Evaluation of host-specific Bacteroidales 16S rRNA gene markers as a complementary tool for detecting fecal pollution in a prairie watershed

The use of E. coli phylogrouping and microbial source tracking (non-species specific, human-specific, bovine-specific bacteroidales markers) to elucidate hydro(geo)logical contamination mechanisms in southeastern Ontario, Canada

In Ontario, monitoring, maintenance, and treatment of private drinking systems (e.g. wells) are the responsibility of the well owner. Fecal contamination of drinking water threatens public health, particularly in rural communities which are often fully reliant on unregulated private groundwater as a primary drinking water source. Private well users face a higher risk of acute gastrointestinal illness compared to those served by municipally operated systems (Murphy et al., 2016). Accordingly, the current study sought to characterize the fecal indicator, E. coli, isolated from southeastern Ontario private groundwater wells, including phylogroups and host source. Results were examined in the context of antecedent climate and local hydrogeological setting to elucidate likely contaminant sources and pathways. A total of 737 E. coli isolates from 260 private wells were assigned to phylogroups using the Clermont PCR phylotyping method, with likely host source determined using host-specific Bacteroidales 16S rRNA RT qPCR assays. Multivariate models were developed for the main E. coli phylogroups (A, B1, B2, and D) and all microbial source tracking markers. Models were coupled for interpretation where possible, based on associations between phylogroups and MST markers. Preferential subsurface flow, and to a lesser degree, overland flow, were likely mechanisms of contamination across all models. Distinct temporal associations were found based on the fecal source. Multiple models were developed and will be discussed, in an attempt to elucidate source-specific contamination mechanisms, in support of risk assessment and appropriate protective actions.

Bacteroidales as a fecal contamination indicator in fresh produce industry: A baseline measurement

Foodborne outbreaks caused by fecal contamination of fresh produce represent a serious concern to public health and the economy. As the consumption of fresh produce increases, public health officials and organizations have pushed for improvements in food safety procedures and environmental assessments to reduce the risk of contamination. Visual inspections and the establishment of "buffer zones" between animal feeding operations and producing fields are the current best practices for environmental assessments. However, a generalized distance guideline and visual inspections may not be enough to account for all environmental risk variables. Here, we report a baseline measurement surveying the background Bacteroidales concentration, as a quantitative fecal contamination indicator, in California's Salinas Valley. We collected a total of 1632 samples from two romaine lettuce commercial fields at the time of harvesting through two seasons in a year. The quantification of Bacteroidales concentration was performed using qPCR, revealing a notably low concentration (0-2.00 copies/cm2) in the commercial fields. To further enhance the applicability of our findings, we developed a user-friendly method for real-world fecal contamination risk assessment that seamlessly integrates with industry practices. Through the generation of heatmaps that visually illustrate varying risk levels across fields, this approach can identify site-specific risks and offer fresh produce stakeholders a more comprehensive understanding of their land. We anticipate this work can encourage the use of Bacteroidales in the fresh produce industry to monitor fecal contamination and prevent future foodborne outbreaks.

Selection of a diagnostic tool for microbial water quality monitoring and management of faecal contamination of water sources in rural communities

The aim of the current study was to evaluate, validate and select microbial water quality monitoring tools to establish their suitability and feasibility for use in rural communities. The monitoring of water quality was performed at three different levels: i) basic level focusing on sanitary inspection and hydrogen sulphide (H2S) test; ii) intermediate level via enumeration of faecal indicator bacteria (faecal coliforms, Escherichia coli, Enterococcus spp. and Clostridium perfringens); and iii) advanced level based on qPCR detecting host-associated genetic markers (BacHum, BacCow, Cytb, Pig-2-Bac, and BacCan) and pathogens (Vibrio cholerae, Escherichia coli O157:H7, and Shiga toxin-producing Escherichia coli). A positive correlation was recorded between sanitary risk and faecal coliforms (r = 0.613 and p < 0.002), E. coli (r = 0.589 and p < 0.003), and Enterococcus spp. (r = 0.625 and p < 0.003). The H2S test showed positive correlations with sanitary risk score (r = 0.623; p < 0.003), faecal coliforms (r = 0.809; p < 0.001), E. coli (r = 0.779; p < 0.001) and Enterococcus spp. (r = 0.799; p < 0.001). Similar correlation patterns were also found with advanced techniques used for detecting host-associated genetic markers, excepted between Clostridium perfringens, and Pig-2-Bac (pig), BacCan (dog), and V. cholerae. The H2S test and sanitary inspections are therefore suitable and cost-effective tools to capacitate rural areas at household level for the monitoring of faecal contamination and management of water sources.

Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly

Escherichia coli are highly diverse bacteria with different pathogenic types, serotypes and phylogenetic types/phylotypes. In recent years, infections with E. coli have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of E. coli. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-β-lactam resistant and the other was multi-drug resistant (resistant to multiple β-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the de-novo approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N50 value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.

Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India

The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.

The prevalence of potential pathogens in ballast water and sediments of oceangoing vessels and implications for management

Ballast water and sediments can serve as prominent vectors for the widespread dispersal of pathogens between geographically distant areas. However, information regarding the diversity and distribution of the bacterial pathogens in ballast water and sediments is highly limited. In this study, using high-throughput sequencing and quantitative PCR, we investigated the composition and abundance of potential pathogens, and their associations with indicator microorganisms. We accordingly detected 48 potential bacterial pathogens in the assessed ballast water and sediments, among which there were significant differences in the compositions and abundances of pathogenic bacterial communities characterizing ballast water and sediments. Rhodococcus erythropolis, Bacteroides vulgatus, and Vibrio campbellii were identified as predominant pathogens in ballast water, whereas Pseudomonas stutzeri, Mycobacterium paragordonae, and Bacillus anthracis predominated in ballast sediments. Bacteroidetes, Vibrio alginolyticus, Vibrio parahaemolyticus, and Escherichia coli were generally detected with median values of 8.54 × 10³-1.22 × 10⁷ gene copies (GC)/100 mL and 1.16 × 10⁷-3.97 × 10⁹ GC/100 g in ballast water and sediments, respectively. Notably, the concentrations of Shigella sp., Staphylococcus aureus, and V. alginolyticus were significantly higher in ballast sediments than in the water. In addition, our findings tend to confirm that the indicator species specified by the International Maritime Organization (IMO) might underestimate the pathogen risk in the ballast water and sediments, as these bacteria were unable to predict some potential pathogens assessed in this study. In summary, this study provides a comprehensive insight into the spectrum of the potential pathogens that transferred by ship ballast tanks and emphasizes the need for the implementation of IMO convention on ballast sediment management.

