Correlation of quantitative PCR for a poultry-specific brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter

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.

Grazing Effects on Bovine-Associated and Background Fecal Indicator Bacteria Levels in Edge-of-Field Runoff

Excessive levels of fecal indicator bacteria are a major cause of water quality impairment. Grazing and its management may significantly impact bacteria concentrations; however, other sources can contribute to water quality issues both in the presence and absence of cattle, thus confounding results. In this study, we utilize Bacteroides markers to evaluate bacteria loading from cattle versus background sources in runoff from rotationally grazed and ungrazed pastures and how grazing management, timing of runoff in relation to grazing events, and stocking rate affect Bacteroides marker (AllBac and BoBac) levels and ratios and their relation to E. coli concentrations in runoff at the small watershed scale. The data suggest that the AllBac and BoBac levels were not significantly impacted by grazing management or stocking rate; however, the timing of runoff events in relation to grazing events significantly impacted the levels of these markers found in runoff. Furthermore, the BoBac/AllBac ratio confirmed that fecal contamination present in runoff when sites were destocked for over two weeks largely originated from sources other than cattle. Thus, the magnitude and proportion of cattle impacts on fecal indicator bacteria in edge-of-field runoff were dramatically reduced shortly after de-stocking. However, background sources continued to contribute significant concentrations of E. coli.

Variable fecal source prioritization in recreational waters routinely monitored with viral and bacterial general indicators

Somatic and F+ coliphage methods are under consideration as potential routine surface water quality monitoring tools to identify unsafe levels of fecal pollution in recreational waters. However, little is known about the cooccurrence of these virus-based fecal indicators and host-associated genetic markers used to prioritize key pollution sources for remediation. In this study, paired measurements of cultivated coliphage (somatic and F+) and bacterial (E. coli and enterococci) general fecal indicators and genetic markers indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), canine (DG3), and avian (GFD) fecal pollution sources were assessed in 365 water samples collected from six Great Lakes Basin beach and river sites over a 15-week recreational season. Water samples were organized into groups based on defined viral and bacterial fecal indicator water quality thresholds and average log10 host-associated genetic marker fecal score ratios were estimated to compare pollutant source inferences based on variable routine water quality monitoring practices. Eligible log10 fecal score ratios ranged from -0.051 (F+ coliphage, GFD) to 2.08 (enterococci, Rum2Bac). Using a fecal score ratio approach, findings suggest that general fecal indicator selection for routine water quality monitoring can influence the interpretation of host-associated genetic marker measurements, in some cases, prioritizing different pollutant sources for remediation. Variable trends were also observed between Great Lake beach and river sites suggesting disparate management practices may be useful for each water type.

Validation of microbial source tracking markers for the attribution of fecal contamination in indoor-household environments of the Peruvian Amazon

The performance of eight microbial source tracking (MST) markers was evaluated in a low-resource, tropical community located in Iquitos, Peru. Fecal samples from humans, dogs, cats, rats, goats, buffalos, guinea-pigs, chickens, ducks, pigeons, and parrots were collected (n = 117). All samples were tested with human (BacHum, HF183-Taqman), dog (BactCan), pig (Pig-2-Bac), and avian (LA35, Av4143, ND5, cytB) markers using quantitative PCR (qPCR). Internal validity metrics were calculated using all animal fecal samples, as well as animal fecal samples contextually relevant for the Peruvian Amazon. Overall, Pig-2-Bac performed best, with 100% sensitivity and 88.5% specificity to detect the correct fecal source. Human-associated markers showed a sensitivity of 80.0% and 76.7%, and specificity of 66.2% and 67.6%. When limiting the analysis to contextually relevant animal fecal samples for the Peruvian Amazon, Av143 surpassed cytB with 95.7% sensitivity and 81.8% specificity. BactCan demonstrated 100% sensitivity and 47.4% specificity. The gene copy number detected by BacHum and HF183-Taqman were positively correlated (Pearson's correlation coefficient: 0.785), as well as avian markers cytB with Av4143 (Pearson's correlation coefficient: 0.508) and nd5 (Pearson's correlation coefficient: 0.949). These findings suggest that markers such as Av4143, Pig2Bac, cytb and BacHum have acceptable performance to be impactful in source attribution studies for zoonotic enteric disease transmission in this and similar low-resource communities.

