Spatiotemporal analysis of Cryptosporidium species/genotypes and relationships with other zoonotic pathogens in surface water from mixed-use watersheds

Acinetobacter calcoaceticus-baumannii complex prevalence, spatial-temporal distribution, and contamination sources in Canadian aquatic environments

Acinetobacter calcoaceticus-baumannii (ACB) complex has been identified as a group of emerging opportunistic pathogens that cause nosocomial infections. The current study investigates the prevalence, distribution, and diversity of pathogenic ACB complex in various aquatic systems with different uses. Of the total 157 agricultural, raw drinking water intake, recreational beach, and wastewater treatment plant (WWTP) effluent samples, acinetobacters were isolated, quantified, and confirmed by genus- and ACB complex-specific PCR assays. Of all agricultural surface water samples, A. calcoaceticus (65%) was more frequently detected than A. pittii (14%), A. nosocomialis (9%), and A. baumannii (3%). In WWTP effluent samples, A. baumannii was more prevalent in de-chlorinated (60%) samples compared to both A. pittii and A. nosocomialis (40%). Interestingly, A. nosocomialis (43%), A. calcoaceticus (29%), and A. baumannii (14%) were detected in raw drinking water intake samples, whereas A. pittii (50%) and A. nosocomialis (25%) were detected in beach samples. Although no sampling location-specific differences were recorded, significant (P < 0.05) seasonal differences were observed when agricultural surface water samples collected in spring were compared with the summer and fall. Whereas effluent chlorination significantly impacted the degree of prevalence of Acinetobacter in WWTP effluent samples, overall, the prevalence of ACB complex in all sampling locations and seasons indicates that these water sources, containing human-associated ACB complex, may pose potential health risks as community-acquired opportunistic infections.IMPORTANCEAcinetobacter calcoaceticus-baumannii (ACB) complex is a group of organisms known to cause problematic nosocomial opportunistic infections. A member of the species complex, A. baumannii, is becoming a global threat to infection treatment as strains are increasingly develop resistance to antibiotics. The prevalence and distribution of potentially pathogenic Acinetobacter calcoaceticus-baumannii complex species remain poorly understood, and there is a need to better understand the occurrence of A. baumannii in non-nosocomial environments. Our research details the spatial-temporal distribution of ACB complex species in a regional watershed and highlights the presence of ACB complex in wastewater effluent that is discharged into a river. These findings deepen our understanding of this group of species in non-nosocomial environments and encourage the development of monitoring programs for these species in regional waters.

Cryptosporidium and agriculture: A review

Cryptosporidiosis is a significant contributor to global foodborne and waterborne disease burden. It is a widespread cause of diarrheal diseases that affect humans and animals worldwide. Agricultural environments can become a source of contamination with Cryptosporidium species through faecal material derived from humans and animals. This review aims to report the main findings of scientific research on Cryptosporidium species related to various agricultural sectors, and highlights the risks of cryptosporidiosis in agricultural production, the contamination sources, the importance of animal production in transmission, and the role of farmed animals as hosts of the parasites. Agricultural contamination sources can cause water pollution in groundwater and different surface waters used for drinking, recreational purposes, and irrigation. The application of contaminated manure, faecal sludge management, and irrigation with inadequately treated water are the main concerns associated with foodborne and waterborne cryptosporidiosis related to agricultural activities. The review emphasizes the public health implications of agriculture concerning the transmission risk of Cryptosporidium parasites and the urgent need for a new concept in the agriculture sector. Furthermore, the findings of this review provide valuable information for developing appropriate measures and monitoring strategies to minimize the risk of infection.

Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water

BACKGROUND

Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites.

RESULTS

All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic.

CONCLUSIONS

The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.

Detection of Cryptosporidium spp. and Giardia spp. in Environmental Water Samples: A Journey into the Past and New Perspectives

Among the major issues linked with producing safe water for consumption is the presence of the parasitic protozoa Cryptosporidium spp. and Giardia spp. Since they are both responsible for gastrointestinal illnesses that can be waterborne, their monitoring is crucial, especially in water sources feeding treatment plants. Although their discovery was made in the early 1900s and even before, it was only in 1999 that the U.S. Environmental Protection Agency (EPA) published a standardized protocol for the detection of these parasites, modified and named today the U.S. EPA 1623.1 Method. It involves the flow-through filtration of a large volume of the water of interest, the elution of the biological material retained on the filter, the purification of the (oo)cysts, and the detection by immunofluorescence of the target parasites. Since the 1990s, several molecular-biology-based techniques were also developed to detect Cryptosporidium and Giardia cells from environmental or clinical samples. The application of U.S. EPA 1623.1 as well as numerous biomolecular methods are reviewed in this article, and their advantages and disadvantages are discussed guiding the readers, such as graduate students, researchers, drinking water managers, epidemiologists, and public health specialists, through the ever-expanding number of techniques available in the literature for the detection of Cryptosporidium spp. and Giardia spp. in water.

Microbial water quality at contrasting recreational areas in a mixed-use watershed in eastern Canada

Recreational water use is an important source of human enteric illness. Enhanced (episodic) surveillance of natural recreational waters as a supplement to beach monitoring can enrich our understanding of human health risks. From 2011 to 2013, water sampling was undertaken at recreational sites on a watershed in eastern Canada. This study compared the prevalence and associations of human enteric pathogens and fecal indicator organisms. Beach water samples had lower pathogen presence than those along the main river, due to different pollution sources and the hydrological disposition. Pathogen profiles identified from the beach sites suggested a more narrow range of sources, including birds, indicating that wild bird management could help reduce public health risks at these sites. The presence and concentration of indicator organisms did not differ significantly between beaches and the river. However, higher concentrations of generic Escherichia coli were observed when Salmonella and Cryptosporidium were present at beach sites, when Salmonella was present at the river recreational site, and when verotoxigenic E. coli were present among all sites sampled. In this watershed, generic E. coli concentrations were good indicators of potential contamination, pathogen load, and elevated human health risk, supporting their use for routine monitoring where enhanced pathogen testing is not possible.