Occurrence and distribution of antibiotic resistant bacteria and genes in the Fuhe urban river and its driving mechanism

Antibiotic resistance genes (ARGs) in urban rivers can affect human health via the food chain and human pathogenic bacteria diffusion. Sediment can be a sink for ARGs, causing second sources of ARG contamination through diffusion. Therefore, we evaluated the effects of total petroleum hydrocarbons (TPHs) and phytoplankton on the distribution of the ARGs in the sediment and water of Fuhe river in Baoding city, China. The ARGs and human pathogenic bacteria in urban river were analyzed, and the phytoplankton and bacterial abundance, TPH, and physicochemical parameters ranked using the partial least squares path modelling (PLS-PM) and aggregated boosted tree (ABT) analysis. The main ARGs in Fuhe river sediment were sulfonamide and tetracycline resistance genes, with sul2 exhibiting the highest level. The main human pathogenic bacteria in the pathogens pool were Clostridium, Bacillus and Burkholderiaceae, with Clostridium demonstrating a positive correlation with SulAfolP01. The PLS-PM analysis confirmed that, among the multiple drivers, water physicochemical factors, TPH, phytoplankton, and heavy metals positively and directly affected the ARG profiles in sediment while sediment heavy metals and bacterial communities did the similar effect. These factors (nutrient factors, heavy metals, and TPH) in water and sediment posed the opposite total effect on ARGs in the sediment, suggesting medium factors should have a conclusive effect on the distribution of ARGs in the sediment. The ABT analysis showed that dissolved oxygen (DO), total nitrogen (TN) and Chlorophyta were the most important factors affecting the ARGs distribution in the water, while TN affected the distribution of the genes in the sediment.

Impacts of granular activated carbon addition on anaerobic granulation in blackwater treatment

Upflow anaerobic sludge blanket (UASB) reactors, with or without granular activated carbon (GAC) amendment, were applied for blackwater treatment. The impact of GAC on the formation of granules and biomethane recovery was assessed. High organic loading rates (OLRs) up to 15.7 ± 2.1 kg COD/(m³d) were achieved with both reactors. Similar chemical oxygen demand (COD) removal and methane production rate were observed with OLRs ranging from 5.1 ± 1.0 to 9.3 ± 1.5 kg COD/(m³d). Under higher OLR conditions (13.6 ± 1.1 to 15.7 ± 2.1 kg COD/(m³d)), the GAC-amended UASB achieved a higher COD reduction than the UASB without GAC addition. Interestingly, volatile suspended solids (VSS) concentrations, granule size, and extracellular polymeric substance concentrations were lower in the GAC-amended UASB reactor as compared to the UASB without GAC. The methanogenesis activity of the granules in the GAC-amended UASB reactor was significantly higher than the methanogenesis activity of the UASB granules. The microbes o_Bacteroidales and Syntrophus were predominant in both reactors. The acetoclastic methanogens dominated in the UASB reactor without GAC addition; while hydrogenotrophic methanogens dominated in the GAC-UASB reactor. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that syntrophic acetate oxidation improved with GAC addition. The co-occurrence network indicated that interactions between dominant bacteria and archaea were higher in the GAC-amended UASB reactor than in the UASB reactor without GAC addition. This study demonstrated the improved blackwater treatment performance as a result of granulation in UASB with the addition of GAC.

Estimating cumulative wastewater treatment plant discharge influences on acesulfame and Escherichia coli in a highly impacted watershed with a fully-integrated modelling approach

Wastewater treatment plant (WWTP) discharge is often considered a principal source of surface water contamination. In this study, a three-dimensional fully-integrated groundwater-surface water model was used to simulate the transport characteristics and cumulative loading of an artificial sweetener (acesulfame) and fecal indicator bacteria (Escherichia coli) from WWTPs within a 6800 km² mixed-use, highly impacted watershed in Ontario, Canada. The model, which employed 3.5 × 10⁶ computational nodes and 15 layers, facilitated a comprehensive assessment of groundwater-surface water interactions under high and low flow conditions; processes typically not accounted for in WWTP cumulative effects models. Simulations demonstrate that the model had significant capacity in reproducing the average and transient multi-year groundwater and surface water flow conditions in the watershed. As a proxy human-specific conservative tracer, acesulfame was useful for model validation and to help inform the representation of watershed-scale transport processes. Using a uniform WWTP acesulfame loading rate of 7.14 mg person^-1 day^-1, the general spatial trends and magnitudes of the acesulfame concentration profile along the main river reach within the watershed were reproduced; however, model performance was improved by tuning individual WWTP loading rates. Although instream dilution and groundwater-surface water interactions were strongly dependent on flow conditions, the main reach primarily consisted of groundwater discharge zones. For this reason, hydrodynamic dispersion in the hyporheic zone is shown as the predominant mechanism driving acesulfame into near-stream shallow groundwater, while under high flow conditions, the simulations demonstrate the potential for advective flushing of the shallow groundwater. Regarding the cumulative impact of the WWTPs on E. coli concentrations in the surface flow system, simulated transient E. coli levels downstream of WWTPs in the watershed were significantly lower than observed values, thus highlighting the potential importance of other sources of E. coli in the watershed.

Analysis of Bacterial Community Characteristics, Abundance of Antibiotics and Antibiotic Resistance Genes Along a Pollution Gradient of Ba River in Xi'an, China

The microbial communities in freshwater have raised concerns about the ecosystem and human health. Many ecological environmental problems have been found in urban river because of the unreasonable use and long-term wastewater discharge. In this study, we explored the bacterial community composition, abundance of 14 antibiotics and 21 antibiotic resistance genes (ARGs), and water environment features in seven water samples and seven sediment samples from Ba River in Xi'an, China. Results showed Proteobacteria and Bacteroidetes were the dominant phyla in all samples, and sediment samples had a higher bacterial diversity and richness than it in water. Bacterial communities of site 5 and 6 were clustered in discrepant patterns compared to those at remaining sites from other samples. It might be influenced by nutrients, heavy metals and antibiotics. Antibiotics concentrations ranged from 1.26 to 1.61 × 10³ ng L^-1 in water samples and 1.55 to 4.05 × 10² μg kg^-1 in sediment samples. Sulfamerazine (SM1) and erythromycin (ERY) were the chief antibiotics in water samples, while the level of oxytetracycline (OTC) and cefazolin (CFZ) were higher in sediment samples. Canonical correspondence analysis showed that trimethoprim (TMP) was significantly related to Acinetobacter in W6, and that SM1 and OTC had positive correlation with Arcobacter in W5. The tetC, bla_{TEM ,} ermF and sul1 had higher pollution abundance ranging from 10^-4 to 10⁰ copies/16S rRNA gene copies in all samples. Significant correlations were observed between ARGs and matching antibiotics, suggesting that antibiotics can pose the selective pressure on ARGs in this river. In summary, these finding might provide some new data to the limited information available on the bacterial community characteristics, abundance of antibiotics and ARGs in urban river of China.

Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds - A review

In New Zealand, there is substantial potential for microbial contaminants from agricultural fecal sources to be transported into waterways. The flow and transport pathways for fecal contaminants vary at a range of scales and is dependent on chemical, physical and biological attributes of pathways, soils, microorganisms and landscape characteristics. Understanding contaminant transport pathways from catchment to stream can aid water management strategies. It is not practical, however to conduct direct field measurement for all catchments on the fate and transport of fecal pathogens due to constraints on time, personnel, and material resources. To overcome this problem, fecal source tracking can be utilised to link catchment characteristics to fecal signatures identifying critical sources. In this article, we have reviewed approaches to identifying critical sources and pathways for fecal microorganisms from agricultural sources, and make recommendations for the appropriate use of these fecal source tracking (FST) tools.