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.

Verification of Bacteroidales 16S rRNA markers as a complementary tool for detecting swine fecal pollution in the Yangtze Delta

To correctly assess and properly manage the public health risks associated with exposure to contaminated water, it is necessary to identify the source of fecal pollution in a watershed. In this study, we evaluated the efficacy of our two previously developed real time-quantitative PCR (qPCR) assays for the detection of swine-associated Bacteroidales genetic markers (gene 1-38, gene 3-53) in the Yangtze Delta watershed of southeastern China. The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy (92.5%, 91.7% conditional probability, respectively) in detecting Bacteroidales spp. in water samples. According to binary logistic regression (BLR), these two swine-associated markers were well correlated (P < 0.05) with fecal indicators (Escherichia coli and Enterococci spp.) and zoonotic pathogens (E. coli O157: H7, Salmonella spp. and Campylobacter spp.) in water samples. In contrast, concentrations of conventional fecal indicator bacteria (FIB) were not correlated with zoonotic pathogens, suggesting that they are noneffective at detecting fecal pollution events. Collectively, the results obtained in this study demonstrated that a swine-targeted qPCR assay based on two Bacteroidales genes markers (gene 1-38, gene 3-53) could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.

Enhanced insights from human and animal host-associated molecular marker genes in a freshwater lake receiving wet weather overflows

This study investigated the magnitude of wet weather overflow (WWO)-driven sewage pollution in an urban lake (Lake Parramatta) located in Sydney, New South Wales, Australia. Water samples were collected during a dry weather period and after two storm events, and tested for a range of novel and established sewage- [Bacteroides HF183, crAssphage CPQ_056 and pepper mild mottle virus (PMMoV)] and animal feces-associated (Bacteroides BacCan-UCD, cowM2 and Helicobacter spp. associated GFD) microbial source tracking marker genes along with the enumeration of culturable fecal indicator bacteria (FIB), namely Escherichia coli (E. coli) and Enterococcus spp. The magnitude of general and source-specific fecal pollution was low in water samples collected during dry weather compared to storm events. The levels of HF183, crAssphage and PMMoV in water samples collected during storm events were as high as 6.39, 6.33 and 5.27 log10 GC/L of water, respectively. Moderate to strong positive correlations were observed among the quantitative occurrence of sewage-associated marker genes. The concentrations of HF183 and PMMoV in most storm water samples exceeded the risk benchmark threshold values established in the literature for primary contact recreators. None of the samples tested was positive for the cowM2 (cow) marker gene, while BacCan-UCD (dog) and GFD (avian) animal-associated markers were sporadically detected in water samples collected from both dry weather and storm events. Based on the results, the ongoing advice that swimming should be avoided for several days after storm events appears appropriate. Further research to determine the decay rates of sewage-associated marker genes in relation to each other and enteric viruses would help refine current advice. Microbial source tracking approaches employed in this study provided insights into sources of contamination over currently used FIB.

Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed

Fecal pollution management remains one of the biggest challenges for water quality authorities worldwide. Advanced fecal pollution source identification technologies are now available that can provide quantitative information from many animal groups. As public interest in these methodologies grows, it is vital to use standardized procedures with clearly defined data acceptance metrics and conduct field studies demonstrating the use of these techniques to help resolve real-world water quality challenges. Here we apply recently standardized human-associated qPCR methods with custom data acceptance metrics (HF183/BacR287 and HumM2), along with established procedures for ruminant (Rum2Bac), cattle (CowM2 and CowM3), canine (DG3 and DG37), and avian (GFD) fecal pollution sources to (i) demonstrate the feasibility of implementing standardized qPCR procedures in a large-scale field study, and (ii) characterize trends in fecal pollution sources in the research area. A total of 602 water samples were collected over a one-year period at 29 sites along the Trask, Kilchis, and Tillamook rivers and tributaries in the Tillamook Bay Watershed (OR, USA). Host-associated qPCR results were combined with high-resolution geographic information system (GIS) land use and general indicator bacteria (E. coli) measurements to elucidate water quality fecal pollution trends. Results demonstrate the feasibility of implementing standardized fecal source identification qPCR methods with established data acceptance metrics in a large-scale field study leading to new investigative leads suggesting that elevated E. coli levels may be linked to specific pollution sources and land use activities in the Tillamook Bay Watershed.

