Distribution and potential significance of a gull fecal marker in urban coastal and riverine areas of southern Ontario, Canada

Decay of Cryptosporidium parvfum DNA in cowpats in subtropical environments determined using qPCR

Cryptosporidium oocysts pose a significant threat to public health due to its ability to contaminate environmental waters, leading to outbreaks of waterborne diseases and emphasizing the crucial need for effective water treatment and monitoring systems. This study aimed to investigate the decay of Cryptosporidium oocyst DNA in cow fecal matter under different environmental conditions prevalent in sub-tropical Southeast Queensland (SEQ) during summer and winter seasons. The effects of ambient sunlight and shaded conditions on the decay rates of C. parvum DNA in cow fecal samples were evaluated. The results showed that measurable levels of C. parvum DNA were observed for up to 60 days during the summer experiments, with a slower decay rate on the surface (k = -0.029) and sub-surface (k = -0.043) of the cowpat under shaded conditions than those on the surface (k = -0.064) and sub-surface (k = -0.079) under sunlight conditions. The decay rates of C. parvum DNA on the surface and sub-surface of the cowpat under shaded conditions were significantly slower (p = 0.004; p = 0.004) than those on the surface and sub-surface under sunlight conditions during summer experiments. During the winter treatments, measurable levels of C. parvum DNA were observed for up to 90 days, and the decay rates were slower on the surface (k = -0.036) and sub-surface (k = -0.034) of the cowpat under shaded conditions than those under sunlight conditions (k = -0.067 for surface and k = -0.057 for sub-surface). The decay rates of C. parvum DNA on the surface and sub-surface of the cowpat under shaded conditions were significantly slower than those on the surface (p = 0.009) and sub-surface (p = 0.041) under sunlight conditions during winter experiments. Moreover, the decay rate in the summer sunlight surface treatment (k = -0.064) was significantly faster from those in the winter shaded surface (k = -0.036; p = 0.018) and sub-surface (k = -0.034; p = 0.011) treatments. Similar results were also observed for summer sunlight sub-surface (k = -0.079), which was significantly faster than winter shaded surface (k = -0.036; p = 0.0008) and sub-surface (k = -0.034; p = 0.0005) treatments. Overall, these findings are important to enhance our understanding on the degradation of C. parvum DNA in cow fecal matter in SEQ, particularly in relation to seasonal variations and environmental conditions.

Climate Change Impacts on Microbiota in Beach Sand and Water: Looking Ahead

Beach sand and water have both shown relevance for human health and their microbiology have been the subjects of study for decades. Recently, the World Health Organization recommended that recreational beach sands be added to the matrices monitored for enterococci and Fungi. Global climate change is affecting beach microbial contamination, via changes to conditions like water temperature, sea level, precipitation, and waves. In addition, the world is changing, and humans travel and relocate, often carrying endemic allochthonous microbiota. Coastal areas are amongst the most frequent relocation choices, especially in regions where desertification is taking place. A warmer future will likely require looking beyond the use of traditional water quality indicators to protect human health, in order to guarantee that waterways are safe to use for bathing and recreation. Finally, since sand is a complex matrix, an alternative set of microbial standards is necessary to guarantee that the health of beach users is protected from both sand and water contaminants. We need to plan for the future safer use of beaches by adapting regulations to a climate-changing world.

A review of the current status of Cryptosporidium in fish

Species of the genus Cryptosporidium (phylum Apicomplexa) infect the epithelium of the gastrointestinal tract of several vertebrate hosts, including humans and domestic and wild animals. In the past 20 years, several studies have focused on Cryptosporidium in fish. To date, a total of four piscine-host-specific species (Cryptosporidium molnari, Cryptosporidium huwi, Cryptosporidium bollandi and Cryptosporidium abrahamseni), nine piscine genotypes and more than 29 unnamed genotypes have been described in fish hosts. In addition, Cryptosporidium species and genotypes typical of other groups of vertebrates have also been identified. This review summarizes the history, biology, pathology and clinical manifestations, as well as the transmission, prevalence and molecular epidemiology of Cryptosporidium in wild, cultured and ornamental fish from both marine and freshwater environments. Finally, the potential role of piscine hosts as a reservoir of zoonotic Cryptosporidium species is also discussed.

