Spatial and temporal drivers of zoonotic pathogen contamination of an agricultural watershed

Veterinary antimicrobials in cattle feedlot environs and irrigation conveyances in a high-intensity agroecosystem in southern Alberta, Canada

The South Saskatchewan River Basin (SSRB) is considered one of the most intensively farmed regions in Canada, with high densities of livestock and expansive areas of irrigated cropland. We measured concentrations of seven veterinary antimicrobials (VAs) in 114 surface water samples from feedlot environs and 219 samples from irrigation conveyances in the SSRB. Overall, detection frequencies in feedlot environs were 100% for chlortetracycline (CTC) and tetracycline (TC), 94% for monensin (MON), 84% for tylosin (TYL), 72% for lincomycin (LIN), 66% for erythromycin (ERY), and 23% for sulfamethazine (SMZ). For irrigation conveyances, detection frequencies for CTC and TC remained high (94-100%), but dropped to 18% for ERY, 15% for TYL, 10% for MON, and 4% for SMZ. Lincomycin was not detected in irrigation conveyance water. Maximum concentrations of VAs ranged from 1384 µg L^-1 (TC) to 17 ng L^-1 (SMZ) in feedlot environs while those in irrigation conveyances were 155 ng L^-1 (TC) to 29 ng L^-1 (ERY). High detection frequencies and median concentrations of VAs in both feedlot environs and irrigation conveyances were associated with high amounts of precipitation. However, an irrigation district (ID) with high livestock density (Lethbridge Northern) did not exhibit higher concentrations of VAs compared to IDs with less livestock, while levels of VAs in irrigation conveyances were less influenced by the degree of surface runoff. The ubiquity of CTC and TC in our study is likely a reflection of its widespread use in intensive livestock operations. Additional investigation is required to link environmental concentrations of VAs with livestock densities and increase our understanding of potential antimicrobial resistance in high-intensity agroecosystems.

A watershed study assessing effects of commercial hog operations on microbial water quality in North Carolina, USA

Commercial Hog Operations (CHOs) produce large amounts of fecal waste, which is often treated in lagoons and sprayed onto fields as fertilizer. The effects of these systems on proximal water quality compared to ambient conditions have not been well-studied, and are particularly important for understanding the dissemination of fecal bacteria and antimicrobial resistance. A longitudinal, case-control watershed study was designed to study effects of CHOs on microbial water quality among watersheds with similar soil, land use, human population, and area. We compared watersheds with (n = 13) and without (n = 9) CHOs over one year measuring fecal indicator bacteria (FIB), microbial source tracking (MST) fecal markers, and antimicrobial resistance in isolated Escherichia coli. E. coli concentrations were higher (p < 0.001) at sites downstream of CHOs (1284 CFU/100 mL, n = 103) compared to background sites (687 CFU/100 mL, n = 74). The human MST marker HF183 was detected at similarly low concentrations (PR = 1.3 (0.91, 1.8), p = 0.30). However, the swine MST marker pig-2-bac was found at more sites downstream of CHOs (PR = 3.5 (0.98, 12), p = 0.035) and at a significantly higher (p = 0.003) mean concentration at sites downstream of CHOs (283 copies/mL) compared to background sites (0.76 copies/mL). The presence of any antimicrobial resistance was observed more often for E. coli isolated downstream from CHOs (19%, n = 556) than background sites (6%, n = 356), with tetracycline resistance observed most often. Nine isolates from four sites downstream of CHOs and one isolate from a background site were confirmed β-lactamase-producing E. coli. Overall, these results show that fecal microbes and antimicrobial resistance from CHOs may be transported off-site, however more research is needed to characterize timing and conditions of off-site transport. Mitigation strategies such as optimizeation of waste treatment, buffers, and antibiotic stewardship could help reduce the contributions of microbial contaminants to surface water.

The Fate of Foodborne Pathogens in Manure Treated Soil

The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.