Enterococcal Concentrations in a Coastal Ecosystem Are a Function of Fecal Source Input, Environmental Conditions, and Environmental Sources

Fecal pollution at coastal beaches requires management efforts to address public health and economic concerns. Feces-borne bacterial concentrations are influenced by different fecal sources, environmental conditions, and ecosystem reservoirs, making their public health significance convoluted. In this study, we sought to delineate the influences of these factors on enterococcal concentrations in southern Maine coastal recreational waters. Weekly water samples and water quality measurements were conducted at freshwater, estuarine, and marine beach sites from June through September 2016. The samples were analyzed for total and particle-associated enterococcal concentrations, total suspended solids, and microbial source tracking markers (PCR: Bac32, HF183, CF128, DF475, and Gull2; quantitative PCR [qPCR]: AllBac, HF183, and GFD). Water, soil, sediment, and marine sediment samples were also subjected to 16S rRNA sequencing and SourceTracker analysis to determine the influence from these environmental reservoirs on water sample microbial communities. Enterococcal and particle-associated enterococcal concentrations were elevated in freshwater, but the concentrations of suspended solids were relatively similar. Mammal fecal contamination was significantly elevated in the estuary, with human and bird fecal contaminant levels similar between sites. A partial least-squares regression model indicated particle-associated enterococcal and mammal marker concentrations had the most significant positive relationships with enterococcal concentrations across marine, estuary, and freshwater environments. Freshwater microbial communities were significantly influenced by underlying sediment, while estuarine/marine beach communities were influenced by freshwater, high tide height, and estuarine sediment. Elevated enterococcal levels were reflective of a combination of increased fecal source input, environmental sources, and environmental conditions, highlighting the need for encompassing microbial source tracking (MST) approaches for managing water quality issues.IMPORTANCE Enterococci have long been the federal standard in determining water quality at estuarine and marine environments. Although enterococci are highly abundant in the intestines of many animals, they are not exclusive to that environment and can persist and grow outside fecal tracts. This presents a management problem for areas that are largely impaired by nonpoint source contamination, as fecal sources might not be the root cause of contamination. This study employed different microbial source tracking methods for delineating the influences from fecal source input, environmental sources, and environmental conditions to determine which combination of variables are influencing enterococcal concentrations in recreational waters at a historically impaired coastal town. The results showed that fecal source input, environmental sources, and conditions all play roles in influencing enterococcal concentrations. This highlights the need to include an encompassing microbial source tracking approach to assess the effects of all important variables on enterococcal concentrations.

Human-Associated Lachnospiraceae Genetic Markers Improve Detection of Fecal Pollution Sources in Urban Waters

The human microbiome contains many organisms that could potentially be used as indicators of human fecal pollution. Here we report the development of two novel human-associated genetic marker assays that target organisms within the family Lachnospiraceae Next-generation sequencing of the V6 region of the 16S rRNA gene from sewage and animal stool samples identified 40 human-associated marker candidates with a robust signal in sewage and low or no occurrence in samples from nonhuman hosts. Two were chosen for quantitative PCR (qPCR) assay development using longer sequences (the V2 to V9 regions) generated from clone libraries. Validation of these assays with these markers, designated Lachno3 and Lachno12, was performed using fecal samples (n = 55) from cat, dog, pig, cow, deer, and gull sources, and the results were compared with those of established host-associated assays (the Lachno2 marker and two human Bacteroides markers, the HB and HF183/BacR287). Each of the established assays cross-reacted with samples from at least one other animal species, including animals common in urban areas. The Lachno3 and Lachno12 markers were primarily human associated; however, the Lachno12 marker demonstrated low levels of cross-reactivity with samples from select cows and nonspecific amplification with samples from pigs. This limitation may not be problematic when testing urban waters. These novel markers resolved ambiguous results from previous investigations of stormwater-impacted waters, demonstrating their utility. The complexity of the microbiome in humans and animals suggests that no single organism is strictly specific to humans, and the use of multiple complementary markers in combination will provide the highest resolution and specificity for assessing fecal pollution sources.IMPORTANCE Traditional fecal indicator bacteria do not distinguish animal from human fecal pollution, which is necessary to evaluate health risks and mitigate pollution sources. Assessing water in urban areas is challenging, since the water can be impacted by sewage, which has a high likelihood of carrying human pathogens, as well as pet and urban wildlife waste. We demonstrate that the Lachno3 and Lachno12 markers are human associated and highly specific for the detection of human fecal pollution from urban sources, offering reliable identification of fecal pollution sources in urban waters.

Validation of host-specific Bacteroidales quantitative PCR assays and their application to microbial source tracking of drinking water sources in the Kathmandu Valley, Nepal

AIMS

To validate host-specific Bacteroidales assays to identify faecal-source contamination of drinking water sources in the Kathmandu Valley, Nepal.

METHODS AND RESULTS

A total of 54 composite faecal-source samples were collected from human sewage, ruminants, pigs, dogs, chickens and ducks, which were analysed by quantitative polymerase chain reaction using human-specific (BacHum, HF183 SYBR, gyrB and HF183 TaqMan), ruminant-specific (BacCow and BacR), pig-specific (Pig2Bac and PF163) and dog-specific assays (BacCan SYBR). The BacHum, BacR and Pig2Bac assays were judged the best performing human-specific, ruminant-specific and pig-specific assays respectively. The BacCan SYBR assay highly cross-reacted with other species, resulting in poor performance. Furthermore, these validated assays were applied to microbial source tracking (MST) of 74 drinking water samples. Out of these, 20, 12 and 4% samples were judged contaminated by human, ruminant and pig faeces respectively. Detection ratios of human and ruminant faecal markers were relatively higher in built-up and agricultural areas respectively.

CONCLUSION

BacHum, BacR and Pig2Bac assays were found suitable for MST and both, human and animal faecal contaminations of drinking water sources were common in the valley.

SIGNIFICANCE AND IMPACT OF THE STUDY

MST could be an effective tool for preparing the faecal pollution strategies as these are site specific.

PCR data and comparative performance of Bacteroidales microbial source tracking genetic markers

We reported modified endpoint PCR results analyzed by universal and human-, swine-, and cattle-specific Bacteroidales gene markers with human sewage and animal fecal samples (i.e., swine, cattle, chicken, goat, sheep, buffalo, and duck) from Tha Chin and Chao Phraya watersheds. Annealing locations of PCR primers were illustrated by maps of 16s rRNA Bacteroidales genes. We also summarized previously published work on the performance of the PCR assays. For further discussion of the data presented here, please refer to Somnark et al., Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds, Environ. Pollut. 236 (2018) 100–110.

Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds

Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixteen endpoint and quantitative PCR (qPCR) assays targeting universal and human-, swine-, and cattle-specific Bacteroidales gene markers were modified for endpoint PCR, evaluated for their performance with sewage and fecal samples from the Tha Chin watershed and subsequently validated with samples from the Chao Phraya watershed, Thailand. Sample sizes of 81 composite samples (from over 1620 individual samples) of farm animals of each type as well as 19 human sewage samples from the Tha Chin watershed were calculated using a stratified random sampling design to achieve a 90% confidence interval and an expected prevalence (i.e., desired assay's sensitivity) of 0.80. The best universal and human-, swine-, and cattle-specific fecal markers were BacUni EP, HF183/BFDrev EP, Pig-2-Bac EP, and Bac3 assays, respectively. The detection limits for these assays ranged from 30 to 3000 plasmid copies per PCR. The positive predictive values were high in universal and swine- and cattle-specific markers (85-100%), while the positive predictive value of the human-specific assay was 52.2%. The negative predictive values in all assays were relatively high (90.8-100%). A suite of PCR assays in Thailand was established for potential MST use in environmental waters, which supports the worldwide applicability of Bacteroidales gene markers. This study also emphasizes the importance of using a proper sample size in assessing the performance of MST markers in a new geographic region.

Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates

Escherichia coli is an important microorganism in the gastrointestinal tract of warm-blooded animals. Commensal populations of E. coli consist of stable genetic isolates, which means that each individual has only one phylogenetic group (phylogroup). We evaluated the frequency of human commensal E. coli phylogroups from 116 people and observed that the majority of isolates belonged to group A. We also evaluated the frequency of phylogroups in wastewater samples and found a strong positive correlation between the phylogroup distribution in wastewater and human hosts. In order to find out if some factors, such as geographical location, and climate could influence the worldwide phylogroup distribution, we performed a meta-analysis of 39 different studies and 24 countries, including different climates, living areas, and feeding habits. Unexpectedly, our results showed no substructuring patterns of phylogroups; indicating there was no correlation between phylogroup distribution and geographic location, climate, living area, feeding habits, or date of collection.

A case study characterizing animal fecal sources in surface water using a mitochondrial DNA marker

Water quality impairment by fecal waste in coastal watersheds is a public health issue. The present study provided evidence for the use of a mitochondrial (mtDNA) marker to detect animal fecal sources in surface water. The accurate identification of fecal pollution is based on the notion that fecal microorganisms preferentially inhabit a host animal's gut environment. In contrast, mtDNA host-specific markers are inherent to eukaryotic host cells, which offers the advantage by detecting DNA from the host rather than its fecal bacteria. The present study focused on sampling water presumably from non-point sources (NPS), which can increase bacterial and nitrogen concentrations to receiving water bodies. Stream sampling sites located within the Piscataqua River Watershed (PRW), New Hampshire, USA, were sampled from a range of sites that experienced nitrogen inputs such as sewer and septic systems and suburban runoff. Three mitochondrial (mtDNA) gene marker assays (human, bovine, and canine) were tested from surface water. Nineteen sites were sampled during an 18-month period. Analyses of the combined single and multiplex assay results showed that the proportion of occurrence was highest for bovine (15.6%; n = 77) compared to canine (5.6%; n = 70) and human (5.7%; n = 107) mtDNA gene markers. For the human mtDNA marker, there was a statistically significant relationship between presence vs. absence and land use (Fisher's test p = 0.0031). This result was evident particularly for rural suburban septic, which showed the highest proportion of presence (19.2%) compared to the urban sewered (3.3%), suburban sewered (0%), and agricultural (0%) as well as forested septic (0%) sites. Although further testing across varied land use is needed, our study provides evidence for using the mtDNA marker in large watersheds.

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments. OTU patterns were found impacted by combined sewer overflows (CSO) through an observed increase in diversity from the sewer to the hyporheic sediments. These changes appeared driven by direct transfers of bacterial contaminants from wastewaters but also by organic inputs favoring previously undetectable bacterial groups among sediments. These NGS datasets appeared more sensitive at tracking community changes than MST markers. The human-specific MST marker HF183 was strictly detected among CSO-impacted surface waters and not river bed sediments. The ruminant-specific DNA marker was more broadly distributed but intense bovine pollution was required to detect transfers from surface water to benthic and hyporheic sediments. Some OTU showed distribution patterns in line with these MST datasets such as those allocated to the Aeromonas, Acinetobacter, and Pseudomonas. Fecal indicators (Escherichia coli and total thermotolerant coliforms) were detected all over the river course but their concentrations were not correlated with MST ones. Overall, MST and NGS datasets suggested a poor colonization of river sediments by bovine and sewer bacterial contaminants. No environmental outbreak of these bacterial contaminants was detected.

Human fecal and pathogen exposure pathways in rural Indian villages and the effect of increased latrine coverage

Efforts to eradicate open defecation and improve sanitation access are unlikely to achieve health benefits unless interventions reduce microbial exposures. This study assessed human fecal contamination and pathogen exposures in rural India, and the effect of increased sanitation coverage on contamination and exposure rates. In a cross-sectional study of 60 villages of a cluster-randomized controlled sanitation trial in Odisha, India, human and domestic animal fecal contamination was measured in community tubewells and ponds (n = 301) and via exposure pathways in homes (n = 354), using Bacteroidales microbial source tracking fecal markers validated in India. Community water sources were further tested for diarrheal pathogens (rotavirus, adenovirus and Vibrio cholerae by quantitative PCR; pathogenic Escherichia coli by multiplex PCR; Cryptosporidium and Giardia by immunomagnetic separation and direct fluorescent antibody microscopy). Exposure pathways in intervention and control villages were compared and relationships with child diarrhea examined. Human fecal markers were rarely detected in tubewells (2.4%, 95%CI: 0.3-4.5%) and ponds (5.6%, 95%CI: 0.8-10.3%), compared to homes (35.4%, 95%CI: 30.4-40.4%). In tubewells, V. cholerae was the most frequently detected pathogen (19.8%, 95%CI: 14.4-25.2%), followed by Giardia (14.8%, 95%CI: 10.0-19.7%). In ponds, Giardia was most often detected (74.5%, 95%CI: 65.7-83.3%), followed by pathogenic E. coli (48.1%, 95%CI: 34.8-61.5%) and rotavirus (44.4%, 95%CI: 34.2-54.7%). At village-level, prevalence of fecal pathogen detection in community drinking water sources was associated with elevated prevalence of child diarrhea within 6 weeks of testing (RR 2.13, 95%CI: 1.25-3.63) while within homes, higher levels of human and animal fecal marker detection were associated with increased risks of subsequent child diarrhea (P = 0.044 and 0.013, respectively). There was no evidence that the intervention, which increased functional latrine coverage and use by 27 percentage points, reduced human fecal contamination in any tested pathway, nor the prevalence of pathogens in water sources. In conclusion, the study demonstrates that (1) improved sanitation alone may be insufficient and further interventions needed in the domestic domain to reduce widespread human and animal fecal contamination observed in homes, (2) pathogens detected in tubewells indicate these sources are microbiologically unsafe for drinking and were associated with child diarrhea, (3) domestic use of ponds heavily contaminated with multiple pathogens presents an under-recognized health risk, and (4) a 27 percentage point increase in improved sanitation access at village-level did not reduce detectable human fecal and pathogen contamination in this setting.

