of suitable markers is challenging due to a lack of understanding of fundamental factors such as sensitivity, specificity, and concentration in target/nontarget hosts, especially in East Asia. In this study, a total of 506 faecal samples comprised of human and 12 nonhuman hosts were collected from 28 cities across China and tested for marker performance characteristics. We firstly tested 40 host-associated markers based on a binary (presence/absence) criterion. Here, 15 markers (7 human-associated, 4 pig-associated, 3 ruminant-associated, and 1 poultry-associated) showed potential applicability in our study area. The selected 15 markers were then tested using qualitative and quantitative methods to characterise their performance. Overall, Bacteroidales markers presented higher sensitivity and concentrations in target samples compared to other bacterial or viral markers, but their specificity was low. Among nontarget samples, pets accounted for 43.7% and 35.7% of cross-reactivity with human-associated and poultry-associated markers, respectively. Noncommon animals, including horse and donkey, contributed 61.3% of cross-reactivity with ruminant-associated markers. When considering the quantitative distribution of markers, their concentration in nontarget samples were 1-3 orders of magnitude lower than in target samples. Moreover, a novel classification method was proposed to classify the nontarget hosts into four groups spanning "no cross-reactivity", "weak cross-reactivity", "moderate cross-reactivity", and "strong cross-reactivity" animal hosts. There were 77.9% nontarget samples identified as no cross-reactivity and weak cross-reactivity hosts, suggesting that these nontarget hosts produce little interference for corresponding markers. Our findings elucidate the performance of host-associated markers around China in a qualitative and quantitative manner, and reveal the interference degree of cross-reactivity from nontarget animals to genetic markers, which will facilitate tracking of multiple faecal pollution sources and planning timely remedial strategies in China.

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.

Sewage-associated marker genes illustrate the impact of wet weather overflows and dry weather leakage in urban estuarine waters of Sydney, Australia

This study investigates the impact of wet weather overflows (WWOs) at three estuarine locations in Sydney, NSW, Australia. WWOs can occur when infiltration of stormwater leads to an excess volume of flow within the sewerage system, resulting in the release of diluted sewage into the environment. Sewage contamination poses a risk to human health due to the presence of pathogens. The magnitude of sewage contamination was monitored using established and novel sewage-associated marker genes, Bacteroides HF183, pepper mild mottle virus (PMMoV), crAssphage CPQ_056, Lachnospiraceae (Lachno3) marker genes along with culturable fecal indicator bacteria (FIB) Escherichia coli (E. coli) and enterococci. Water samples were collected at two water depths (0.5 m below the water surface and 1 m above the bottom surface) during one dry weather and two storm events. Analysis of sewage-associated marker genes showed greater (i.e., 3-5 orders of magnitude) concentrations in water samples collected during the storm events compared to dry weather event. Water samples were also analysed for four animal feces-associated marker genes targeting avian (GFD), dog (BacCan-UCD), cow (cowM2) and horse (HoF597) species to determine the extent of animal fecal contamination. Among the four marker genes, cowM2 and HoF597 could not be detected, while GFD marker gene was consistently present and BacCan-UCD was occasionally detected. Overall results suggested that after rainfall, untreated sewage from WWOs was present at sampling locations. In addition, microbial source tracking (MST) monitoring was able to distinguish the presence of a leaking sewer impacting on the recreational area during dry weather condition. This study demonstrated the capability of the MST monitoring approach to understand sources (sewage or animal) of fecal contamination. This capability will greatly enhance management decisions assisting in the prioritisation of remediation efforts of the sewerage system to improve estuarine bathing water quality and diminish human health risk.

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

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

Integrating Bayesian Analysis and Cumulative Probability Generates High Confidence Using a Single Microbial Source Tracking Marker

Microbial source tracking can identify waterbodies at risk of contamination using host-associated molecular markers. No assay used for microbial source tracking is both 100% host-specific and sensitive for human or animal fecal contamination. Using literature sensitivity and specificity values, Bayes' Theorem for conditional probability was applied to the human fecal-associated HF183 marker in a microbial source tracking context. Type I and Type II error rates were examined across a range of priors. Conditional probabilities were investigated using two human-associated markers, HF183 and HumM2, concurrently. Cumulative probability analysis was used to explore the likelihood of true contaminant detection using multiple samples. Probability of human fecal contamination was calculated for all combinations of positive and negative marker results given three samples. Results demonstrate the respective influence that specificity and sensitivity values exert on the likelihood of true positive and true negative. Using practical priors, high levels of confidence (99%) in results were observed when HF183 and HumM2 were used concurrently. Cumulative probability analyses showed that multiple samples from a single location can provide a >95% level of confidence in positive and negative results, suggesting that when multiple samples are necessary to account for in situ variability, a single marker can yield sufficiently reliable results.

Use of Escherichia coli genes associated with human sewage to track fecal contamination source in subtropical waters

Escherichia coli (E. coli) is frequently used in assessment and regulation of recreational water quality, but it is a general fecal indicator that provides no information about fecal contamination source. Sewage-associated microorganisms and related marker genes have proven useful for microbial source tracking (MST) applications that link fecal contamination to host sources, but many MST marker genes are carried in taxa not used in regulatory contexts. A more direct connection with regulatory concerns, including human health risk and total maximum daily load (TMDL) assessments, could be accomplished with tools such as the human-associated marker genes of E. coli. We evaluated the performance of E. coli H8, H12, H14, and H24 marker genes for detection of domestic sewage at the E. coli isolate level in Florida. E. coli isolates (n = 1, 380) from reference fecal and wastewater samples were first tested by binary PCR for the presence of each H marker gene. H8 and H12 were >90% specific and sensitive for domestic sewage, while H14 and H24 were ≤86% specific. Therefore, quantitative PCR (qPCR) assays were used to quantify H8 and H12 marker genes at the sample level. Specificity values for the H8 and H12 qPCR assays were 96 and 93%, respectively, while both marker genes showed 100% sensitivity. H12 concentrations were tenfold lower in wastewater than H8 (~6-7 log₁₀ gene copies (GC)/100 mL). H8 concentrations in wastewater and contaminated environmental water samples were correlated with the sewage-associated Bacteroides HF183 marker gene. This study suggests that E. coli H genes, and H8 in particular, can be useful for sewage contamination tracking and TMDL development in subtropical waters.