Antimicrobial Resistance in Escherichia coli and Enterococcal Isolates From Irrigation Return Flows in a High-Desert Watershed

Irrigation return flows (IRFs) collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential source of pollutants. The purpose of this study was to determine antimicrobial susceptibility among Escherichia coli and enterococcal isolates that were collected from IRFs in a south-central Idaho watershed. Environmental isolates can be a potentially important source of antimicrobial resistance (AMR) and IRFs may be one way resistance genes are transported out of agroecosystems. Water samples were collected from nine IRFs and one background site (canal water from Snake River) on a biweekly basis during 2018. Escherichia coli and enterococci were enumerated via a most probable number (MPN) technique, then subsamples were plated on selective media to obtain isolates. Isolates of E. coli (187) or enterococci (185) were tested for antimicrobial susceptibility using Sensititre broth microdilution plates. For E. coli, 13% (25/187) of isolates were resistant to tetracycline, with fewer numbers being resistant to 13 other antimicrobials, with none resistant to gentamicin. While 75% (141/187) of the E. coli isolates were pan-susceptible, 12 multidrug resistance (MDR) patterns with 17 isolates exhibiting resistance to up to seven drug classes (10 antimicrobials). For the enterococcal species, only 9% (16/185) of isolates were pan-susceptible and the single highest resistance was to lincomycin (138/185; 75%) followed by nitrofurantoin (56/185; 30%) and quinupristin/dalfopristin (34/185; 18%). In addition, 13 enterococcal isolates belonging to Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, and Enterococcus thailandicus, were determined to be MDR to up to six different antimicrobial drug classes. None of the enterococcal isolates were resistant to gentamycin, linezolid, tigecycline, and vancomycin.

Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling

The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal defense tissue against pathogens, as manifested by the presence of the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of multifactorial gill pathologies has increased significantly, causing substantial losses in Atlantic salmon aquaculture. The transition from healthy to unhealthy gill phenotypes and the progression of multifactorial gill pathologies, such as proliferative gill disease (PGD), proliferative gill inflammation (PGI) and complex gill disorder (CGD), are commonly characterized by epithelial hyperplasia, lamellar fusion and inflammation. Routine monitoring for PGD relies on visual inspection and non-invasive scoring of the gill tissue (gross morphology), coupled with histopathological examination of gill sections. To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). Our results strongly suggested that the changes in PGD scores of the gill tissue were not associated with the changes in gene expression or histopathology. In contrast, integration of the gill RNA-seq data with the gill histopathology enabled us to identify common gene expression patterns associated with multifactorial gill disease, independently from the origin of samples. We demonstrated that the gene expression patterns associated with multifactorial gill disease were dominated by two processes: a range of immune responses driven by pro-inflammatory cytokines and the events associated with tissue damage and repair, driven by caspases and angiogenin.

Differential Effects of Drinking Water Quality on Phagocyte Responses of Broiler Chickens Against Fungal and Bacterial Challenges

Combinatorial effects of xenobiotics in water on health may occur even at levels within current acceptable guidelines for individual chemicals. Herein, we took advantage of the sensitivity of the immune system and an avian animal model to examine the impact of xenobiotic mixtures on animal health. Water was derived from an underground well in Alberta, Canada and met guidelines for consumption, but contained a number of contaminants. Changes to chicken immunity were evaluated following acute (7d) exposure to contaminated water under basal and immune challenged conditions. An increase in resident macrophages and a decrease in CD8+ lymphocytes were identified in the abdominal cavity, which served as a relevant site where immune leukocytes could be examined. Subsequent intra-abdominal immune stimulation detected differential in vivo acute inflammatory responses to fungal and bacterial challenges. Leukocyte recruitment into the challenge site and activation of phagocyte antimicrobial responses were affected. These functional responses paralleled molecular changes in the expression for pro-inflammatory and regulatory genes. In all, this study primarily highlights dysregulation of phagocyte responses following acute (7d) exposure of poultry to contaminated water. Given that production food animals hold a unique position at the interface of animal, environmental and human health, this emphasizes the need to consider the impact of xenobiotic mixtures in our assessments of water quality.