Human density is associated with the increased prevalence of a generalist zoonotic parasite in mammalian wildlife

Macroecological approaches can provide valuable insight into the epidemiology of globally distributed, multi-host pathogens. Toxoplasma gondii is a zoonotic protozoan that infects any warm-blooded animal, including humans, in almost every ecosystem worldwide. There is substantial geographical variation in T. gondii prevalence in wildlife populations and the mechanisms driving this variation are poorly understood. We implemented Bayesian phylogenetic mixed models to determine the association between species' ecology, phylogeny and climatic and anthropogenic factors on T. gondii prevalence. Toxoplasma gondii prevalence data were compiled for free-ranging wild mammal species from 202 published studies, encompassing 45 079 individuals from 54 taxonomic families and 238 species. We found that T. gondii prevalence was positively associated with human population density and warmer temperatures at the sampling location. Terrestrial species had a lower overall prevalence, but there were no consistent patterns between trophic level and prevalence. The relationship between human density and T. gondii prevalence is probably mediated by higher domestic cat abundance and landscape degradation leading to increased environmental oocyst contamination. Landscape restoration and limiting free-roaming in domestic cats could synergistically increase the resiliency of wildlife populations and reduce wildlife and human infection risks from one of the world's most common parasitic infections.

Changes in Escherichia coli to enteric protozoa ratios in rivers: Implications for risk-based assessment of drinking water treatment requirements

Minimum treatment requirements are set in response to established or anticipated levels of enteric pathogens in the source water of drinking water treatment plants (DWTPs). For surface water, contamination can be determined directly by monitoring reference pathogens or indirectly by measuring fecal indicators such as Escherichia coli (E. coli). In the latter case, a quantitative interpretation of E. coli for estimating reference pathogen concentrations could be used to define treatment requirements. This study presents the statistical analysis of paired E. coli and reference protozoa (Cryptosporidium, Giardia) data collected monthly for two years in source water from 27 DWTPs supplied by rivers in Canada. E. coli/Cryptosporidium and E. coli/Giardia ratios in source water were modeled as the ratio of two correlated lognormal variables. To evaluate the potential of E. coli for defining protozoa treatment requirements, risk-based critical mean protozoa concentrations in source water were determined with a reverse quantitative microbial risk assessment (QMRA) model. Model assumptions were selected to be consistent with the World Health Organization (WHO) Guidelines for drinking-water quality. The sensitivity of mean E. coli concentration trigger levels to identify these critical concentrations in source water was then evaluated. Results showed no proportionalities between the log of mean E. coli concentrations and the log of mean protozoa concentrations. E. coli/protozoa ratios at DWTPs supplied by small rivers in agricultural and forested areas were typically 1.0 to 2.0-log lower than at DWTPs supplied by large rivers in urban areas. The seasonal variations analysis revealed that these differences were related to low mean E. coli concentrations during winter in small rivers. To achieve the WHO target of 10^-6 disability-adjusted life year (DALY) per person per year, a minimum reduction of 4.0-log of Cryptosporidium would be required for 20 DWTPs, and a minimum reduction of 4.0-log of Giardia would be needed for all DWTPs. A mean E. coli trigger level of 50 CFU 100 mL^-1 would be a sensitive threshold to identify critical mean concentrations for Cryptosporidium but not for Giardia. Treatment requirements higher than 3.0-log would be needed at DWTPs with mean E. coli concentrations as low as 30 CFU 100 mL^-1 for Cryptosporidium and 3 CFU 100 mL^-1 for Giardia. Therefore, an E. coli trigger level would have limited value for defining health-based treatment requirements for protozoa at DWTPs supplied by small rivers in rural areas.

Land use associated with Cryptosporidium sp. and Giardia sp.in surface water supply in the state of São Paulo, Brazil

Land use/Land cover (LULC) associated with Cryptosporidium sp. and Giardia sp. quantification and distribution can provide identification of the environmental circulation patterns of these parasites. The aim of this research was to relate the occurrence and circulation of these parasites to the LULC watershed with poor sanitation infrastructure and livestock as important economic activity. The study involved 11 municipalities in the state of São Paulo, located in southeastern Brazil. Sampling was carried out at the catchment sites of each water supply on a monthly basis, starting in December 2014 and lasting until November 2015, totalizing 128 samples. Protozoans were quantified according to the 1623.1 US. EPA Method. For watershed delimitation, the hydrographic network was extracted from the hydrology tool of ArcGIS 10.1. The frequency of occurrence of these pathogens and the high concentrations were evidenced in the municipality with the largest urban area (16.2%) and intense livestock activity (39%) near the catchment site. The municipality that showed the lowest frequency of occurrence presented the smallest urban area (0.87%) and absence of livestock activity near the catchment site. The high concentration of pathogens suggests a correlation between the impact on water supply networks and river basin degradation caused by urban activity and livestock.

Does land use affect pathogen presence in New Zealand drinking water supplies?

Four microbes (Campylobacter spp., Escherichia coli, Cryptosporidium spp. and Giardia spp.) were monitored in 16 waterways that supply public drinking water for 13 New Zealand towns and cities. Over 500 samples were collected from the abstraction point at each study site every three months between 2009 and 2019. The waterways represent a range from small to large, free flowing to reservoir impoundments, draining catchments of entirely native vegetation to those dominated by pastoral agriculture. We used machine learning algorithms to explore the relative contribution of land use, catchment geology, vegetation, topography, and water quality characteristics of the catchment to determining the abundance and/or presence of each microbe. Sites on rivers draining predominantly agricultural catchments, the Waikato River, Oroua River and Waiorohi Stream had all four microbes present, often in high numbers, throughout the sampling interval. Other sites, such as the Hutt River and Big Huia Creek in Wellington which drain catchments of native vegetation, never had pathogenic microbes detected, or unsafe levels of E. coli. Boosted Regression Tree models could predict abundances and presence/absence of all four microbes with good precision using a wide range of potential environmental predictors covering land use, geology, vegetation, topography, and nutrient concentrations. Models were more accurate for protozoa than bacteria but did not differ markedly in their ability to predict abundance or presence/absence. Environmental drivers of microbe abundance or presence/absence also differed depending on whether the microbe was protozoan or bacterial. Protozoa were more prevalent in waterways with lower water quality, higher numbers of ruminants in the catchment, and in September and December. Bacteria were more abundant with higher rainfall, saturated soils, and catchments with greater than 35% of the land in agriculture. Although modern water treatment protocols will usually remove many pathogens from drinking water, several recent outbreaks of waterborne disease due to treatment failures, have highlighted the need to manage water supplies on multiple fronts. This research has identified potential catchment level variables, and thresholds, that could be better managed to reduce the potential for pathogens to enter drinking water supplies.