Contamination with bacterial zoonotic pathogen genes in U.S. streams influenced by varying types of animal agriculture

Animal waste, stream water, and streambed sediment from 19 small (<32km(2)) watersheds in 12U.S. states having either no major animal agriculture (control, n=4), or predominantly beef (n=4), dairy (n=3), swine (n=5), or poultry (n=3) were tested for: 1) cholesterol, coprostanol, estrone, and fecal indicator bacteria (FIB) concentrations, and 2) shiga-toxin producing and enterotoxigenic Escherichia coli, Salmonella, Campylobacter, and pathogenic and vancomycin-resistant enterococci by polymerase chain reaction (PCR) on enrichments, and/or direct quantitative PCR. Pathogen genes were most frequently detected in dairy wastes, followed by beef, swine and poultry wastes in that order; there was only one detection of an animal-source-specific pathogen gene (stx1) in any water or sediment sample in any control watershed. Post-rainfall pathogen gene numbers in stream water were significantly correlated with FIB, cholesterol and coprostanol concentrations, and were most highly correlated in dairy watershed samples collected from 3 different states. Although collected across multiple states and ecoregions, animal-waste gene profiles were distinctive via discriminant analysis. Stream water gene profiles could also be discriminated by the watershed animal type. Although pathogen genes were not abundant in stream water or streambed samples, PCR on enrichments indicated that many genes were from viable organisms, including several (shiga-toxin producing or enterotoxigenic E. coli, Salmonella, vancomycin-resistant enterococci) that could potentially affect either human or animal health. Pathogen gene numbers and types in stream water samples were influenced most by animal type, by local factors such as whether animals had stream access, and by the amount of local rainfall, and not by studied watershed soil or physical characteristics. Our results indicated that stream water in small agricultural U.S. watersheds was susceptible to pathogen gene inputs under typical agricultural practices and environmental conditions. Pathogen gene profiles may offer the potential to address both source of, and risks associated with, fecal pollution.

Temporal variation in the prevalence and species richness of Campylobacter spp. in a prairie watershed impacted by urban and agricultural mixed inputs

Campylobacter spp. are a substantial cause of gastroenteritis worldwide. Human infection can result from ingestion of contaminated food or water from a variety of sources, including the consumption of fresh produce that is contaminated with the pathogen via the use of contaminated irrigation water. Using molecular methods, we investigated the occurrence of Campylobacter in the Qu’Appelle River watershed, an important source of irrigation water for vegetable producers in southern Saskatchewan, Canada. Water samples were collected from 7 sampling sites from April to September 2009 (145 samples), and from 5 sampling sites from May to October 2013 (116 samples). Campylobacter was detected in 57% and 16% of the samples collected in 2009 and 2013, respectively. Campylobacter detection was highest in May and June for both sampling years. In 2009, the predominant species were Campylobacter lari and Campylobacter jejuni, with prevalences of 84% and 41%, respectively. Other Campylobacter spp. were detected less frequently. Only C. lari was detected in 2013. The results in 2009 demonstrate the species richness of Campylobacter in water sources within the watershed. The occurrence of Campylobacter in the study area also underscores the importance of monitoring irrigation water used to irrigate fresh produce from a public health prospective.

Fecal pollution source tracking in waters intended for human supply based on archaeal and bacterial genetic markers

The determination of fecal pollution sources in aquatic ecosystems is essential to estimate associated health risks. In this study, we evaluate eight microbial source tracking (MST) markers including host-specific Bacteroidales and Methanobrevibacter spp. for discrimination between human, bovine, equine, and swine fecal contamination in waters intended for human supply. Overall, the novel host-specific archaeal and bacterial primers proposed in this study demonstrated high sensitivity and specificity. Markers for the Archaea domain were more prevalent in the fecal and water samples studied. We conclude that the investigations regarding the sources of fecal pollution in public water supplies can contribute to improve the quality of human health. To our knowledge, this is the first analysis using both archaeal and bacterial fecal MST markers on tropical water bodies of Rio de Janeiro city, Brazil.

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts.

Evaluation of molecular- and culture-dependent MST markers to detect fecal contamination and indicate viral presence in good quality groundwater

Microbial contamination of groundwater represents a significant health risk to resource users. Culture-dependent Bacteroides phage and molecular-dependent Bacteroidales 16S rRNA assays are employed in microbial source tracking (MST) studies globally, however little is known regarding how these important groups relate to each other in the environment and which is more suitable to indicate the presence of waterborne fecal pollution and human enteric viruses. This study addresses this knowledge gap by examining 64 groundwater samples from sites with varying hydrogeological properties using a MST toolbox containing two bacteriophage groups (phage infecting GB-124 and ARABA-84), and two Bacteroidales 16S rRNA markers (Hf183 and BacR); those were compared to fecal indicator bacteria, somatic coliphage, Bacteroidales 16S rRNA marker AllBac, four human enteric viruses (norovirus GI and II, enterovirus and group A rotavirus) and supplementary hydrogeological/chemical data. Bacteroidales 16S rRNA indicators offered a more sensitive assessment of both human-specific and general fecal contamination than phage indicators, but may overestimate the risk from enteric viral pathogens. Comparison with hydrogeological and land use site characteristics as well as auxiliary microbiological and chemical data proved the plausibility of the MST findings. Sites representing karst aquifers were of significantly worse microbial quality than those with unconsolidated or fissured aquifers, highlighting the vulnerability of these hydrogeological settings.

An environmental survey of surface waters using mitochondrial DNA from human, bovine and porcine origin as fecal source tracking markers

Fecal contamination of surface waters is one the major sources of waterborne pathogens and consequently, is an important concern for public health. For reliable fecal source tracking (FST) monitoring, there is a need for a multi-marker toolbox as no single all-encompassing method currently exists. Mitochondrial DNA (mtDNA) as a source tracking marker has emerged as a promising animal-specific marker. However, very few comprehensive field studies were done on the occurrence of this marker in surface waters. In this report, water samples were obtained from 82 sites in different watersheds over a six year period. The samples were analyzed for the presence of human, bovine and porcine mtDNA by endpoint nested PCR, along with the human-specific Bacteroidales HF183 marker. These sites represented a mix of areas with different anthropogenic activities, natural, urban and agricultural. The occurrences of mitoHu (human), mitoBo (bovine), mitoPo (porcine) and HF183 specific PCR amplifications from the samples were 46%, 23%, 6% and 50%, respectively. The occurrence of mitoHu and HF183 was high in all environment types with higher occurrence in the natural and urban areas, whereas the occurrence of mitoBo was higher in agricultural areas. FST marker concentrations were measured by real-time PCR for samples positive for these markers. The concentration of the mitoHu markers was one order of magnitude lower than HF183. There was co-linearity between the concentrations of the mitoHu and HF183 markers. Co-linearity was also observed between HF183 concentration and fecal coliform levels. Such a relationship was not observed between the mitoHu concentration and fecal coliform levels. In summary, our results showed a high incidence of human fecal pollution throughout the environment while demonstrating the potential of mtDNA as suitable FST markers.

Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters

Untreated sewage discharges and limited agricultural manure management practices contribute to fecal pollution in rural Brazilian waterways. Most microbial source tracking studies have focused on Bacteroidales, and few have tested host-specific indicators in underdeveloped regions. Sequencing of sewage and human and animal feces with Illumina HiSeq revealed Prevotellaceae as the most abundant family in humans, with Lachnospiraceae and Ruminococcaceae also comprising a large proportion of the microbiome. These same families were also dominant in animals. Bacteroides, the genus containing the most commonly utilized human-specific marker in the United States was present in very low abundance. We used oligotyping to identify Prevotella and Blautia sequences that can distinguish human fecal contamination. Thirty-five of 61 Blautia oligotypes and 13 of 108 Prevotella oligotypes in humans were host-specific or highly abundant (i.e. host-preferred) compared to pig, dog, horse and cow sources. Certain human Prevotella and Blautia oligotypes increased more than an order of magnitude along a polluted river transect in rural Brazil, but traditional fecal indicator levels followed a steady or even decreasing trend. While both Prevotella and Blautia oligotypes distinguished human and animal fecal pollution in Brazil surface waters, Blautia appears to contain more discriminatory and globally applicable markers for tracking sources of fecal pollution.