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

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

Evaluating the risks associated with Shiga-toxin-producing Escherichia coli (STEC) in private well waters in Canada

Shiga-toxin-producing Escherichia coli (STEC) represent a major concern for waterborne disease outbreaks associated with consumption of contaminated groundwater. Over 4 million people rely on private groundwater systems as their primary drinking water source in Canada; many of these systems do not meet current standards for water quality. This manuscript provides a scoping overview of studies examining STEC prevalence and occurrence in groundwater, and it includes a synopsis of the environmental variables affecting survival, transport, persistence, and overall occurrence of these important pathogenic microbes in private groundwater wells used for drinking purposes.

A Review of Potential Public Health Impacts Associated With the Global Dairy Sector

Strong demand for dairy products has led to a global increase in dairy production. In many parts of the world, dairy systems are undergoing rapid intensification. While increased production may contribute to food security, higher dairy stocking rates in some regions have resulted in increased pressure on natural resources with the potential to affect public health and wellbeing. The aim of this review was to identify and describe the potential health harms and benefits associated with dairy production and consumption. Electronic databases Medline, Embase, Scopus, Web of Science, PubMed, and Google Scholar were searched for published literature that investigated human health impacts of dairy production and consumption. Occupational hazards, environmental health impacts, ecosystem health impacts, foodborne hazards, and diet-related chronic diseases were identified as potential public health hazards. Some impacts, notably climate change, extend beyond directly exposed populations. Dairy production and consumption are also associated with important health benefits through the provision of nutrients and economic opportunities. As the global dairy sector increases production, exposure to a range of hazards must be weighed with these benefits. The review of impacts presented here can provide an input into decision making about optimal levels of dairy production and consumption, local land use, and identification and management of specific hazards from this sector. Future research should consider multiple exposure routes, socioeconomic implications, and environmental factors, particularly in regions heavily dependent on dairy farming.

Climate-driven QMRA model for selected water supply systems in Norway accounting for raw water sources and treatment processes

Formulating effective management intervention measures for water supply systems requires investigation of potential long-term impacts. This study applies an integrated multiple regression, random forest regression, and quantitative microbial risk assessment (QMRA) modelling approach to assess the effect of climate-driven precipitation on pathogen infection risks in three drinking water treatment plants (WTPs) in Norway. Pathogen removal efficacies of treatment steps were calculated using process models. The results indicate that while the WTPs investigated generally meet the current water safety guidelines, risks of Norovirus and Cryptosporidium infection may be of concern in the future. The pathogen infections attributable to current projections of average precipitation in the study locations may be low. However, the pathogen increases in the drinking water sources due to the occurrence of extreme precipitation events in the catchments could substantially increase the risks of pathogen infections. In addition, without optimal operation of the UV disinfection steps in the WTPs, both the present and potential future infection risks could be high. Therefore, the QMRA models demonstrated the need for improved optimization of key treatment steps in the WTPs, as well as implementation of stringent regulations in protecting raw water sources in the country. The variety of models applied and the pathogen: E. coli used in the study introduce some uncertainties in the results, thus, management decisions that will be based on the results should consider these limitations. Nevertheless, the integration of predictive models with QMRA as applied in this study could be a useful method for climate impact assessment in the water supply industry.

Real-Time Estimates of Escherichia coli Concentrations Using Ultraviolet-Visible Spectrometers

Substantial effort has been invested in the development and testing of methods to rapidly measure the concentration of indicator bacteria in recreational waters. These efforts are driven by the need to quickly determine whether waters are contaminated and may pose excessive public health risks. In situ ultraviolet-visible (UV-vis) spectrometers have been used to monitor levels of multiple contaminants in surface waters by relating the absorption spectra to the measured concentrations using regression models. In this study, three different regression models were tested to see if spectroscopy could be used to rapidly predict concentrations in a freshwater stream. The regression models did not produce acceptable results when tested for all of the samples collected during an 11-mo period ( < 0.2). When divided into multiple subsets based on temperature, concentration, or rainfall, models produced adequate results for subsets of samples collected in the cooler months ( = 0.72) or on days when rainfall occurred ( = 0.58). Pairing a UV-vis spectrometer with regression models did not result in a model that could be used to estimate levels throughout the year, but the results promote further testing of this method when flow data is available in freshwaters, on beaches where rainfall causes elevated bacteria levels, and in shellfish growing waters.