Real-time quantitative PCR assay development and application for assessment of agricultural surface water and various fecal matter for prevalence of Aliarcobacter faecis and Aliarcobacter lanthieri

BACKGROUND

Aliarcobacter faecis and Aliarcobacter lanthieri are recently identified as emerging human and animal pathogens. In this paper, we demonstrate the development and optimization of two direct DNA-based quantitative real-time PCR assays using species-specific oligonucleotide primer pairs derived from rpoB and gyrA genes for A. faecis and A. lanthieri, respectively. Initially, the specificity of primers and amplicon size of each target reference strain was verified and confirmed by melt curve analysis. Standard curves were developed with a minimum quantification limit of 100 cells mL^- 1 or g^- 1 obtained using known quantities of spiked A. faecis and A. lanthieri reference strains in autoclaved agricultural surface water and dairy cow manure samples.

RESULTS

Each species-specific qPCR assay was validated and applied to determine the rate of prevalence and quantify the total number of cells of each target species in natural surface waters of an agriculturally-dominant and non-agricultural reference watershed. In addition, the prevalence and densities were determined for human and various animal (e.g., dogs, cats, dairy cow, and poultry) fecal samples. Overall, the prevalence of A. faecis for surface water and feces was 21 and 28%, respectively. The maximum A. faecis concentration for water and feces was 2.3 × 10⁷ cells 100 mL^{- 1} and 1.2 × 10⁷ cells g^- 1, respectively. A. lanthieri was detected at a lower frequency (2%) with a maximum concentration in surface water of 4.2 × 10⁵ cells 100 mL^- 1; fecal samples had a prevalence and maximum density of 10% and 2.0 × 10⁶ cells g^- 1, respectively.

CONCLUSIONS

The results indicate that the occurrence of these species in agricultural surface water is potentially due to fecal contamination of water from livestock, human, or wildlife as both species were detected in fecal samples. The new real-time qPCR assays can facilitate rapid and accurate detection in < 3 h to quantify total numbers of A. faecis and A. lanthieri cells present in various complex environmental samples.

Chlorophyll-a, dissolved organic carbon, turbidity and other variables of ecological importance in river basins in southern Ontario and British Columbia, Canada

Optical sensing of chlorophyll-a (chl-a), turbidity, and fluorescent dissolved organic matter (fDOM) is often used to characterize the quality of water. There are many site-specific factors and environmental conditions that can affect optically sensed readings; notwithstanding the comparative implication of different procedures used to measure these properties in the laboratory. In this study, we measured these water quality properties using standard laboratory methods, and in the field using optical sensors (sonde-based) at water quality monitoring sites located in four watersheds in Canada. The overall objective of this work was to explore the relationships among sonde-based and standard laboratory measurements of the aforementioned water properties, and evaluate associations among these eco-hydrological properties and land use, environmental, and ancillary water quality variables such as dissolved organic carbon (DOC) and total suspended solids (TSS). Differences among sonde versus laboratory relationships for chl-a suggest such relationships are impacted by laboratory methods and/or site specific conditions. Data mining analysis indicated that interactive site-specific factors predominately impacting chl-a values across sites were specific conductivity and turbidity (variables with positive global associations with chl-a). The overall linear regression predicting DOC from fDOM was relatively strong (R² = 0.77). However, slope differences in the watershed-specific models suggest laboratory DOC versus fDOM relationships could be impacted by unknown localized water quality properties affecting fDOM readings, and/or the different standard laboratory methods used to estimate DOC. Artificial neural network analyses (ANN) indicated that higher relative chl-a concentrations were associated with low to no tree cover around sample sites and higher daily rainfall in the watersheds examined. Response surfaces derived from ANN indicated that chl-a concentrations were higher where combined agricultural and urban land uses were relatively higher.

Modelling the fate and transport of Cryptosporidium, a zoonotic and waterborne pathogen, in the Daning River watershed of the Three Gorges Reservoir Region, China

Oospores of Cryptosporidium, a waterborne pathogen of great concern, are widely distributed in surface waters in China and pose a threat to human health. This study seeks to explore the spatio-temporal patterns of Cryptosporidium concentrations. We focus on the Daning River watershed (4166 km²) of the Three Gorges Reservoir Region (TGR) during the period 2008 to 2013 and use the SWAT (Soil and Water Assessment Tool) model to test two mitigation scenarios. Based on data on animal husbandry, population, agriculture and WWTPs (wastewater treatment plants), Cryptosporidium transport in the Daning River watershed was simulated using a calibrated hydrological and sediment transport model. Our model results showed that the average annual concentration of oocysts in the whole watershed was 9.5 oocysts/10L, but high spatial variability occurred, ranging from 0.7 to 33.4 oocysts/10L. Highest monthly mean oocysts concentrations at the outlets of the sub-basins were found at high runoff and high fertilization or at the lowest flow, while minimum monthly mean oocysts concentrations were recorded at high runoff only. A model parameter sensitivity analysis showed that the Cryptosporidium soil partitioning coefficient (BACTKDQ) and the temperature adjustment factor for Cryptosporidium die-off (THBACT) were the only two sensitive parameters among the microbial parameters. The construction of multiple WWTPs throughout the watershed and composting of 50% of the feces from rural citizens and livestock up to 56 days before its application as fertilizer could significantly reduce the concentration of oocysts. Our Cryptosporidium transport model and simulation results may assist in the establishment of better pollution control countermeasures in the Daning River and other similar watersheds.