Applicability of universal Bacteroidales genetic marker for microbial monitoring of drinking water sources in comparison to conventional indicators

Water quality monitoring is essential for the provision of safe drinking water. In this study, we compared a selection of fecal indicators with universal Bacteroidales genetic marker to identify fecal pollution of a variety of drinking water sources. A total of 60 samples were collected from water sources. The microbiological parameters included total coliforms, fecal coliforms, Escherichia coli and fecal streptococci as the fecal indicator bacteria (FIB), Clostridium perfringens and H2S bacteria as alternative indicators, universal Bacteroidales genetic marker as a promising alternative fecal indicator, and Salmonella spp., Shigella spp., and E. coli O157 as pathogenic bacteria. From 60 samples analyzed, Bacteroidales was the most frequently detected indicator followed by total coliforms. However, the Bacteroidales assay failed to detect the marker in nine samples positive for FIB and other alternative indicators. The results of our study showed that the absence of Bacteroidales is not necessarily an evidence of fecal and pathogenic bacteria absence and may be unable to ensure the safety of the water. Further research, however, is required for a better understanding of the use of a Bacteroidales genetic marker as an indicator in water quality monitoring programs.

Baseline and storm event monitoring of Bacteroidales marker concentrations and enteric pathogen presence in a rural Canadian watershed

Bacteroidales 16S rRNA gene markers were evaluated for their use as a microbial source tracking tool in a well characterized 750 ha agricultural watershed in Nova Scotia, Canada. Water quality monitoring was conducted following the validation of host-specific and universal Bacteroidales (AllBac) markers for their proficiency in this particular geographic region, which provided further evidence that these markers are geographically stable. Increasing Escherichia coli concentrations were positively correlated (p < 0.01) with concentrations of the AllBac marker in water samples, suggesting that this universal marker is more suited as a positive DNA control rather than as an indicator of recent fecal contamination. Ruminant (BacR) and bovine (CowM2) specific marker detection was associated with increased runoff due to precipitation in sub-watersheds putatively impacted by cattle farming, demonstrating that the BacR and CowM2 markers can be used to detect the recent introduction of fecal matter from cattle farming activities during rainfall events. However, the human associated marker (BacH) was only detected once in spite of numerous on-site residential wastewater treatment systems in the watershed, suggesting that this assay is not sensitive enough to detect this type of human sewage source. E. coli O157:H7 and Salmonella spp. DNA was not detected in any of the 149 watershed samples; however, 114 (76.5%) of those samples tested positive for Campylobacter spp. No significant correlation (p > 0.05) was found between Campylobacter spp. presence and either E. coli or AllBac marker levels. Further studies should be conducted to assess the origins of Campylobacter spp. in these types of watersheds, and to quantify pathogen cell numbers to allow for a human health risk assessment.

Long-term monitoring of waterborne pathogens and microbial source tracking markers in paired agricultural watersheds under controlled and conventional tile drainage management

Surface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig) Bacteroidales markers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences of Salmonella spp. and Arcobacter spp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the level P = 0.06. The odds of Salmonella spp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet for Arcobacter spp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization.

Environmental fate of tetracycline resistance genes originating from swine feedlots in river water

Tetracyclines are antibiotics commonly used in swine farms to treat disease and promote growth. However, there are growing concerns regarding the discharge of animal feces into the environment owing to the potential for development and dissemination of tetracycline resistance genes (TRGs). In this study, farming wastewater from one Chinese swine farm as well as river water from seven locations downstream of the farm was sampled. Polymerase chain reaction (PCR) showed that 12 TRGs, including six efflux pump genes (tet(B), tet(C), tet(D), tet(E), tet(G) and tet(L)), five ribosomal protection proteins (RPPs) genes (tet(O), tet(M), tet(Q), tet(W) and tet(S)), and one enzymatic modification gene (tet(X)), were present in all wastewater and river water samples. Quantitative real-time PCR (qPCR) showed that the abundance of tet(C), tet(X), tet(O), tet(M), tet(Q) and tet(W) decreased with downstream flow. Among the detected TRGs, tet(C) had the highest abundance, ranging from 459.5 copies/16S rRNA gene copies in wastewater to 33.8 copies/16S rRNA gene copies in river water samples collected from the last location. Furthermore, pig-specific Bacteroidales 16S rRNA genetic marker was quantified by qPCR to determine the level of fecal pollution in the river water. Bivariate correlation analysis confirmed that the total relative abundance of the six TRGs was significantly correlated with the level of swine feces in the aquatic environment (R(2) = 0.63, P < 0.05), suggesting that swine feces mainly contributed to the spread of TRGs in the river water.

Microbial water quality in freshwater lakes with different land use

AIMS

The relationship between land use (undeveloped, cattle grazing, urban), faecal indicator bacteria (FIB) levels and microbial source tracking (MST) marker detection was investigated in lakes created following phosphate mining.

METHODS AND RESULTS

Faecal coliforms and enterococci were cultured, and MST markers were detected by PCR [Methanobrevibacter smithii, human polyomaviruses (HPyVs), ruminant, human (HF183) and general Bacteroidales]. FIB levels varied significantly by sampling date and were correlated with antecedent rainfall. FIB levels varied with land use category only in the case of faecal coliform levels in sediments of urban lakes, which were significantly greater than those in undeveloped or cattle-impacted lakes. Ruminant Bacteroidales were detected consistently in cattle-impacted lakes (57%) and rarely in other lakes. HPyVs was the only human source marker detected.

CONCLUSIONS

Rainfall was more strongly associated with FIB levels than land use category. The detection frequency of only the ruminant MST marker was associated with land use.

SIGNIFICANCE AND IMPACT OF STUDY

Microbial source tracking (MST) can fine-tune the assessment of human health risk from recreational use of inland waters, particularly when similar FIB levels but different surrounding land use and probable impacts exist.

Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes

Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.

Coherence among different microbial source tracking markers in a small agricultural stream with or without livestock exclusion practices

Over 1,400 water samples were collected biweekly over 6 years from an intermittent stream protected and unprotected from pasturing cattle. The samples were monitored for host-specific Bacteroidales markers, Cryptosporidium species/genotypes, viruses and coliphages associated with humans or animals, and bacterial zoonotic pathogens. Ruminant Bacteroidales markers did not increase within the restricted cattle access reach of the stream, whereas the ruminant Bacteroidales marker increased significantly in the unrestricted cattle access reach. Human Bacteroidales markers significantly increased downstream of homes where septic issues were documented. Wildlife Bacteroidales markers were detected downstream of the cattle exclusion practice where stream and riparian habitat was protected, but detections decreased after the unrestricted pasture, where the stream and riparian zone was unprotected from livestock. Detection of a large number of human viruses was shown to increase downstream of homes, and similar trends were observed for the human Bacteroidales marker. There was considerable interplay among biomarkers with stream flow, season, and the cattle exclusion practices. There were no to very weak associations with Bacteroidales markers and bacterial, viral, and parasitic pathogens. Overall, discrete sample-by-sample coherence among the different microbial source tracking markers that expressed a similar microbial source was minimal, but spatial trends were physically meaningful in terms of land use (e.g., beneficial management practice) effects on sources of fecal pollution.