Novel crAssphage marker genes ascertain sewage pollution in a recreational lake receiving urban stormwater runoff

Considerable efforts have been made in recent years in developing novel marker genes for fecal pollution tracking in environmental waters. CrAssphage are recently discovered DNA bacteriophage that are highly abundant in human feces and untreated sewage. In this study, we evaluated the host-sensitivity and -specificity of the newly designed crAssphage qPCR assays (Stachler et al., 2017) CPQ_056 and CPQ_064 (i.e., marker genes) in fecal samples collected from various human and several animal host groups in Australia. We also investigated the utility of these marker genes to detect sewage pollution in an urban recreational lake (i.e., Lake Parramatta) in Sydney, NSW. The mean concentrations of CPQ_056 and CPQ_064 marker genes in untreated sewage were 9.43 ± 0.14 log₁₀ GC/L and 8.91 ± 0.17 log₁₀ GC/L, respectively, 2 to 3 orders of magnitude higher than other sewage-associated viruses used in microbial source tracking studies. Among 177 animal fecal samples tested from 11 species, the host-specificity values for CPQ_056 and CPQ_064 marker genes were 0.95 and 0.93, respectively. Limited cross-reactivity was observed with cat fecal and cattle wastewater samples. Abundance of crAssphage markers were monitored in an urban lake that receives stormwater runoff. The concentrations of both markers were higher (CPQ_056 ranging from 3.40 to 6.04 log₁₀ GC/L and CPQ_064 ranging from 2.90 to 5.47 log₁₀ GC/L) in 20 of 20 (for CPQ_056) and 18 of 20 (for CPQ_064) samples collected after storm events with gauged sewer overflows compared to dry weather event (10 of 10 samples were qPCR negative for the CPQ_056 and 8 of 10 were negative for the CPQ_064 marker genes) suggesting sewage pollution was transported by urban stormwater runoff to Lake Parramatta. The results of the study may provide context for management of sewage pollution from gauged overflow points of the sewerage system in the catchment.

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

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

Toward Forensic Uses of Microbial Source Tracking

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

Transport and attenuation of Salmonella enterica, fecal indicator bacteria and a poultry litter marker gene are correlated in soil columns

Millions of tons of fecal-contaminated poultry litter are applied to U.S. agricultural fields annually. Precipitation and irrigation facilitate transport of fecal-derived pathogens and fecal indicator bacteria (FIB) to groundwater. The goal of this study was to compare transport of pathogens, FIB, and a microbial source tracking marker gene for poultry litter (LA35) in a simulated soil-to-groundwater system. Nine laboratory soil columns containing four different soil types were used to evaluate microbial transport to groundwater via infiltration. Quantitative polymerase chain reaction was used to monitor Salmonella enterica Typhimurium, Escherichia coli, Enterococcus spp., Brevibacterium sp. LA35 and Bacteroidales leached from soil columns inoculated with poultry litter. S. enterica was correlated with LA35 poultry litter marker gene and FIB concentrations in column soils containing organic matter, but not in acid washed sands. In contrast, S. enterica was found to correlate with LA35 and FIB in the leachate from columns containing sand, but not with leachate from organic soil columns. The majority of recovered DNA was found in leachate of predominately sandy soil columns, and in the soil of loamy columns. At least 90% of the DNA retained in soils for each microbial target was found in the top 3cm of the column. These studies suggest that poultry litter associated pathogens and FIB are rapidly released from litter, but are influenced by complex attenuation mechanisms during infiltration, including soil type. This study advances our understanding of the potential for subsurface transport of poultry litter associated pathogens and FIB, and support the use of the LA35 marker gene for evaluating poultry litter impacts on groundwater.