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.

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.

Explaining and modeling the concentration and loading of Escherichia coli in a stream-A case study

Escherichia coli (E. coli) level in streams is a public health indicator. Therefore, being able to explain why E. coli levels are sometimes high and sometimes low is important. Using citizen science data from Fall Creek in central NY we found that complementarily using principal component analysis (PCA) and partial least squares (PLS) regression provided insights into the drivers of E. coli and a mechanism for predicting E. coli levels, respectively. We found that stormwater, temperature/season and shallow subsurface flow are the three dominant processes driving the fate and transport of E. coli. PLS regression modeling provided very good predictions under stormwater conditions (R² = 0.85 for log (E. coli concentration) and R² = 0.90 for log (E. coli loading)); predictions under baseflow conditions were less robust. But, in our case, both E. coli concentration and E. coli loading were significantly higher under stormwater condition, so it is probably more important to predict high-flow E. coli hazards than low-flow conditions. Besides previously reported good indicators of in-stream E. coli level, nitrate-/nitrite-nitrogen and soluble reactive phosphorus were also found to be good indicators of in-stream E. coli levels. These findings suggest management practices to reduce E. coli concentrations and loads in-streams and, eventually, reduce the risk of waterborne disease outbreak.

Understanding human infectious Cryptosporidium risk in drinking water supply catchments

Treating drinking water appropriately depends, in part, on the robustness of source water quality risk assessments, however quantifying the proportion of infectious, human pathogenic Cryptosporidium oocysts remains a significant challenge. We analysed 962 source water samples across nine locations to profile the occurrence, rate and timing of infectious, human pathogenic Cryptosporidium in surface waters entering drinking water reservoirs during rainfall-runoff conditions. At the catchment level, average infectivity over the four-year study period reached 18%; however, most locations averaged <5%. The maximum recorded infectivity fraction within a single rainfall runoff event was 65.4%, and was dominated by C. parvum. Twenty-two Cryptosporidium species and genotypes were identified using PCR-based molecular techniques; the most common being C. parvum, detected in 23% of water samples. Associations between landuse and livestock stocking characteristics with Cryptosporidium were determined using a linear mixed-effects model. The concentration of pathogens in water were significantly influenced by flow and dominance of land-use by commercial grazing properties (as opposed to lifestyle properties) in the catchment (p < 0.01). Inclusion of measured infectivity and human pathogenicity data into a quantitative microbial risk assessment (QMRA) could reduce the source water treatment requirements by up to 2.67 log removal values, depending on the catchment, and demonstrated the potential benefit of collating such data for QMRAs.

Temporal trends in Giardia occurrence in the Grand River and surrounding tributaries, Waterloo, Ontario (2005-2013), a retrospective analysis of surveillance data

Giardia contamination in the Grand River Watershed (south-western Ontario, Canada) was monitored from 2005 to 2013 as part of FoodNet Canada. Our study objectives were to describe the temporal pattern of Giardia occurrence and determine whether water quality parameters and bacterial indicators could act as effective markers for Giardia occurrence. Water samples were collected monthly from the Grand River near a drinking water intake point (2005-2013) and also collected intermittently from other areas in the watershed during the study period. Samples were tested for Giardia cysts using the US EPA method 1623. Samples were also tested for chemical and microbial water quality indicators. Univariable and multivariable linear regression models were built to examine whether temporal, water quality and bacterial indicators were associated with Giardia cyst concentration. Giardia cysts were identified in 89% of samples (n = 228), with highest measured concentrations downstream of a waste water treatment plant outfall. Year and season were found to be predictors for Giardia occurrence. Concentrations were significantly higher in the winter and fall compared to the summer, and significantly higher in 2007 compared to other study years. After controlling for season, year and sampling location, dissolved oxygen was the only variable significantly associated with Giardia cyst concentration. Seasonal peaks in Giardia cyst concentrations in samples collected near the intake for the drinking water plant did not align with the seasonal peak in human Giardiasis cases in this region that are reported annually by public health authorities. This suggests that the risk of contracting Giardiasis from treated drinking water in this community is possibly low when the treatment plant is functioning adequately. Instead, waterborne exposure is likely the result of seasonal behaviours surrounding recreational water use. Therefore, the collective findings of our study are important to help inform future risk management studies and guide public health protection policies.

Rodents as a reservoir of infection caused by multiple zoonotic species/genotypes of C. parvum, C. hominis, C. suis, C. scrofarum, and the first evidence of C. muskrat genotypes I and II of rodents in Europe

Cryptosporidium spp. is an important causative agent of intestinal parasitoses-induced diarrhoea in humans and animals worldwide. Rodents (small mammals), the main reservoir of infections, are globally expanded and overpopulated, which increases the risk of transfer of human and zoonotic pathogens from the genus Cryptosporidium. In this study, Cryptosporidium was detected in wild immunocompetent asymptomatic small mammals. Altogether 262 fecal samples were collected from five areas in Eastern Slovakia from four different rodent species (Myodes glareolus, Apodemus agrarius, Apodemus flavicollis, Rattus norvegicus), eight samples originated from two insectivore species (Sorex araneus, Crocidura suaveolens), and two sample from a carnivore Mustela nivalis. The samples were examined using a method modified in our laboratory, based on the use of specific primers on a small subunit rRNA (18S rRNA) gene for species identification, and amplification of GP60 gene coding 60-kDa glycoprotein for genotype determination. The following species were identified: Cryptosporidium parvum (n=15), genotypes IIaA18G3R1 (n=11; KU311673), IIaA10G1R1 (n=1; KU311670), IIcA5G3a (n=1; KU311669), IIiA10 (n=2; KU311672); Cryptosporidium suis (n=4; KU311671); Cryptosporidium scrofarum (n=28); Cryptosporidium environment sp. (n=12; KU311677); Cryptosporidium muskrat genotype I (n=3; KU311675); Cryptosporidium muskrat genotype II (n=3; KU311676). From one of the rodent, the species Cryptosporidium hominis genotype IbA10G2 (KU311668) was identified for the first time. The results of this study indicate low host specificity of the detected Cryptosporidium species and imply the importance of free-living small mammals in urban and suburban habitats as a potential source of human cryptosporidiosis.