Qualitative and Quantitative Beach Cleanliness Assessment to Support Marine Litter Management in Tropical Destinations

In addition to its ecological and recreational relevance, beach cleanliness is also one of the five most important aspects (i.e., the “Big Five”) for beach visitors around the world. Nonetheless, few efforts have been carried out to guide the sound management of this rising issue. This paper presents a quantitative and qualitative method to assess the level of beach cleanliness, in order to allow managers to focus their attention on the environmental management of the most frequent and relevant types of litter in tropical areas. In a first step, a survey on users’ perception was applied to 361 beachgoers in eight beaches in Colombia to identify the most relevant types of beach litter and the weighting factors to obtain quantitative calculations. In a second step, the thirteen categories of litter identified were analyzed in relation to beach cleanliness, origin of litter, and environmental impact, to define its individual weighting importance. Some categories were also selected according to particularities of tropical countries, such as the presence of abundant natural vegetation debris and gross polystyrene items, largely transported by rivers in great quantities. In a third step, the method was then tested at eight beaches in the Caribbean coast of Colombia through a period of four months, during which 192 transect samplings were carried out. The qualitative module of the proposed technique, named Beach Litter Assessment Technique—Qualitative and Quantitative (BLAT-QQ), identified the main types of beach litter and the quantitative module gave an overview on the state of beach cleanliness. The method is demonstrated to be quick and effective in diagnosing beach cleanliness, providing a simple instrument to carry out sound environmental management actions in coastal destinations.

Untreated sewage contamination of beach sand from a leaking underground sewage system

Thirty people (mostly children) experienced an episode of skin rash days after a sand sifting beach operation at Porto Pim Beach in Faial, Azores during June 2019. An environmental and epidemiologic investigation was conducted to identify the cause of the outbreak of skin rash. The epidemiologic investigation found that some of the patients experiencing symptoms had never entered the beach water. During the pollution period and throughout the epidemiologic investigation, faecal indicator bacteria levels (94 CFU/100 ml for intestinal enterococci and 61 CFU/100 ml for Escherichia coli) in water remained under the limits used for the ninety-five percentile calculation of an Excellent coastal and transitional bathing water defined in the Portuguese Legislation (100 CFU/100 ml for intestinal enterococci and 250 CFU/100 ml for Escherichia coli). Thus sand contact was considered as a likely primary exposure route. Sand microbiological analysis for faecal indicator organisms and electron microscopy strongly suggested faecal contamination. Chemical analysis of the sand also revealed a concomitant substance compatible with sodium-hypochlorite as analysed using gas chromatography and subsequently confirmed by free chlorine analysis. Inspection of the toilet facilities and sewage disposal system revealed a leaking sewage distribution box. Collectively, results suggest that the cause of the outbreak was the leaking underground sewage distribution box that serviced the beach toilet facilities (40 m from beach), where sodium-hypochlorite was used for cleaning and disinfection. This sewage then contaminated the surficial sands to which beach goers were exposed. Chlorine being an irritant substance, was believed to have been the cause of the symptoms given the sudden presentation and dissipation of skin rashes. No gastro-intestinal illness was reported during this episode and during the following 30 days. Like water, beach sand should also be monitored for safety, especially for areas serviced by aged infrastructure.

Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan

Shoreline sand harbors high concentrations of fecal indicator bacteria (FIB) that may be resuspended into the water column through washing and resuspension. Studies have explored coastal processes that influence this sand-water flux for FIB, but little is known about how microbial markers of contamination or the bacterial community interact in the sand-water interface. In this study, we take a three-tiered approach to explore the relationship between bacteria in sand, sediment, and overlying water at three shoreline sites and two associated rivers along an extended freshwater shoreline. Samples were collected over two years and analyzed for FIB, two microbial source tracking (MST) markers (Catellicoccus marimammalium, Gull2; Bacteroides HF183), and targeted metagenomic 16S rRNA gene analysis. FIB was much higher in sand than in water at all three sites. Gull2 marker was abundant in shoreline sand and water while HF183 marker was mostly present in rivers. Overall bacterial communities were dissimilar between sand/sediment and water, indicating little interaction. Sediment composition was generally unfavorable to bacterial resuspension. Results show that FIB and MST markers were effective estimates of short-term conditions at these locations, and bacterial communities in sand and sediment reflected longer-term conditions. Findings are useful for locating contamination sources and targeting restoration by evaluating scope of shoreline degradation.

Spatial and temporal distribution of E. coli contamination on three inland lake and recreational beach systems in the upper Midwestern United States

Swimming advisories are commonly posted at public beaches across the United States every year. In Iowa, weekly monitoring of public swimming areas at state and county beaches have resulted in the impairment of numerous lakes for fecal indicator bacteria (FIB) contamination, as detected by E. coli. An extensive study was established to assess the relationships between E. coli contamination of nearshore beach water environments, open lake conditions and beach sands in three recreational beach/lake systems currently impaired for FIB contamination across Iowa. A transect/grab sample based sampling design was implemented across the systems with collections spanning from April through October of 2015 and 2016. Collections of E. coli along water transects identified strong near to far shore gradients of decreasing concentrations in all systems. Results indicate that concentrations of E. coli observed in swimming waters consistently disassociate with concentrations in the broader lake environment. Swimming water E. coli concentrations correlated with elevated beach sand E. coli, samples collected from beach sands uncovered concentrations up to 86,500 times higher than adjacent swimming waters. Results from this study indicate that foreshore beach sands and other beach proximate FIB sources serve as the major contributing source for swimming zone advisories. The current methodology used by state and federal officials includes impairing entire lake waterbodies for FIB contamination of the swimming area. These impairment listings do not accurately reflect the condition(s) of the larger lake environment outside the swimming area and fail to account for beach proximate conditions in the assessment process. Further, this approach provides potentially misleading information to the public and may undermine implementation strategies deployed by resource managers aimed at addressing FIB contamination at recreational swimming areas. Views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the Iowa Department of Natural Resources.

Bacterial quality of groundwater downgradient of onsite wastewater disposal systems and the influence on eastern Long Island's embayments

Onsite wastewater disposal systems (OWDS) can introduce bacterial and chemical contaminants, via groundwater, into aquifers and adjacent waterways. We evaluated the concentration of fecal indicator bacteria (FIB) and antibiotic resistant bacteria (ARB) in the shallow groundwater of Eastern Long Island, New York, downgradient of OWDS using cultivation approaches and analysis of 16 S rRNA genes. While FIB and ARB were detected in 80% and 67% of groundwater samples, respectively, concentrations were low, suggesting that, at least at the time of sampling, groundwater was not a large-scale source of fecal bacterial contamination to adjacent embayments. ARB isolates did not include common fecal associated genera and the concentration of FIB and ARB did not correlate well with the concentration of pharmaceutical contaminants, suggesting that bacterial contaminants were poorly linked to OWDS discharge. Concentrations of FIB in the studied embayments were significantly greater in nearshore compared to mid-channel environments, suggesting that land-based sources are likely to be the major contributors of bacterial contamination.