Spatiotemporal variation of bacterial water quality and the relationship with pasture land cover

Pathogens are a major cause of water quality impairment and public health concern world-wide. In the United States, each state is tasked with developing water quality standards (WQS) to protect the designated use(s) of waterbodies. Several streams in the Illinois River Watershed in northwest Arkansas are currently listed as impaired due to elevated levels of pathogens. Our objective was to evaluate Escherichia coli (E. coli) numbers at 29 stream sites, compare these numbers to the applicable WQS, and investigate the relationship between E. coli numbers and land cover variables. E. coli numbers in samples collected at most sites were within allowable limits, although there were several instances of violations of the WQS. Violations were variable from year to year at some sites, and elevated levels of E. coli were spatially localized during baseflow. Violations also were positively related to pasture land cover in the drainage area, and particularly within the riparian buffer area. This relationship was non-linear, or threshold based, where there was a significant increase in the mean E. coli exceedances when riparian pasture land cover was greater than approximately 50%. These results can be used to identify specific stream reaches where E. coli numbers might be elevated and the implementation of best management practices can be geographically targeted.

Within-House Spatial Distribution of Fecal Indicator Bacteria in Poultry Litter

Land application of poultry litter is often considered to be a major source of water pollutants in poultry-producing regions. However, reported levels of fecal indicator microorganisms in litter vary widely, with considerable variation possible within houses and across farms, depending on management practices. Therefore, a study was conducted to determine the levels and distribution of indicator microorganisms within 12 broiler farms representing three companies. Within each house, litter samples were collected from around the feed line, water line, north wall, cool pad end, middle, and fan end. Litter moisture content was significantly different within the houses, with the litter being driest around the feed line (19.8%) and wettest around the water line (40.7%). Mean levels of total coliforms, , enterococci, and were 3.7, 3.3, 6.4, and 4.0 log colony-forming units g dry litter, respectively. Levels of total coliforms, , and were positively correlated with litter moisture content, but enterococci levels were not. Consequently, levels of total coliforms, , and , as well as enterococci, were highest around the water line and lowest around the feed line. These results indicate that areas with higher litter water content are more likely to contain higher levels of most fecal indicator microorganisms. Approaches to reduce litter water content in these areas would not only benefit the microbial quality of litter for land application but would also likely improve in-house disease control.

Utility of Helicobacter spp. associated GFD markers for detecting avian fecal pollution in natural waters of two continents

Avian fecal droppings may negatively impact environmental water quality due to the presence of high concentrations of fecal indicator bacteria (FIB) and zoonotic pathogens. This study was aimed at evaluating the performance characteristics and utility of a Helicobacter spp. associated GFD marker by screening 265 fecal and wastewater samples from a range of avian and non-avian host groups from two continents (Brisbane, Australia and Florida, USA). The host-prevalence and -specificity of this marker among fecal and wastewater samples tested from Brisbane were 0.58 and 0.94 (maximum value of 1.00). These values for the Florida fecal samples were 0.30 (host-prevalence) and 1.00 (host-specificity). The concentrations of the GFD markers in avian and non-avian fecal nucleic acid samples were measured at a test concentration of 10 ng of nucleic acid at Brisbane and Florida laboratories using the quantitative PCR (qPCR) assay. The mean concentrations of the GFD marker in avian fecal nucleic acid samples (5.2 × 10(3) gene copies) were two orders of magnitude higher than non-avian fecal nucleic acid samples (8.6 × 10(1) gene copies). The utility of this marker was evaluated by testing water samples from the Brisbane River, Brisbane and a freshwater creek in Florida. Among the 18 water samples tested from the Brisbane River, 83% (n = 18) were positive for the GFD marker, and the concentrations ranged from 6.0 × 10(1)-3.2 × 10(2) gene copies per 100 mL water. In all, 92% (n = 25) water samples from the freshwater creek in Florida were also positive for the GFD marker with concentrations ranging from 2.8 × 10(1)-1.3 × 10(4) gene copies per 100 mL water. Based on the results, it can be concluded that the GFD marker is highly specific to avian host groups, and could be used as a reliable marker to detect the presence and amount of avian fecal pollution in environmental waters.