Comparative predictive modelling of the occurrence of faecal indicator bacteria in a drinking water source in Norway

Presently, concentrations of fecal indicator bacteria (FIB) in raw water sources are not known before water undergoes treatment, since analysis takes approximately 24h to produce results. Using data on water quality and environmental variables, models can be used to predict real time concentrations of FIB in raw water. This study evaluates the potentials of zero-inflated regression models (ZI), Random Forest regression model (RF) and adaptive neuro-fuzzy inference system (ANFIS) to predict the concentration of FIB in the raw water source of a water treatment plant in Norway. The ZI, RF and ANFIS faecal indicator bacteria predictive models were built using physico-chemical (pH, temperature, electrical conductivity, turbidity, color, and alkalinity) and catchment precipitation data from 2009 to 2015. The study revealed that pH, temperature, turbidity, and electrical conductivity in the raw water were the most significant factors associated with the concentration of FIB in the raw water source. Compared to the other models, the ANFIS model was superior (Mean Square Error=39.49, 0.35, 0.09, 0.23CFU/100ml respectively for coliform bacteria, E. coli, Intestinal enterococci and Clostridium perfringens) in predicting the variations of FIB in the raw water during model testing. However, the model was not capable of predicting low counts of FIB during both training and testing stages of the models. The ZI and RF models were more consistent when applied to testing data, and they predicted FIB concentrations that characterized the observed FIB concentrations. While these models might need further improvement, results of this study indicate that ZI and RF regression models have high prospects as tools for the real-time prediction of FIB in raw water sources for proactive microbial risk management in water treatment plants.

Occurrence, characterization, and potential predictors of verotoxigenic Escherichia coli, Listeria monocytogenes, and Salmonella in surface water used for produce irrigation in the Lower Mainland of British Columbia, Canada

Produce has become a major source of foodborne illness, and may become contaminated through surface water irrigation. The objectives of this study were to (i) determine the frequency of verotoxigenic E. coli (VTEC), Listeria monocytogenes, and Salmonella in surface waters used for irrigation in the Lower Mainland of British Columbia, (ii) assess the suitability of fecal coliforms and generic E. coli as hygiene indicators, and (iii) investigate the correlations of environmental factors with pathogen occurrence. Water samples were collected semi-monthly for 18 months from seven irrigation ditches across the Serpentine and Sumas watersheds. VTEC colonies on water filters were detected using a verotoxin colony immunoblot, and the presence of virulence genes vt1 and vt2 was ascertained via multiplex PCR. Detection of L. monocytogenes and Salmonella was completed using standard, Health Canada Compendium of Analytical Methods. Fecal coliforms and generic E. coli were enumerated by 3M™ Petrifilm™ and filtration methods, and meteorological and geographic data were collected from government records. VTEC, L. monocytogenes, and Salmonella were detected in 4.93%, 10.3%, and 2.69% of 223 samples, respectively. L. monocytogenes occurrence was greatest in the Serpentine watershed (χ2; p < 0.05), and was most common during the winter and fall (Fisher exact test; p < 0.05). Site dependence of VTEC and Salmonella occurrence was observed within watersheds (Fisher's exact test; p < 0.10). Pathogen occurrence correlated with fecal coliform counts (r = 0.448), while VTEC occurrence also correlated with precipitation over the five days before sampling (r = 0.239). The density of upstream livestock correlated with VTEC (rs = 0.812), and L. monocytogenes (rs = 0.841) detection. These data show that foodborne pathogens are present in the waters used for irrigation in the Lower Mainland of British Columbia, but their frequency may depend on spatial and temporal factors.