Quantitative multi-year elucidation of fecal sources of waterborne pathogen contamination in the South Nation River basin using bacteroidales microbial source tracking markers

Over a seven-year period (2004-2010) 1095 water samples were obtained from the South Nation River basin at multiple watershed monitoring sites (Ontario, Canada). Real-time PCR using Bacteroidales specific markers was used to identify the origin (human (10% prevalence), ruminant (22%), pig (~2%), Canada goose (4%) and muskrat (7%)) of fecal pollution. In parallel, the distribution of fecal indicator bacteria and waterborne pathogens (Cryptosporidium oocysts, Giardia cysts, Escherichia coli O157:H7, Salmonella enterica and Campylobacter spp.) was evaluated. Associations between the detection of specific Bacteroidales markers and the presence of fecal indicator bacteria, pathogens, and distinct land use or environmental variables were evaluated. Linear correlations between Bacteroidales markers and fecal indicator bacteria were weak. However, mean marker densities, and the presence and absence of markers could be discriminated on the basis of threshold fecal indicator densities. The ruminant-specific Bacteroidales marker was the most frequently detected marker in water, consistent with the large number of dairy farms in the study area. Detection of the human or the ruminant markers were associated with a slightly higher risk of detecting S. enterica. Detection of the muskrat marker was related to more frequent Campylobacter spp. detections. Important positive associations between markers and pathogens were found among: i) total Bacteroidales and Cryptosporidium and Giardia, ii) ruminant marker and S. enterica, and iii) muskrat and Campylobacter spp.

Sewage reflects the distribution of human faecal Lachnospiraceae

Faecal pollution contains a rich and diverse community of bacteria derived from animals and humans, many of which might serve as alternatives to the traditional enterococci and Escherichia coli faecal indicators. We used massively parallel sequencing (MPS) of the 16S rRNA gene to characterize microbial communities from wastewater treatment plant (WWTP) influent sewage from 12 cities geographically distributed across the USA. We examined members of the Clostridiales, which included the families Clostridiaceae, Lachnospiraceae and Ruminococcaceae for their potential as sewage indicators. Lachnospiraceae was one of the most abundant groups of faecal bacteria in sewage, and several Lachnospiraceae high-abundance sewage pyrotags occurred in at least 46 of 48 human faecal samples. Clone libraries targeting Clostridium coccoides (C. coccoides) in sewage samples demonstrated that Lachnospiraceae-annotated V6 pyrotags encompassed the previously reported C. coccoides group. We used oligotyping to profile the genus Blautia within Lachnospiraceae and found oligotypes comprised of 24 entropy components that showed patterns of host specificity. These findings suggest that indicators based on Blautia might have the capacity to discriminate between different faecal pollution sources. Development of source-specific alternative indicators would enhance water quality assessments, which leads to improved ecosystem health and reduced human health risk due to waterborne disease.

Differential recovery of phylogenetically disparate microbes from spacecraft-qualified metal surfaces

Universal and species-specific quantitative polymerase chain reaction-based methods were employed to compare the effectiveness of four distinct materials used to collect biological samples from metal surfaces. Known cell densities of a model microbial community (MMC) were deposited onto metal surfaces and subsequently collected with cotton and nylon-flocked swabs for small surface areas and biological sampling kits (BiSKits) and polyester wipes for large surface areas. Ribosomal RNA gene-based quantitative PCR (qPCR) analyses revealed that cotton swabs were superior to nylon-flocked swabs for recovering nucleic acids (i.e., DNA) from small surface areas. Similarly, BiSKits outperformed polyester wipes for sampling large surface areas. Species-specific qPCR results show a differential recovery of rRNA genes of the various MMC constituents, seemingly dependent on the type of sampling device employed. Both cotton swabs and BiSKits recovered the rDNA of all nine of the MMC constituent microbes assayed, whereas nylon-flocked swabs and polyester wipes recovered the rDNA of only six and four of these MMC strains, respectively. The findings of this study demonstrate the importance and proficiency of molecular techniques in gauging the effectiveness and efficiency of various modes of biological sample collection from metal surfaces.

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.

Geographic setting influences Great Lakes beach microbiological water quality

Understanding of factors that influence Escherichia coli (EC) and enterococci (ENT) concentrations, pathogen occurrence, and microbial sources at Great Lakes beaches comes largely from individual beach studies. Using 12 representative beaches, we tested enrichment cultures from 273 beach water and 22 tributary samples for EC, ENT, and genes indicating the bacterial pathogens Shiga-toxin producing E. coli (STEC), Shigella spp. , Salmonella spp , Campylobacter jejuni/coli , and methicillin-resistant Staphylococcus aureus , and 108-145 samples for Bacteroides human, ruminant, and gull source-marker genes. EC/ENT temporal patterns, general Bacteroides concentration, and pathogen types and occurrence were regionally consistent (up to 40 km), but beach catchment variables (drains/creeks, impervious surface, urban land cover) influenced exceedances of EC/ENT standards and detections of Salmonella and STEC. Pathogen detections were more numerous when the EC/ENT Beach Action Value (but not when the Geometric Mean and Statistical Threshold Value) was exceeded. EC, ENT, and pathogens were not necessarily influenced by the same variables. Multiple Bacteroides sources, varying by date, occurred at every beach. Study of multiple beaches in different geographic settings provided new insights on the contrasting influences of regional and local variables, and a broader-scale perspective, on significance of EC/ENT exceedances, bacterial sources, and pathogen occurrence.

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.

Microbial source tracking to identify human and ruminant sources of faecal pollution in an ephemeral Florida river

AIMS

Levels and sources of faecal indicator bacteria (FIB) in an ephemeral Florida river were assessed under different rainfall/flow patterns to explore the effects of rainfall on water quality.

METHODS AND RESULTS

Quantitative PCR for sewage markers [human-associated Bacteroides HF183 and human polyomaviruses (HPyVs)] and PCR for ruminant faecal markers were used to explore contamination sources. Escherichia coli, faecal coliform and enterococci levels consistently exceeded recreational water quality criteria, and sediment FIB levels were about 100-fold higher compared with water. HPyVs detections cooccurred with HF183, which was frequently detected near septic systems. Ruminant markers were detected only in livestock-grazing areas. Significantly greater faecal coliform and E. coli concentrations were observed under no-flow conditions and the levels of faecal coliforms in water column and sediments were negatively correlated with duration since last rain event.

CONCLUSIONS

Septic systems and cattle grazing in this watershed contributed to the formation of FIB reservoirs in sediments, which were persistent following prolonged rainfall.

SIGNIFICANCE AND IMPACT OF THE STUDY

Ephemeral water bodies that flow only under the direct influence of recent rainfall are rarely studied. FIB levels in the New River in Florida were greater during dry weather than wet weather, which contrasts with most observations and may be attributed to bacterial reservoirs formed in still pool, sediments and water-saturated soils in this subtropical environment.