LA35 Poultry Fecal Marker Persistence Is Correlated with That of Indicators and Pathogens in Environmental Waters

Disposal of fecally contaminated poultry litter by land application can deliver pathogens and fecal indicator bacteria (FIB) into receiving waters via runoff. While water quality is regulated by FIB enumeration, FIB testing provides inadequate information about contamination source and health risk. This microbial source tracking (MST) study compared the persistence of the Brevibacterium sp. strain LA35 16S rRNA gene (marker) for poultry litter with that of pathogens and FIB under outdoor, environmentally relevant conditions in freshwater, marine water, and sediments over 7 days. Salmonella enterica, Campylobacter jejuni, Campylobacter coli, Bacteroidales, and LA35 were enumerated by quantitative PCR (qPCR), and Enterococcus spp. and E. coli were quantified by culture and qPCR. Unlike the other bacteria, C. jejuni was not detectable after 48 h. Bacterial levels in the water column consistently declined over time and were highly correlated among species. Survival in sediments ranged from a slow decrease over time to growth, particularly in marine microcosms and for Bacteroidales. S. enterica also grew in marine sediments. Linear decay rates in water (k) ranged from -0.17 day(-1) for LA35 to -3.12 day(-1) for C. coli. LA35 levels correlated well with those of other bacteria in the water column but not in sediments. These observations suggest that, particularly in the water column, the fate of LA35 in aquatic environments is similar to that of FIB, C. coli, and Salmonella, supporting the hypothesis that the LA35 marker gene can be a useful tool for evaluating the impact of poultry litter on water quality and human health risk.

Run-off studies demonstrate parallel transport behaviour for a marker of poultry fecal contamination and Staphylococcus aureus

AIMS

To determine whether poultry litter marker gene LA35 is correlated with pathogens and fecal indicator bacteria (FIB) in run-off from poultry litter-amended plots.

METHODS AND RESULTS

A rainfall simulator with various vegetative filter strip lengths was employed to evaluate the correlation of a microbial source tracking (MST) marker for poultry feces/litter (the 16S rRNA gene of Brevibacterium sp. LA35 [LA35] measured by quantitative PCR) with pathogens and FIB in run-off. LA35 was correlated with Staphylococcus aureus, Escherichia coli, Enterococcus spp. and Bacteroidales levels. Salmonella was present at low concentration in litter, but became undetectable by qPCR in run-off. Escherichia coli, LA35 and Staph. aureus exhibited mass-based first flush behaviour in the run-off.

CONCLUSIONS

Correlation of LA35 with FIB and pathogens in run-off from poultry litter-amended fields suggest comparable transport mechanisms and that LA35 is a useful tracer for harmful bacteria in the environment released from poultry litter.

SIGNIFICANCE AND IMPACT OF THE STUDY

To protect human health, an effective marker for poultry fecal contamination should exhibit similar fate and transport characteristics compared to pathogens. This study is among the first to demonstrate such a relationship in run-off for a MST marker.