Cryptosporidium spp. and Giardia spp. in feces and water and the associated exposure factors on dairy farms

The aims of this study were to verify the prevalence of Cryptosporidium spp. and Giardia spp. in animal feces and drinking water on dairy farms and to identify a possible relation between the exposure factors and the presence of these parasites. Fecal samples from cattle and humans and water samples were collected on dairy farms in Paraná, Brazil. Analysis of (oo)cysts in the feces was performed by the modified Ziehl-Neelsen staining and centrifugal flotation in zinc sulfate. Test-positive samples were subjected to nested PCR amplification of the 18SSU ribosomal RNA gene for identification of Cryptosporidium and Giardia and of the gp60 gene for subtyping of Cryptosporidium. Microbiological analysis of water was carried out by the multiple-tube method and by means of a chromogenic substrate, and parasitological analysis was performed on 31 samples by direct immunofluorescence and nested PCR of the genes mentioned above. Identification of the species of Cryptosporidium was performed by sequencing and PCR with analysis of restriction fragment length polymorphisms. The prevalence of Giardia and Cryptosporidium was higher in calves than in adults. Among the samples of cattle feces, Cryptosporidium parvum was identified in 41 (64%), C. ryanae in eight (12.5%), C. bovis in four (6.3%), C. andersoni in five (7.8%), and a mixed infection in 20 samples (31.3%). These parasites were not identified in the samples of human feces. Thermotolerant coliform bacteria were identified in 25 samples of water (45.5%). Giardia duodenalis and C. parvum were identified in three water samples. The gp60 gene analysis of C. parvum isolates revealed the presence of two strains (IIaA20G1R1 and IIaA17G2R2) in the fecal samples and one (IIaA17G2R1) in the water samples. The presence of coliforms was associated with the water source, structure and degradation of springs, rain, and turbidity. The prevalence of protozoa was higher in calves up to six months of age. C. parvum and G. duodenalis were identified in the water of dairy farms, as were thermotolerant coliforms; these findings point to the need for guidance on handling of animals, preservation of water sources, and water treatment.

Waterborne Viruses and F-Specific Coliphages in Mixed-Use Watersheds: Microbial Associations, Host Specificities, and Affinities with Environmental/Land Use Factors

From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml^-1, respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml^-1 delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment.

IMPORTANCE

This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets.

Towards a more accurate quantitative assessment of seasonal Cryptosporidium infection risks in surface waters using species and genotype information

Many Cryptosporidium species/genotypes are not considered infectious to humans, and more realistic estimations of seasonal infection risks could be made using human infectious species/genotype information to inform quantitative microbial risk assessments (QMRA). Cryptosporidium oocyst concentration and species/genotype data were collected from three surface water surveillance programs in two river basins [South Nation River, SN (2004-09) and Grand River, GR (2005-13)] in Ontario, Canada to evaluate seasonal infection risks. Main river stems, tributaries, agricultural drainage streams, water treatment plant intakes, and waste water treatment plant effluent impacted sites were sampled. The QMRA employed two sets of exposure data to compute risk: one assuming all observed oocysts were infectious to humans, and the other based on the fraction of oocysts that were C. hominis and/or C. parvum (dominant human infectious forms of the parasite). Viability was not considered and relative infection risk was evaluated using a single hypothetical recreational exposure. Many sample site groupings for both river systems, had significant seasonality in Cryptosporidium occurrence and concentrations (p ≤ 0.05); occurrence and concentrations were generally highest in autumn for SN, and autumn and summer for GR. Mean risk values (probability of infection per exposure) for all sites combined, for each river system, were roughly an order of magnitude lower (avg. of SN and GR 5.3 × 10^-5) when considering just C. parvum and C. hominis oocysts, in relation to mean infection risk (per exposure) assuming all oocysts were infectious to humans (5.5 × 10^-4). Seasonality in mean risk (targeted human infectious oocysts only) was most strongly evident in SN (e.g., 7.9 × 10^-6 in spring and 8.1 × 10^-5 in summer). Such differences are important if QMRA is used to quantify effects of water safety/quality management practices where inputs from a vast array of fecal pollution sources can readily occur. Cryptosporidium seasonality in water appears to match the seasonality of human infections from Cryptosporidium in the study regions. This study highlights the importance of Cryptosporidium species/genotype data to help determine surface water pollution sources and seasonality, as well as to help more accurately quantify human infection risks by the parasite.

Molecular detection of Toxoplasma gondii in water samples from Scotland and a comparison between the 529bp real-time PCR and ITS1 nested PCR

Waterborne transmission of Toxoplasma gondii is a potential public health risk and there are currently no agreed optimised methods for the recovery, processing and detection of T. gondii oocysts in water samples. In this study modified methods of T. gondii oocyst recovery and DNA extraction were applied to 1427 samples collected from 147 public water supplies throughout Scotland. T. gondii DNA was detected, using real time PCR (qPCR) targeting the 529bp repeat element, in 8.79% of interpretable samples (124 out of 1411 samples). The samples which were positive for T. gondii DNA originated from a third of the sampled water sources. The samples which were positive by qPCR and some of the negative samples were reanalysed using ITS1 nested PCR (nPCR) and results compared. The 529bp qPCR was the more sensitive technique and a full analysis of assay performance, by Bayesian analysis using a Markov Chain Monte Carlo method, was completed which demonstrated the efficacy of this method for the detection of T. gondii in water samples.