Identification of Factors Affecting Fecal Pollution in Beaver Lake Reservoir

Standard methods for the evaluation of recreational water quality rely on generic bacterial indicators such as . However, does not provide enough information to determine fecal source or public health risk. The stsudy objective was to determine factors influencing the presence of and host-specific markers (HSM) from upstream to downstream in Beaver Lake Reservoir (BLR). From February 2014 to September 2015, 420 base flow and rain event samples were collected from seven sites-two sites from streams (White River [WR] and War Eagle Creek) draining into BLR and five sites from within BLR. Each sample was analyzed for and by quantitative polymerase chain reaction for HSM related to human, bovine, and poultry. The data indicate that overall levels of were significantly greater in the WR and significantly lower at the most downstream sampling location in BLR. is more likely present during spring (adjusted odds ratio [aOR] = 1.86), at the WR sampling site (aOR = 3.39), or during a rain event (aOR = 2.73). Moreover, the HSM HumM2 is more likely present (aOR = 1.99) when is present. These same factors were associated with concentrations >126 most probable number 100 mL (aOR = 2.76-12.48), except the poultry marker CL was more likely associated (aOR = 3.81) than HumM2. This study revealed that both seasonal and locational factors are important variables for fecal pollution in BLR. Moreover, these same factors may apply to fecal pollution in manmade reservoirs within similar types of watersheds across the United States, as well as internationally.

Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment

AIM

Investigate dynamics of culturable mesophilic bacteria and selected food-contaminating bacteria from three herbs and their production environment.

METHODS AND RESULTS

Marjoram, basil and thyme were investigated during one growing season by sampling plants, organic fertilizers, soil, irrigation water and marketed products. Mesophilic bacteria and selected food-contaminating bacteria (Escherichia coli, Enterococcus spp., Bacillus cereus group) were cultured and identified by MALDI biotyping. Culturable mesophilic bacteria on marjoram and basil plants decreased over time by two orders of magnitude starting at above 10⁶ colony forming units per gram (CFU per g), while they remained constant on thyme (~10⁴  CFU per g). Compared to the last field sample, mesophilic bacteria were increased on all market-ready products by one order of magnitude. Marjoram and basil were dominated by B. cereus group, Enterobacter spp. and Pseudomonas spp., thyme by Bacillus spp. and Pseudomonas spp. All selected food-contaminating bacteria were detected in soil and reservoir-sourced irrigation water, whereas in municipal water, only B. cereus group and rarely Enterococcus spp. were found. Escherichia coli was detected only on young marjoram and basil plants (5 × 10² and 5 × 10¹  CFU per g, respectively), whereas Enterococcus spp. and B. cereus group were consistently detected on these two herbs. Thyme plants only contained B. cereus group consistently (above 10³ CFU per g). Marketed marjoram and thyme contained Enterococcus spp. (5 × 10² and 10⁴ CFU per g) and B. cereus group (~5 × 10² CFU per g), while no selected food-contaminating bacteria were found on marketed basil.

CONCLUSIONS

Overall, culturable mesophilic bacteria were dominated by Pseudomonas spp. and Bacillus spp., with increased numbers on market-ready products. Selected food-contaminating bacteria were readily detectable, however, only the B. cereus group was found throughout in all systems.

SIGNIFICANCE AND IMPACT OF THE STUDY

Insight into composition and development of mesophilic bacterial communities and selected food-contaminating bacteria of fresh herbs contributes to estimating consumer exposure.

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.

Detection of hepatitis E virus and other livestock-related pathogens in Iowa streams

Manure application is a source of pathogens to the environment. Through overland runoff and tile drainage, zoonotic pathogens can contaminate surface water and streambed sediment and could affect both wildlife and human health. This study examined the environmental occurrence of gene markers for livestock-related bacterial, protozoan, and viral pathogens and antibiotic resistance in surface waters within the South Fork Iowa River basin before and after periods of swine manure application on agricultural land. Increased concentrations of indicator bacteria after manure application exceeding Iowa's state bacteria water quality standards suggest that swine manure contributes to diminished water quality and may pose a risk to human health. Additionally, the occurrence of HEV and numerous bacterial pathogen genes for Escherichia coli, Enterococcus spp., Salmonella sp., and Staphylococcus aureus in both manure samples and in corresponding surface water following periods of manure application suggests a potential role for swine in the spreading of zoonotic pathogens to the surrounding environment. During this study, several zoonotic pathogens were detected including Shiga-toxin producing E. coli, Campylobacter jejuni, pathogenic enterococci, and S. aureus; all of which can pose mild to serious health risks to swine, humans, and other wildlife. This research provides the foundational understanding required for future assessment of the risk to environmental health from livestock-related zoonotic pathogen exposures in this region. This information could also be important for maintaining swine herd biosecurity and protecting the health of wildlife near swine facilities.