Assessing microbial risk through event-based pathogen loading and hydrodynamic modelling

The aim of this study was to assess the variability of microbial risk associated with drinking water under various contaminant loading conditions in a drinking water source. For this purpose, a probabilistic-deterministic approach was applied to estimate the loadings of Cryptosporidium, Giardia, and Escherichia coli (E. coli) from fecal contamination sources during both dry and wet weather conditions. The relative importance of loads originating from various fecal contamination sources was also determined by a probabilistic approach. This study demonstrates that water resource recovery facilities were the dominant source of Giardia, yet rivers were more important with regards to Cryptosporidium. Estimated loadings were used as input to a three-dimensional hydrodynamic model of Lake Ontario; the fate and transport of microbial organisms were simulated at the influent of a drinking water intake. Discharge-based hydrodynamic modelling results were compared to observed concentrations. Simulated probability distributions of concentrations at the intake were used as an input to a quantitative microbial risk assessment (QMRA) model such that the variability of microbial risk in the context of drinking water could be examined. Depending on wind and currents, higher levels of fecal contamination reached the intake during wet weather loading scenarios. Probability distribution functions of Cryptosporidium, Giardia and E. coli concentrations at the intake were significantly higher during wet weather conditions when compared to dry conditions (p < 0.05). For all contaminants studied, the QMRA model showed a higher risk during wet weather (over 1 order of magnitude) compared to dry weather conditions. When considering sewage by-pass scenarios, risks remained below 2.7 × 10^-7 person^-1 day^-1 for Giardia and E. coli O157:H7. Limited data were available for Cryptosporidium in by-pass effluents and the risk is unknown; hence it is critical to obtain reliable loading data for the riskiest scenarios, such as those associated with water resource recovery facility by-passes.

To clean or not to clean? A critical review of beach cleaning methods and impacts

Cleaning is a fundamental concern of beach managers in many destinations as well as an important requirement in beach quality awards. However, it has been largely neglected in the literature. This paper provides an overview of empirical studies on beach cleaning and analyzes cleaning-related requirements of 11 beach awards that generate controversy in the literature. This study comments on key aspects of beach cleaning, resolves various misconceptions, and provides new perspectives by integrating related topics drawn from a wide range of literature. The arguments based on both the ecological and tourism managerial perspectives are presented, indicating the gaps and proposing research solutions. The paper calls for empirical studies with regard to the efficiency of different cleaning approaches on beaches with varying levels of use intensity and for methodological designs that separate the impacts of mechanical grooming from those of trampling, dune destruction, shore armoring, artificial lighting, among others.

Microbial Source Tracking Using Quantitative and Digital PCR To Identify Sources of Fecal Contamination in Stormwater, River Water, and Beach Water in a Great Lakes Area of Concern

Areas of concern (AOCs) around the Great Lakes are characterized by historic and ongoing problems with microbial water quality, leading to beneficial use impairments (BUIs) such as beach postings and closures. In this study, we assessed river and beach sites within the Rouge River watershed, associated stormwater outfalls, and at Rouge Beach. The concentrations of Escherichia coli as well as human- and gull-specific qPCR microbial source tracking (MST) markers were assessed at all sites. A preliminary comparison of digital PCR (dPCR) methodologies for both MST markers was conducted regarding sensitivity and specificity. Within the watershed, the outfalls were found to be a prominent source of human fecal contamination, with two outfalls particularly affected by sewage cross-connections. However, the occurrence of human fecal contamination along Rouge Beach and in the lower portions of the watershed was largely dependent on rain events. Gull fecal contamination was the predominant source of contamination at the beach, particularly during dry weather. The multiplex human/gull dPCR methodology used in this study tended to be more sensitive than the individual quantitative PCR (qPCR) assays, with only a slight decrease in specificity. Both dPCR and qPCR methodologies identified the same predominance of human and gull markers in stormwater and beach locations, respectively; however, the dPCR multiplex assay was more sensitive and capable of detecting fecal contamination that was undetected by qPCR assays. These results demonstrate the dPCR assay used in this study could be a viable tool for MST studies to increase the ability to identify low levels of fecal contamination.IMPORTANCE Fecal contamination of recreational water poses a persistent and ongoing problem, particularly in areas of concern around the Great Lakes. The identification of the source(s) of fecal contamination is essential for safeguarding public health as well as guiding remediation efforts; however, fecal contamination may frequently be present at low levels and remain undetectable by certain methodologies. In this study, we utilized microbial source tracking techniques using both quantitative and digital PCR assays to identify sources of contamination. Our results indicated high levels of human fecal contamination within stormwater outfalls, while lower levels were observed throughout the watershed. Additionally, high levels of gull fecal contamination were detected at Rouge Beach, particularly during drier sampling events. Furthermore, our results indicated an increased sensitivity of the digital PCR assay to detect both human and gull contamination, suggesting it could be a viable tool for future microbial source tracking studies.