Fine-Scale Spatial Heterogeneity in the Distribution of Waterborne Protozoa in a Drinking Water Reservoir

Background: The occurrence of faecal pathogens in drinking water resources constitutes a threat to the supply of safe drinking water, even in industrialized nations. To efficiently assess and monitor the risk posed by these pathogens, sampling deserves careful design, based on preliminary knowledge on their distribution dynamics in water. For the protozoan pathogens Cryptosporidium and Giardia, only little is known about their spatial distribution within drinking water supplies, especially at fine scale. Methods: Two-dimensional distribution maps were generated by sampling cross-sections at meter resolution in two different zones of a drinking water reservoir. Samples were analysed for protozoan pathogens as well as for E. coli, turbidity and physico-chemical parameters. Results: Parasites displayed heterogeneous distribution patterns, as reflected by significant (oo)cyst density gradients along reservoir depth. Spatial correlations between parasites and E. coli were observed near the reservoir inlet but were absent in the downstream lacustrine zone. Measurements of surface and subsurface flow velocities suggest a role of local hydrodynamics on these spatial patterns. Conclusion: This fine-scale spatial study emphasizes the importance of sampling design (site, depth and position on the reservoir) for the acquisition of representative parasite data and for optimization of microbial risk assessment and monitoring. Such spatial information should prove useful to the modelling of pathogen transport dynamics in drinking water supplies.

Development and Evaluation of Three Real-Time PCR Assays for Genotyping and Source Tracking Cryptosporidium spp. in Water

The occurrence of Cryptosporidium oocysts in drinking source water can present a serious public health risk. To rapidly and effectively assess the source and human-infective potential of Cryptosporidium oocysts in water, sensitive detection and correct identification of oocysts to the species level (genotyping) are essential. In this study, we developed three real-time PCR genotyping assays, two targeting the small-subunit (SSU) rRNA gene (18S-LC1 and 18S-LC2 assays) and one targeting the 90-kDa heat shock protein (hsp90) gene (hsp90 assay), and evaluated the sensitivity and Cryptosporidium species detection range of these assays. Using fluorescence resonance energy transfer probes and melt curve analysis, the 18S-LC1 and hsp90 assays could differentiate common human-pathogenic species (C. parvum, C. hominis, and C. meleagridis), while the 18S-LC2 assay was able to differentiate nonpathogenic species (such as C. andersoni) from human-pathogenic ones commonly found in source water. In sensitivity evaluations, the 18S-LC2 and hsp90 genotyping assays could detect as few as 1 Cryptosporidium oocyst per sample. Thus, the 18S-LC2 and hsp90 genotyping assays might be used in environmental monitoring, whereas the 18S-LC1 genotyping assay could be useful for genotyping Cryptosporidium spp. in clinical specimens or wastewater samples.

Prevalence, species identification and genotyping Cryptosporidium from livestock and deer in a catchment in the Cairngorms with a history of a contaminated public water supply

Background

The apicomplexan parasite Cryptosporidium represents a threat to water quality and public health. An important zoonotic species involved in human cryptosporidiosis from contaminated water is Cryptosporidium parvum (C. parvum), the main reservoirs of which are known to be farm livestock particularly neonatal calves, although adult cattle, sheep, lambs and wildlife are also known to contribute to catchment loading of C. parvum. This study aimed to establish Cryptosporidium prevalence, species and genotype in livestock, deer and water in a catchment with a history of Cryptosporidium contamination in the public water supply.

Methods

A novel method of processing adult ruminant faecal sample was used to concentrate oocysts, followed by a nested species specific multiplex (nssm) PCR, targeting the 18S rRNA gene, to speciate Cryptosporidium. A multilocus fragment typing (MLFT) tool was used, in addition to GP60 sequencing, to genotype C. parvum positive samples.

Results

A very high prevalence of Cryptosporidium was detected, with speciation identifying a predominance of C. parvum in livestock, deer and water samples. Four GP60 subtypes were detected within C. parvum with the majority IIaA15G2R1 which was detected in all host species and on all farms. Multilocus fragment typing further differentiated these into 6 highly related multilocus genotypes.

Conclusion

The high prevalence of Cryptosporidium detected was possibly due to a combination of the newly developed sample processing technique used and a reflection of the high rates of the parasite present in this catchment. The predominance of C. parvum in livestock and deer sampled in this study suggested that they represented a significant risk to water quality and public health. Genotyping results suggested that the parasite is being transmitted locally within the study area, possibly via free-roaming sheep and deer. Further studies are needed to verify particular host associations with subtypes/MLGs. Land and livestock management solutions to reduce Cryptosporidium on farm and in the catchment are planned with the aim to improve animal health and production as well as water quality and public health.

Cryptosporidium and Giardia in surface water: a case study from Michigan, USA to inform management of rural water systems

Cryptosporidium and Giardia pose a threat to human health in rural environments where water supplies are commonly untreated and susceptible to contamination from agricultural animal waste/manure, animal wastewater, septic tank effluents and septage. Our goals for this paper are to: (1) explore the prevalence of these protozoan parasites, where they are found, in what quantities, and which genotypes are present; (2) examine relationships between disease and land use comparing human health risks between rural and urban environments; and (3) synthesize available information to gain a better understanding of risk and risk management for rural water supplies. Our results indicate that Cryptosporidium and Giardia were more prevalent in rural versus urban environments based on the number of positive samples. Genotyping showed that both the human and animal types of the parasites are found in rural and urban environments. Rural areas had a higher incidence of disease compared to urban areas based on the total number of disease cases. Cryptosporidiosis and giardiasis were both positively correlated (p < 0.001) with urban area, population size, and population density. Finally, a comprehensive strategy that creates knowledge pathways for data sharing among multiple levels of management may improve decision-making for protecting rural water supplies.