Persistence of host-associated Bacteroidales gene markers and their quantitative detection in an urban and agricultural mixed prairie watershed

Microbial source tracking is an emerging tool developed to protect water sources from faecal pollution. In this study, we evaluated the suitability of real time-quantitative PCR (qPCR) Taqman assays developed for detection of host-associated Bacteroidales markers in a prairie watershed. The qPCR primers and probes used in this study exhibited high accuracy (88-96% sensitivity and ≥ 99% host specificity) in detecting Bacteroidales spp. that are associated with faeces from humans, ruminants, bovines, and horses. The ruminant- and human-associated markers were also found in high concentrations within individual faecal samples, ranging from 3.4 to 7.3 log(10) marker copy numberg(-1) of individual host faeces. Following validation of host sensitivity and specificity, the host-associated Bacteroidales markers were detected in the Qu'Appelle Valley watershed of Saskatchewan, Canada which experiences a diversity of anthropogenic inputs. Concentrations of the ruminant marker were well-correlated with proximity to cattle operations and there was a correlation between the marker and Escherichia coli concentrations at these sites. Low concentrations of the human faecal marker were measured throughout the sampling sites, and may indicate a consistent influx of human faecal pollution into the watershed area. Persistence of each of the Bacteroidales host-associated marker was also studied in situ. The results indicated that the markers persist for shorter periods of time (99% decay in <8 days) compared with the conventional E. coli marker (99% decay in >15 days), suggesting they are effective at detecting recent faecal contamination events. The levels of Bacteroidales markers and E. coli counts did not correlate with the presence of the pathogenic bacteria, Salmonella spp. or Campylobacter spp. detected in the Qu'Appelle Valley. Collectively, the results obtained in this study demonstrated that the qPCR approach for detecting host-associated Bacteroidales spp. markers can be a useful tool in helping to determine host-specific impacts of faecal pollution into a prairie watershed.

Decay of Bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources

The implementation of microbial fecal source tracking (MST) methods in drinking water management is limited by the lack of knowledge on the transport and decay of host-specific genetic markers in water sources. To address these limitations, the decay and transport of human (BacH) and ruminant (BacR) fecal Bacteroidales 16S rRNA genetic markers in a drinking water source (Lake Rådasjön in Sweden) were simulated using a microbiological model coupled to a three-dimensional hydrodynamic model. The microbiological model was calibrated using data from outdoor microcosm trials performed in March, August, and November 2010 to determine the decay of BacH and BacR markers in relation to traditional fecal indicators. The microcosm trials indicated that the persistence of BacH and BacR in the microcosms was not significantly different from the persistence of traditional fecal indicators. The modeling of BacH and BacR transport within the lake illustrated that the highest levels of genetic markers at the raw water intakes were associated with human fecal sources (on-site sewers and emergency sewer overflow). This novel modeling approach improves the interpretation of MST data, especially when fecal pollution from the same host group is released into the water source from different sites in the catchment.

Comparison of gull feces-specific assays targeting the 16S rRNA genes of Catellicoccus marimammalium and Streptococcus spp

Two novel gull-specific quantitative PCR (qPCR) assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR green assay targeting Streptococcus spp. (gull3) and a hydrolysis TaqMan assay targeting Catellicoccus marimammalium (gull4). The objectives of this study were to compare the host specificity of a previous C. marimammalium qPCR assay (gull2) with that of the new markers and to examine the presence of the three gull markers in environmental water samples from different geographic locations. Most of the gull fecal samples tested (n = 255) generated positive signals with the gull2 and gull4 assays (i.e., >86%), whereas only 28% were positive with gull3. Low prevalence and abundance of tested gull markers (0.6 to 15%) were observed in fecal samples from six nonavian species (n = 180 fecal samples), whereas the assays cross-reacted to some extent (13 to 31%) with other (nongull) avian fecal samples. The gull3 assay was positive against fecal samples from 11 of 15 avian species, including gull. Of the presumed gull-impacted water samples (n = 349), 86%, 59%, and 91% were positive with the gull2, the gull3, and the gull4 assays, respectively. Approximately 5% of 239 non-gull-impacted water samples were positive with the gull2 and the gull4 assays, whereas 21% were positive witg the gull3 assay. While the relatively high occurrence of gull2 and gull4 markers in waters impacted by gull feces suggests that these assays could be used in environmental monitoring studies, the data also suggest that multiple avian-specific assays will be needed to accurately assess the contribution of different avian sources in recreational waters.

Improving the performance of an end-point PCR assay commonly used for the detection of Bacteroidales pertaining to cow feces

Bacteroidales are normal gut flora of warm-blooded animals. Since each host species carries a different diversity of Bacteroidales, the detection of host-associated gene markers of Bacteroidales has emerged as a promising tool for the tracking of the source of fecal pollution in aquatic ecosystems. To detect cow-associated Bacteroidales, a commonly used method has been an end-point PCR assay with the 16S rRNA genes primers CF128F (cow-associated) and Bac708R (all Bacteroidales). The PCR assay has demonstrated high rates of true-positive detection (i.e., high sensitivity) in all previous studies. However, the assay also had high rates of false-positive detection to the samples of non-target hosts in some cases (i.e., low specificity). In opposite to the reason many investigators have proposed, our results suggested that false detection was not necessarily due to the presence of the target sequence of CF128F in the feces of non-target hosts. Instead, we found sequences of non-target hosts having single internal mismatches with CF128F. Those mismatches were well tolerated in PCR, partly due to the universality of Bac708R. To improve the detection performance, we designed a novel primer CF592R (targeting the same clade of sequences as CF128F) to substitute Bac708R. The use of CF529R alleviated false detection and also led to a tenfold reduction in detection limit in the samples tested, compared to the use of Bac708R. Many other end-point PCR assays that detect the 16S rRNA genes in Bacteroidales also use a host-associated primer to couple with Bac708R, and low specificity or sensitivity has been reported. Based on our findings for CF128F, we suggest that the suitability of Bac708R in those PCR assays needs to be revisited.

High diversity and differential persistence of fecal Bacteroidales population spiked into freshwater microcosm

Bacteroidales markers are promising indicators of fecal pollution and are now widely used in microbial source tracking (MST) studies. However, a thorough understanding of the persistence of Bacteroidales population after being released into environmental waters is lacking. We investigated the persistence of two host specific markers (HF183 and CF193) and temporal change of Bacteroidales population over 14 days in freshwater microcosms seeded with human or bovine feces. The concentrations of HF183/CF193 and Escherichia coli were determined using quantitative polymerase chain reaction (qPCR) and standard cultivation method, respectively. Shifts in the Bacteroidales population structure were fingerprinted using PCR-denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing analysis targeting both 16S rDNA and rRNA-transcribed cDNA. Both HF183 and CF193 decayed significantly faster than E. coli but the decay curves fit poorly with first-order model. High diversity of Bacteroidales population was observed for both microcosms, and persistence of different species in the population varied. Sequence analysis indicated that most of the bovine Bacteroidales populations in our study are unexplored. DGGE and decay curve indicated that RNA decayed faster than DNA, further supporting the use of rRNA as indicator of metabolically active Bacteroidales population. Evaluations with more realistic scenarios are warranted prior to extending the results of this study to real field settings.