Cryptosporidium and Giardia in Wastewater and Surface Water Environments

and spp. are significant contributors to the global waterborne disease burden. Waterways used as sources of drinking water and for recreational activity can become contaminated through the introduction of fecal materials derived from humans and animals. Multiple studies have reported the occurence or concentrations of these pathogens in the environment. However, this information has not been comprehensively reviewed. Quantitative microbial risk assessment (QMRA) for and can be beneficial, but it often relies on the concentrations in environmental sources reported from the literature. A thorough literature review was conducted to develop an inventory of reported and concentrations in wastewater and surface water available in the literature. This information can be used to develop QMRA inputs. and (oo)cyst concentrations in untreated wastewater were up to 60,000 oocysts L and 100,000 cysts L, respectively. The maximum reported concentrations for and in surface water were 8400 oocysts L and 1000 cysts L, respectively. A summary of the factors for interpretation of concentration information including common quantification methods, survival and persistence, biofilm interactions, genotyping, and treatment removal is provided in this review. This information can help in identifying assumptions implicit in various QMRA parameters, thus providing the context and rationale to guide model formulation and application. Additionally, it can provide valuable information for water quality practitioners striving to meet the recreational water quality or treatment criteria. The goal is for the information provided in the current review to aid in developing source water protection and monitoring strategies that will minimize public health risks.

Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China

Larus ridibundus, a migratory wild bird, has become one of the most popular gull species in southwest China in recent years. There has been no information on the gut microbiota and intestinal pathogenic bacteria configuration in wild L. ridibundus, even though the public are in close contact with this bird. In this study, 16S rRNA amplicon‐sequencing methods were used to describe the microbial community structure and intestinal pathogenic bacteria were isolated to identify their characteristics. The taxonomic results revealed that Firmicutes (86%), Proteobacteria (10%), and Tenericutes (3%) were the three most abundant phyla in the gut of L. ridibundus. Enterococcaceae, Enterobacteriaceae, and Mycoplasmataceae were the most predominant families, respectively. The number of operational taxonomic units (OTUs), the richness estimates and diversity indices of microbiota, was statistically different (p < 0.05). However, beta diversity showed that no statistical significance (p > 0.05) between all the fecal samples. The most frequently isolated intestinal pathogenic bacteria from L. ridibundus were enteropathogenic Escherichia coli (32%) and Salmonella (21%). Pulsed‐field gel electrophoresis (PFGE) results of Salmonella species revealed a high degree of similarity between isolates, which was not observed for other species. None of the potentially pathogenic isolates were identical to human‐isolated counterparts suggesting that there was little cross‐infection between humans and gulls, despite close proximity. In brief, this study provided a baseline for future L. ridibundus microbiology analysis, and made an understanding of the intestinal bacterial community structure and diversity.

Potential for gulls to transport bacteria from human waste sites to beaches

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape.