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected as independent variables that correctly classified Shiga toxin occurrences in water and sediment (54%-87%), and Salmonella occurrences in water (96%). Relationships between pathogens and indicator variables were generally inconsistent and no single indicator adequately described occurrence of all pathogens. Because of inconsistent relationships between individual pathogens and FIB/MST markers, incorporating a combination of FIB, water quality measurements, and MST markers may be the best way to assess microbial water quality in mixed land use systems.

Microbial Transport, Retention, and Inactivation in Streams: A Combined Experimental and Stochastic Modeling Approach

Long-term survival of pathogenic microorganisms in streams enables long-distance disease transmission. In order to manage water-borne diseases more effectively we need to better predict how microbes behave in freshwater systems, particularly how they are transported downstream in rivers. Microbes continuously immobilize and resuspend during downstream transport owing to a variety of processes including gravitational settling, attachment to in-stream structures such as submerged macrophytes, and hyporheic exchange and filtration within underlying sediments. We developed a stochastic model to describe these microbial transport and retention processes in rivers that also accounts for microbial inactivation. We used the model to assess the transport, retention, and inactivation of Escherichia coli in a small stream and the underlying streambed sediments as measured from multitracer injection experiments. The results demonstrate that the combination of laboratory experiments on sediment cores, stream reach-scale tracer experiments, and multiscale stochastic modeling improves assessment of microbial transport in streams. This study (1) demonstrates new observations of microbial dynamics in streams with improved data quality than prior studies, (2) advances a stochastic modeling framework to include microbial inactivation processes that we observed to be important in these streams, and (3) synthesizes new and existing data to evaluate seasonal dynamics.

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.

Effects of future climate and land use scenarios on riverine source water quality

Surface water quality is particularly sensitive to land use practices and climatic events that affect its catchment. The relative influence of a set of watershed characteristics (climate, land use, morphology and pedology) and climatic variables on two key water quality parameters (turbidity and fecal coliforms (FC)) was examined in 24 eastern Canadian catchments at various spatial scales (1 km, 5 km, 10 km and the entire catchment). A regression analysis revealed that the entire catchment was a better predictor of water quality. Based on this information, linear mixed effect models for predicting turbidity and FC levels were developed. A set of land use and climate scenarios was considered and applied within the water quality models. Four land use scenarios (no change, same rate of variation, optimistic and pessimistic) and three climate change scenarios (B1, A1B and A2) were tested and variations for the near future (2025) were assessed and compared to the reference period (2000). Climate change impacts on water quality remained low annually for this time horizon (turbidity: +1.5%, FC: +1.6%, A2 scenario). On the other hand, the influence of land use changes appeared to predominate. Significant benefits for both parameters could be expected following the optimistic scenario (turbidity: -16.4%, FC: -6.3%; p < 0.05). However, pessimistic land use scenario led to significant increases on an annual basis (turbidity: +11.6%, FC: +15.2%; p < 0.05). Additional simulations conducted for the late 21st century (2090) revealed that climate change impacts could become equivalent to those modeled for land use for this horizon.

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.

Weather and livestock risk factors for Escherichia coli O157 human infection in Alberta, Canada

This study investigated the extent to which proximity to cattle and weather events in Alberta predispose human populations to E. coli O157 disease. Cases of human E. coli O157 infection in Alberta between 2004 and 2011 were obtained from the province's Communicable Disease Reporting System and Discharge Abstract Database. Regression models based on spatial area incorporated human infection data with livestock and weather covariates. A variety of regression models were applied (i.e. least squares, spatial lag/error, Poisson, negative binomial) to test the most appropriate approach. Ratios for the total number of calves, bulls and beef cows to human population were highlighted as significant cattle density variables in all final best-fitting models. Weather variables were not significant in final regression models averaged over the full study period. Our results provide evidence of a significant association between measures of cattle density and human E. coli O157 disease in Alberta.