A national investigation of the prevalence and diversity of thermophilic Campylobacter species in agricultural watersheds in Canada

The occurrence and diversity of thermophilic Campylobacter species (C. jejuni, coli, and lari) were studied in water samples from four river basins located across Canada. These basins located in Quebec (Bras d'Henri), Alberta (Oldman), Ontario (South Nation), and British Columbia (Sumas) represented some of the most intensive farming areas in Canada for hog, beef cattle, dairy cattle, and poultry, respectively. This study analyzed 769 water samples collected from 23 monitoring sites with agricultural influence, and four reference sites with limited or no agricultural influence. Water samples were collected bi-weekly over two years and analyzed for Campylobacter using a semi-quantitative minimum probable number (MPN) enrichment protocol. Putative isolates were confirmed by genus- and species-specific multiplex polymerase chain reaction (PCR) assays. A total of 377 (49%) water samples were positive for campylobacters with 355 samples having a cell density ranging from 4 to 4000 MPN L(-1). Campylobacters were more common at agricultural than reference sites in each river basin, although this difference was not significant in the Oldman and South Nation (p > 0.05). Campylobacter was significantly more common in the Bras d'Henri and Sumas (63%) compared to the South Nation (45%) and Oldman (33%) River basins (p < 0.05). C. jejuni, C. coli and C. lari were detected in each river basin, and these species occurred in 45% (n = 168), 34% (n = 128) and 19% (n = 73), of all Campylobacter positive samples, respectively. The remaining Campylobacter positive water samples without these three species (n = 67; 18%) were identified as other Campylobacter species. C. jejuni was the predominant species occurring in the Sumas, Oldman and South Nation River basins. However, in the Bras d'Henri River basin with intensive hog production, C. coli was the predominant species. This study found campylobacters to be common in some agricultural systems with intensive livestock farming activities, and different river basins could have strikingly different profiles of either C. jejuni or C. coli as the predominant waterborne thermophilic Campylobacter species.

The impact of major earthquakes and subsequent sewage discharges on the microbial quality of water and sediments in an urban river

A series of large earthquakes struck the city of Christchurch, New Zealand in 2010-2011. Major damage sustained by the sewerage infrastructure required direct discharge of up to 38,000 m(3)/day of raw sewage into the Avon River of Christchurch for approximately six months. This allowed evaluation of the relationship between concentrations of indicator microorganisms (Escherichia coli, Clostridium perfringens and F-RNA phage) and pathogens (Campylobacter, Giardia and Cryptosporidium) in recreational water and sediment both during and post-cessation of sewage discharges. Giardia was the pathogen found most frequently in river water and sediment, although Campylobacter was found at higher levels in water samples. E. coli levels in water above 550 CFU/100 mL were associated with increased likelihood of detection of Campylobacter, Giardia and Cryptosporidium, supporting the use of E. coli as a reliable indicator for public health risk. The strength of the correlation of microbial indicators with pathogen detection in water decreased in the following order: E. coli>F-RNA phage>C. perfringens. All the microorganisms assayed in this study could be recovered from sediments. C. perfringens was observed to accumulate in sediments, which may have confounded its usefulness as an indicator of fresh sewage discharge. F-RNA phage, however, did not appear to accumulate in sediment and in conjunction with E. coli, may have potential as an indicator of recent human sewage discharge in freshwater. There is evidence to support the low-level persistence of Cryptosporidium and Giardia, but not Campylobacter, in river sediments after cessation of sewage discharges. In the event of disturbances of the sediment, it is highly probable that there could be re-mobilisation of microorganisms beyond the sediment-water exchange processes occurring under base flow conditions. Re-suspension events do, therefore, increase the potential risk to human health for those who participate in recreational and work-related activities in the river environment.

Receiver-operating characteristics analysis: a new approach to predicting the presence of pathogens in surface waters

Fecal indicator microbes are used to monitor the public health risks of recreating in surface waters. However, the importance of indicator tests as predictors of waterborne pathogens has been unclear. Numerous studies have also shown that the survival and growth of indicator organisms may depend on location-specific factors that cannot be broadly generalized. We used receiver-operating characteristic (ROC) methods to determine whether fecal indicator species are capable of predicting the presence of Giardia and Cryptosporidium in fresh surface waters in the Chicago area. We also derived recreational water quality criteria specific to our location with respect to this end point. We considered five fecal indicators: enterococci measured by culture and quantitative polymerase chain reaction (qPCR), Escherichia coli measured by culture, somatic coliphage, and F+ coliphage. All fecal indicators were found to predict the presence and absence of protozoan pathogens. The test for enterococci measured by culture was the poorest predictor of the presence of pathogens. The test for enterococci measured by qPCR was the best predictor of the presence of Giardia, but not an important predictor of the presence of Cryptosporidium. The test for somatic coliphage was a relatively strong predictor of the presence of both pathogens. This analysis supports the use of qPCR-based assays over culture-based assays for predicting the presence of Giardia in fresh surface water. Our criteria were optimized for the prediction of the presence of Giardia and Cryptosporidium in our location and were closely aligned with criteria of the U.S. Environmental Protection Agency derived from epidemiological risk assessment. The ROC approach is flexible and can inform location-specific interpretation of water quality monitoring data and decision making.

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.

Using SWAT, Bacteroidales microbial source tracking markers, and fecal indicator bacteria to predict waterborne pathogen occurrence in an agricultural watershed

Developing the capability to predict pathogens in surface water is important for reducing the risk that such organisms pose to human health. In this study, three primary data source scenarios (measured stream flow and water quality, modelled stream flow and water quality, and host-associated Bacteroidales) are investigated within a Classification and Regression Tree Analysis (CART) framework for classifying pathogen (Escherichia coli 0157:H7, Salmonella, Campylobacter, Cryptosporidium, and Giardia) presence and absence (P/A) for a 178 km(2) agricultural watershed. To provide modelled data, a Soil Water Assessment Tool (SWAT) model was developed to predict stream flow, total suspended solids (TSS), total N and total P, and fecal indicator bacteria loads; however, the model was only successful for flow and total N and total P simulations, and did not accurately simulate TSS and indicator bacteria transport. Also, the SWAT model was not sensitive to an observed reduction in the cattle population within the watershed that may have resulted in significant reduction in E. coli concentrations and Salmonella detections. Results show that when combined with air temperature and precipitation, SWAT modelled stream flow and total P concentrations were useful for classifying pathogen P/A using CART methodology. From a suite of host-associated Bacteroidales markers used as independent variables in CART analysis, the ruminant marker was found to be the best initial classifier of pathogen P/A. Of the measured sources of independent variables, air temperature, precipitation, stream flow, and total P were found to be the most important variables for classifying pathogen P/A. Results indicate a close relationship between cattle pollution and pathogen occurrence in this watershed, and an especially strong link between the cattle population and Salmonella detections.