Development and small-scale validation of a novel pigeon-associated mitochondrial DNA source tracking marker for the detection of fecal contamination in harvested rainwater

The current study was aimed at designing and validating (on a small-scale) a novel pigeon mitochondrial DNA (mtDNA) microbial source tracking (MST) marker for the detection of pigeon fecal matter in harvested rainwater. The pigeon mtDNA MST marker was designed to target the mtDNA Cytochrome b gene by employing mismatch amplification mutation assay kinetics. The pigeon marker was validated by screening 69 non-pigeon and 9 pigeon fecal samples. The host-sensitivity of the assay was determined as 1.00 while the host-specificity of the assay was 0.96. Harvested rainwater samples (n=60) were screened for the prevalence of the marker with the mtDNA Cytochrome b marker detected in 78% of the samples. Bayes' theorem was applied to calculate the conditional probability of the marker detecting true pigeon contamination and the marker subsequently displayed a 99% probability of detecting true pigeon contamination in the harvested rainwater samples. In addition, the mtDNA Cytochrome b marker displayed high concurrence frequencies versus heterotrophic bacteria (78.3%), E. coli (73.3%), total coliforms (71.1%) and fecal coliforms (66.7%). This study thus validates that targeting mtDNA for the design of source tracking markers may be a valuable tool to detect avian fecal contamination in environmental waters.

Estimating the probability of illness due to swimming in recreational water with a mixture of human- and gull-associated microbial source tracking markers

Beaches often receive fecal contamination from more than one source. Human sources include untreated sewage as well as treated wastewater effluent, and animal sources include wildlife such as gulls. Different contamination sources are expected to pose different health risks to swimmers. Genetic microbial source tracking (MST) markers can be used to detect bacteria that are associated with different animal sources, but the health risks associated with a mixture of MST markers are unknown. This study presents a method for predicting these health risks, using human- and gull-associated markers as an example. Quantitative Microbial Risk Assessment (QMRA) is conducted with MST markers as indicators. We find that risks associated with exposure to a specific concentration of a human-associated MST marker (HF) are greater if the HF source is untreated sewage rather than treated wastewater effluent. We also provide a risk-based threshold of HF from untreated sewage at a beach, to stay below a predicted illness risk of 3 per 100 swimmers, that is a function of gull-associated MST marker (CAT) concentration.

Genetic characterization of fecal impacts of seagull migration on an urban scenery lake

A microbial source tracking scheme was devised to differentiate fecal impacts of seagulls from that of human activities on an urban scenery lake in southern China, which is a major wintering ground for the black-headed seagull. Fecal contamination of seagulls was characterized by quantifying a novel genetic marker targeting Catellicoccus marimamalium. Quantification of this marker was combined with those of Escherichia coli, human-associated Bacteroidales, thermophilic Campylobacter and Helicobacter. Findings of a year-round study indicate that C. marimamalium levels correlated strongly, both spatially and temporally, with seagull migration. A steady increase in C. marimammalium concentrations was recorded between October 2014 and March 2015, which peaked at about 5-log copies/100 mL in January. However, a background level of about 2.1-log copies/100 mL was noticeable from April through September when seagulls were absent, probably due to other host sources or secondary habitats for C. marimammalium. Seagull migration also caused an apparent elevation of E. coli concentrations (86% and 60%, respectively for qPCR and culture method; p < 0.001) as well as Campylobacter and Helicobacter (66% and 68%, respectively; p < 0.001). Nonetheless, in contrast to the declining levels of E. coli, Campylobacter and Helicobacter, the human-specific Bacteroidales marginally increased in the seagull-absent season, indicating a limited influence of human activities, compared with seagull migration, on the seasonal variations in microbial water quality of the lake. The elevated levels of FIB, Campylobacter and Helicobacter along with C. marimammalium may imply human health risk of the lake water due to seasonal seagull migration, which requires further investigation for risk assessment.