Influence of seasonal and inter-annual hydro-meteorological variability on surface water fecal coliform concentration under varying land-use composition

Quantifying the influence of hydro-meteorological variability on surface source water fecal contamination is critical to the maintenance of safe drinking water. Historically, this has not been possible due to the scarcity of data on fecal indicator bacteria (FIB). We examined the relationship between hydro-meteorological variability and the most commonly measured FIB, fecal coliform (FC), concentration for 43 surface water sites within the hydro-climatologically complex region of British Columbia. The strength of relationship was highly variable among sites, but tended to be stronger in catchments with nival (snowmelt-dominated) hydro-meteorological regimes and greater land-use impacts. We observed positive relationships between inter-annual FC concentration and hydro-meteorological variability for around 50% of the 19 sites examined. These sites are likely to experience increased fecal contamination due to the projected intensification of the hydrological cycle. Seasonal FC concentration variability appeared to be driven by snowmelt and rainfall-induced runoff for around 30% of the 43 sites examined. Earlier snowmelt in nival catchments may advance the timing of peak contamination, and the projected decrease in annual snow-to-precipitation ratio is likely to increase fecal contamination levels during summer, fall, and winter among these sites. Safeguarding drinking water quality in the face of such impacts will require increased monitoring of FIB and waterborne pathogens, especially during periods of high hydro-meteorological variability. This data can then be used to develop predictive models, inform source water protection measures, and improve drinking water treatment.

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.

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.

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.

Evaluating the occurrence of host-specific , general fecal indicators, and bacterial pathogens in a mixed-use watershed

Fecal contamination of water is very common, and, in the United States, prevention is complicated by the colossal span of waterways (>3.5 million miles), heterogeneous sources of pollution, and competing interests in water monitoring. The focus of this study was the Upper Sugar Creek Watershed, a mixed-use watershed with many headwater streams and one of the most contaminated waterways in Ohio. Quantitative polymerase chain reaction (qPCR) and host-specific PCR for were evaluated for the potential to discern sources of fecal contamination. Pathogen-specific qPCR and culturable by most probable number (MPN) were compared at 21 established water quality monitoring sites in the watershed headwaters. Lower numbers of ruminant-specific markers were detected in the base flow water samples compared with the human-specific marker, suggesting the presence of hotspots of human fecal contamination. qPCR and MPN showed significant correlation ( = 0.57; < 0.001). Correlation between general fecal indicator and pathogen concentrations was weak or nonexistent. Coexistence of and human-specific was common ( = 0.015). qPCR may have a greater potential for predicting fecal contamination due to its sensitivity, rapid analysis, and availability of host-specific assays. However, the lack of a strong correlation between pathogens and general fecal indicators suggests that assessment of health risk associated with fecal contamination will require a complement of approaches.

Impact of mixed land-use practices on the microbial water quality in a subtropical coastal watershed

Surface runoff water is an important non-point source of fecal pollution to downstream water; however, there is a lack of systematic studies on the microbial quality of surface runoff water from watersheds with mixed land uses. In this study water samples from 12 surface runoff holding water bodies (SRW), which collected runoff from various patterns of land use within the St. Lucie watershed along the southeastern coastline of Florida, were collected monthly for 22 months. The concentration of fecal indicator bacteria (FIB) and frequency of detection of Salmonella and host specific markers (HF183, CF128, CF193, and HS-esp) were determined, and their associations with land use, rainfall, and water physico-chemical parameters were investigated. Higher FIB concentrations were observed from urban land and cattle ranch sites. Within the same primary land use pattern, different sub-patterns did not have the same level of FIB: golf communities contributed less to fecal pollution than residential areas, and plant nursery sites contained relative higher FIB concentrations than other agricultural sites. Salmonella, CF128, and CF193 markers were more frequently detected from the cattle ranch sites. In contrast the frequency of detecting human specific markers (HF183 and HS-esp) was much higher in residential sites. Rainfall positively affected the concentration of FIB and occurrence of Salmonella, possibly by providing more inputs or mobilizing the sources from sediments. Water temperature, dissolved organic carbon (DOC), and nutrient levels were positively correlated with FIB concentrations and occurrence in SRW, possibly by promoting their growth and survival. This study indicated the need for site specific mitigation strategies to improve SRW and downstream water quality.