Comparison of two poultry litter qPCR assays targeting the 16S rRNA gene of Brevibacterium sp

Chicken feces commonly contain human pathogens and are also important sources of fecal pollution in environmental waters. Consequently, methods that can detect chicken fecal pollution are needed in public health and environmental monitoring studies. In this study, we compared a previously developed SYBR green qPCR assay (LA35) to a novel TaqMan qPCR assay (CL) for the environmental detection of poultry-associated fecal pollution. We tested both assays against chicken litter (n = 40), chicken fecal samples (n = 186), non-chicken fecal sources (n = 484), and environmental water samples (n = 323). Most chicken litter samples (i.e., ≥ 98%) were positive for both assays with relatively high signal intensities, whereas only 23% and 12% of poultry fecal samples (n = 186) were positive with the LA35 and the CL assays, respectively. Data using fecal samples from non-target animal species showed that the assays are highly host-associated (≥ 95%). Bayesian statistical models showed that the two assays are associated with relatively low probability of false-positive and false-negative signals in water samples. The CL marker had a lower prevalence than the LA35 assay when tested against environmental water samples (i.e., 21% vs. 31% positive signals). However, by combining the results from the two assays the detection levels increased to 41%, suggesting that using multiple assays can improve the detection of chicken-fecal pollution in environmental waters.

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.

Sewage pollution in urban stormwater runoff as evident from the widespread presence of multiple microbial and chemical source tracking markers

The concurrence of human sewage contamination in urban stormwater runoff (n=23) from six urban catchments across Australia was assessed by using both microbial source tracking (MST) and chemical source tracking (CST) markers. Out of 23 stormwater samples human adenovirus (HAv), human polyomavirus (HPv) and the sewage-associated markers; Methanobrevibacter smithii nifH and Bacteroides HF183 were detected in 91%, 56%, 43% and 96% of samples, respectively. Similarly, CST markers paracetamol (87%), salicylic acid (78%) acesulfame (96%) and caffeine (91%) were frequently detected. Twenty one samples (91%) were positive for six to eight sewage related MST and CST markers and remaining two samples were positive for five and four markers, respectively. A very good consensus (>91%) observed between the concurrence of the HF183, HAv, acesulfame and caffeine suggests good predictability of the presence of HAv in samples positive for one of the three markers. High prevalence of HAv (91%) also suggests that other enteric viruses may also be present in the stormwater samples which may pose significant health risks. This study underscores the benefits of employing a set of MST and CST markers which could include monitoring for HF183, adenovirus, caffeine and paracetamol to accurately detect human sewage contamination along with credible information on the presence of human enteric viruses, which could be used for more reliable public health risk assessments. Based on the results obtained in this study, it is recommended that some degree of treatment of captured stormwater would be required if it were to be used for non-potable purposes.

Evaluation of bovine feces-associated microbial source tracking markers and their correlations with fecal indicators and zoonotic pathogens in a Brisbane, Australia, reservoir

This study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB), Campylobacter spp., Escherichia coli O157, and Salmonella spp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for the Campylobacter 16S rRNA and E. coli O157 rfbE genes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens.

Tracking the primary sources of fecal pollution in a tropical watershed in a one-year study

A study was conducted to determine the primary sources of fecal pollution in a subtropical watershed using host-specific assays developed in temperate regions. Water samples (n = 534) from 10 different sites along the Rio Grande de Arecibo (RGA) watershed were collected mostly on a weekly basis (54 sampling events) during 13 months. DNA extracts from water samples were used in PCR assays to determine the occurrence of fecal bacteria (Bacteroidales, Clostridium coccoides, and enterococci) and human-, cattle-, swine-, and chicken-specific fecal sources. Feces from 12 different animals (n = 340) and wastewater treatment samples (n = 16) were analyzed to determine the specificity and distribution of host-specific assays. The human-specific assay (HF183) was found to be highly specific, as it did not cross-react with nontarget samples. The cattle marker (CF128) cross-reacted to some extent with swine, chicken, and turkeys and was present in 64% of the cattle samples tested. The swine assays showed poor host specificity, while the three chicken assays showed poor host distribution. Differences in the detection of host-specific markers were noted per site. While human and cattle assays showed moderate average detection rates throughout the watershed, areas impacted by wastewater treatment plants and cattle exhibited the highest prevalence of these markers. When conditional probability for positive signals was determined for each of the markers, the results indicated higher confidence levels for the human assay and lower levels for all the other assays. Overall, the results from this study suggest that additional assays are needed, particularly to track cattle, chicken, and swine fecal pollution sources in the RGA watershed. The results also suggest that the geographic stability of genetic markers needs to be determined prior to conducting applied source tracking studies in tropical settings.