Sources and persistence of fecal indicator bacteria and Bacteroidales in sand as measured by culture-based and culture-independent methods: A case study at Santa Monica Pier, California

This study investigated causes of persistent fecal indicator bacteria (FIB) in beach sand under the pier in Santa Monica, CA. FIB levels were up to 1,000 times higher in sand underneath the pier than that collected from adjacent to the pier, with the highest concentrations under the pier in spring and fall. Escherichia coli (EC) and enterococci (ENT) under the pier were significantly positively correlated with moisture (ρ = 0.61, p < 0.001, n = 59; ρ = 0.43, p < 0.001, n = 59, respectively), and ENT levels measured by qPCR (qENT) were much higher than those measured by membrane filtration (cENT). Microcosm experiments tested the ability of EC, qENT, cENT, and general Bacteroidales (GenBac) to persist under in-situ moisture conditions (10% and 0.1%). Decay rates of qENT, cENT, and GenBac were not significantly different from zero at either moisture level, while decay rates for EC were relatively rapid during the microcosm at 10% moisture (k = 0.7 days-1). Gull/pelican marker was detected at eight of 12 sites and no human-associated markers (TaqHF183 and HumM2) were detected at any site during a one-day site survey. Results from this study indicate that the high levels of FIB observed likely stem from environmental sources combined with high persistence of FIB under the pier.

Transport of Fecal Indicators from Beach Sand to the Surf Zone by Recirculating Seawater: Laboratory Experiments and Numerical Modeling

Recirculating seawater is an important component of submarine groundwater discharge, yet its role in transporting microbial contaminants from beach sand to coastal water is unknown. This study investigated the extent to which recirculating seawater carries fecal indicators, Enterococcus and bird-associated Catellicoccus, through the beach subsurface. Laboratory experiments and numerical modeling were performed to characterize the transport of fecal indicators suspended in seawater through medium-grained beach sand under transient and saturated flow conditions. Enterococcus was measured both by culture (cENT) and DNA assay (tENT), and Catellicoccus (CAT) by DNA assay. There were differences between transport of tENT and CAT compared to cENT through laboratory columns containing beach sands. Under transient flow conditions, first-order attachment rate coefficients (k_att) of DNA markers were greater (∼10 h^-1) than k_att of cENT (∼1 h^-1), although under saturated conditions k_att values were similar (∼1 h^-1). First-order detachment rate coefficients, k_det, of DNA markers were greater (∼1 h^-1) than k_det of cENT (∼0.1h^-1) under both types of flow conditions. Incorporating the rate coefficients into field-scale subsurface transport simulations showed that, in this sand type, the contribution of recirculating seawater to surf zone contamination is likely to be minimal unless bird feces are deposited close to the land-sea interface.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls

Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log₁₀ copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log₁₀ CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log₁₀ CFU/100 ml, and 7.65 log₁₀ CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds.

IMPORTANCE

Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls

Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log₁₀ copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log₁₀ CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log₁₀ CFU/100 ml, and 7.65 log₁₀ CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds.

IMPORTANCE

Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination.

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches

Avian and possum fecal droppings may negatively impact roof-harvested rainwater (RHRW) water quality due to the presence of zoonotic pathogens. This study was aimed at evaluating the performance characteristics of a possum feces-associated (PSM) marker by screening 210 fecal and wastewater samples from possums (n = 20) and a range of nonpossum hosts (n = 190) in Southeast Queensland, Australia. The host sensitivity and specificity of the PSM marker were 0.90 and 0.95 (maximum value, 1.00), respectively. The mean concentrations of the GFD marker in possum fecal DNA samples (8.8 × 10(7) gene copies per g of feces) were two orders of magnitude higher than those in the nonpossum fecal DNA samples (5.0 × 10(5) gene copies per g of feces). The host sensitivity, specificity, and concentrations of the avian feces-associated GFD marker were reported in our recent study (W. Ahmed, V. J. Harwood, K. Nguyen, S. Young, K. Hamilton, and S. Toze, Water Res 88:613-622, 2016, http://dx.doi.org/10.1016/j.watres.2015.10.050). The utility of the GFD and PSM markers was evaluated by testing a large number of tank water samples (n = 134) from the Brisbane and Currumbin areas. GFD and PSM markers were detected in 39 of 134 (29%) and 11 of 134 (8%) tank water samples, respectively. The GFD marker concentrations in PCR-positive samples ranged from 3.7 × 10(2) to 8.5 × 10(5) gene copies per liter, whereas the concentrations of the PSM marker ranged from 2.0 × 10(3) to 6.8 × 10(3) gene copies per liter of water. The results of this study suggest the presence of fecal contamination in tank water samples from avian and possum hosts. This study has established an association between the degradation of microbial tank water quality and avian and possum feces. Based on the results, we recommend disinfection of tank water, especially for tanks designated for potable use.