Bacteria, viruses, and parasites in an intermittent stream protected from and exposed to pasturing cattle: prevalence, densities, and quantitative microbial risk assessment

Over 3500 individual water samples, for 131 sampling times, targeting waterborne pathogens/fecal indicator bacteria were collected during a 7-year period from 4 sites along an intermittent stream running through a small livestock pasture system with and without cattle access-to-stream restriction measures. The study assessed the impact of cattle pasturing/riparian zone protection on: pathogen (bacterial, viral, parasite) occurrence, concentrations of fecal indicators, and quantitative microbial risk assessments (QMRA) of the risk of Cryptosporidium, Giardia and Escherichia coli O157:H7 infection in humans. Methodologies were developed to compute QMRA mean risks on the basis of water samples exhibiting potentially human infectious Cryptosporidium and E. coli based on genotyping Crytosporidium, and E. coli O157:H7 presence/absence information paired with enumerated E. coli. All Giardia spp. were considered infectious. No significant pasturing treatment effects were observed among pathogens, with the exception of Campylobacter spp. and E. coli O157:H7. Campylobacter spp. prevalence significantly decreased downstream through pasture treatments and E. coli O157:H7 was observed in a few instances in the middle of the unrestricted pasture. Densities of total coliform, fecal coliform, and E. coli reduced significantly downstream in the restricted pasture system, but not in the unrestricted system. Seasonal and flow conditions were associated with greater indicator bacteria densities, especially in the summer. Norovirus GII was detected at rates of 7-22% of samples for all monitoring sites, and rotavirus in 0-7% of samples for all monitoring sites; pasture treatment trends were not evident, however. Seasonal and stream flow variables (and their interactions) were relatively more important than pasture treatments for initially stratifying pathogen occurrence and higher fecal indicator bacteria densities. Significant positive associations among fecal indicator bacteria and Campylobacter spp. detection were observed. For QMRA, adjusting for the proportion of Cryptosporidium spp. detected that are infectious for humans reduces downstream risk estimates by roughly one order of magnitude. Using QMRA in this manner provides a more refined estimate of beneficial management practice effects on pathogen exposure risks to humans.

Assessment of a new Bacteroidales marker targeting North American beaver (Castor canadensis) fecal pollution by real-time PCR

In many settings wildlife can be a significant source of fecal pathogen input into surface water. The North American beaver (Castor canadensis) is a zoonotic reservoir for several human pathogens including Cryptosporidium spp. and Giardia spp. In order to specifically detect fecal pollution by beavers, we have developed and validated a beaver-specific Bacteroidales marker, designated Beapol01, based on the 16S rRNA gene. The marker is suitable for quantifying pollution using real-time PCR. The specificity and sensitivity of the marker was excellent, Beaver signal was detected in water of a mixed-activity watershed harbouring this rodent. Overall, Beapol01 will be useful for a better understanding of fecal source inputs in drainage basins inhabited by the beaver.

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.

Using Campylobacter spp. and Escherichia coli data and Bayesian microbial risk assessment to examine public health risks in agricultural watersheds under tile drainage management

Human campylobacteriosis is the leading bacterial gastrointestinal illness in Canada; environmental transmission has been implicated in addition to transmission via consumption of contaminated food. Information about Campylobacter spp. occurrence at the watershed scale will enhance our understanding of the associated public health risks and the efficacy of source water protection strategies. The overriding purpose of this study is to provide a quantitative framework to assess and compare the relative public health significance of watershed microbial water quality associated with agricultural BMPs. A microbial monitoring program was expanded from fecal indicator analyses and Campylobacter spp. presence/absence tests to the development of a novel, 11-tube most probable number (MPN) method that targeted Campylobacter jejuni, Campylobacter coli, and Campylobacter lari. These three types of data were used to make inferences about theoretical risks in a watershed in which controlled tile drainage is widely practiced, an adjacent watershed with conventional (uncontrolled) tile drainage, and reference sites elsewhere in the same river basin. E. coli concentrations (MPN and plate count) in the controlled tile drainage watershed were statistically higher (2008-11), relative to the uncontrolled tile drainage watershed, but yearly variation was high as well. Escherichia coli loading for years 2008-11 combined were statistically higher in the controlled watershed, relative to the uncontrolled tile drainage watershed, but Campylobacter spp. loads for 2010-11 were generally higher for the uncontrolled tile drainage watershed (but not statistically significant). Using MPN data and a Bayesian modelling approach, higher mean Campylobacter spp. concentrations were found in the controlled tile drainage watershed relative to the uncontrolled tile drainage watershed (2010, 2011). A second-order quantitative microbial risk assessment (QMRA) was used, in a relative way, to identify differences in mean Campylobacter spp. infection risks among monitoring sites for a hypothetical exposure scenario. Greater relative mean risks were obtained for sites in the controlled tile drainage watershed than in the uncontrolled tile drainage watershed in each year of monitoring with pair-wise posterior probabilities exceeding 0.699, and the lowest relative mean risks were found at a downstream drinking water intake reference site. The second-order modelling approach was used to partition sources of uncertainty, which revealed that an adequate representation of the temporal variation in Campylobacter spp. concentrations for risk assessment was achieved with as few as 10 MPN data per site. This study demonstrates for the first time how QMRA can be implemented to evaluate, in a relative sense, the public health implications of controlled tile drainage on watershed-scale water quality.

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.