Molecular diversity of Bacteroidales in fecal and environmental samples and swine-associated subpopulations

Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600 bp in length) Bacteroidales 16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major Bacteroidales populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive to swine fecal sources and detected in swine-contaminated waters. Phylogenetic and diversity analyses revealed that some markers previously believed to be highly specific to swine populations are shared by multiple hosts, potentially explaining the cross-amplification signals obtained with nontargeted hosts. These data suggest that while many Bacteroidales populations are cosmopolitan, others exhibit a preferential host distribution and may be able to survive different environmental conditions. This study further demonstrates the importance of elucidating the diversity patterns of targeted bacterial groups to develop more inclusive fecal source tracking applications.

Evaluation of the nifH gene marker of Methanobrevibacter smithii for the detection of sewage pollution in environmental waters in Southeast Queensland, Australia

This study aimed at evaluating the host-specificity and -sensitivity of the nifH gene marker of Methanobrevibacter smithii by screening 272 fecal and wastewater samples from 11 animal species including humans in Southeast Queensland (SEQ), Australia. In addition, environmental water samples (n = 21) were collected during the dry and wet weather conditions and tested for the presence of the nifH marker along with other sewage-associated markers, namely, enterococci surface protein (esp) found in Enterococci faecium, Bacteroides HF183, adenoviruses (AVs), and polyomaviruses (PVs). The overall host-specificity of the nifH marker to differentiate between human and animal feces was 0.96 (maximum value of 1), while the overall sensitivity of this marker in human sourced feces and wastewater was 0.81 (maximum value of 1). Among the 21 environmental water samples tested, 2 (10%), 3 (14%), 12 (57%), 6 (29%), and 6 (29%) were positive for the nifH, esp, HF183, AVs and PVs markers, respectively. The prevalence of the nifH marker in environmental water samples, however, was low compared to other markers, suggesting that the use of this marker alone may not be sensitive enough to detect fecal pollution in environmental waters. The nifH marker, however, appears to be sewage-specific in SEQ, Australia, and therefore, it is recommended that this marker should be used as an additional marker in combination with the HF183 or viral markers such as AVs or PVs for accurate and sensitive detection of fecal pollution in SEQ waterways.

Test of direct and indirect effects of agrochemicals on the survival of fecal indicator bacteria

Water bodies often receive agrochemicals and animal waste carrying fecal indicator bacteria (FIB) and zoonotic pathogens, but we know little about the effects of agrochemicals on these microbes. We assessed the direct effects of the pesticides atrazine, malathion, and chlorothalonil and inorganic fertilizer on Escherichia coli and enterococcal survival in simplified microcosms held in the dark. E. coli strain composition in sediments and water column were positively correlated, but none of the agrochemicals had significant direct effects on E. coli strain composition or on densities of culturable FIBs. In a companion study, microcosms with nondisinfected pond water and sediments were exposed to or shielded from sunlight to examine the potential indirect effects of atrazine and inorganic fertilizer on E. coli. The herbicide atrazine had no effect on E. coli in dark-exposed microcosms containing natural microbial and algal communities. However, in light-exposed microcosms, atrazine significantly lowered E. coli densities in the water column and significantly increased densities in the sediment compared to controls. This effect appears to be mediated by the effects of atrazine on algae, given that atrazine significantly reduced phytoplankton, which was a positive and negative predictor of E. coli densities in the water column and sediment, respectively. These data suggest that atrazine does not directly affect the survival of FIB, rather that it indirectly alters the distribution and abundance of E. coli by altering phytoplankton and periphyton communities. These results improve our understanding of the influence of agricultural practices on FIB densities in water bodies impacted by agricultural runoff.