IMPORTANCE

The use of roof-harvested rainwater (RHRW) for domestic purposes is a globally accepted practice. The presence of pathogens in rainwater tanks has been reported by several studies, supporting the necessity for the management of potential health risks. The sources of fecal pollution in rainwater tanks are unknown. However, the application of microbial source tracking (MST) markers has the potential to identify the sources of fecal contamination in a rainwater tank. In this study, we provide evidence of avian and possum fecal contamination in tank water samples using molecular markers. This study established a potential link between the degradation of the microbial quality of tank water and avian and possum feces.

Evaluation of three full-scale stormwater treatment systems with respect to water yield, pathogen removal efficacy and human health risk from faecal pathogens

In this study, three full-scale, operational stormwater harvesting systems located in Melbourne, Australia were evaluated with respect to water yields; pathogen removal performance by analysis of native surrogate data (Escherichiacoli, somatic coliphages and Clostridium perfringens); and potential human health risk associated with exposures to faecal pathogens using Quantitative Microbial Risk Assessment (QMRA). The water yield assessment confirmed variation between design and measured yields. Faecal contamination of urban stormwater was site specific and variable. Different treatment removal performance was observed between each of the microbial surrogates and varied between event and baseline conditions, with negligible removal of viruses during event conditions. Open storages that provide a habitat for waterfowl may lead to elevated risk due to the potential for zoonotic transmission. Nevertheless, in the Australian urban setting studied, the potential for human faecal contamination of the separated stormwater system was a critical driver of risk. If the integrity of the sewerage system can be ensured, then predicted health risks are dramatically reduced.

Comparison of the occurrence and survival of fecal indicator bacteria in recreational sand between urban beach, playground and sandbox settings in Toronto, Ontario

While beach sands are increasingly being studied as a reservoir of fecal indicator bacteria (FIB), less is known about the occurrence of FIB in other recreational sands (i.e., sandboxes and playgrounds). In this study, different culture-based FIB enumeration techniques were compared and microbial source tracking assays were conducted on recreational sand samples from beaches, playgrounds and sandboxes around Toronto, ON. FIB were detected in every sand sample (n=104) with concentrations not changing significantly over the five month sampling period. Concentrations of FIB and a gull-specific DNA marker were significantly higher in foreshore beach sands, and indicated these were a more significant reservoir of FIB contamination than sandbox or playground sands. Human- and dog-specific contamination markers were not detected. All culture-based FIB enumeration techniques were consistent in identifying the elevated FIB concentrations associated with foreshore beach sands. However, significant differences between differential agar media, IDEXX and Aquagenx Compartment Bag Test were observed, with DC media and Enterolert being the most sensitive methods to detect Escherichia coli and enterococci, respectively. To better understand the elevated occurrence of E. coli in foreshore sands, microcosm survival experiments were conducted at two different temperatures (15 °C and 28 °C) using non-sterile saturated foreshore beach sands collected from two urban freshwater beaches with different sand type (fine grain and sand-cobble). Microcosms were inoculated with a mixture of eight sand-derived E. coli strains and sampled over a 28-day period. E. coli levels were found to decline in all microcosms, although survival was significantly greater in the finer sand and at the cooler temperature (15 °C). These results indicate that FIB can be widespread in any type of recreational sand and, while E. coli can survive for many weeks, it is most likely to accumulate in cooler fine-grain sand as occurs below the foreshore sand surface.

Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems

Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment.

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

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

A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems

Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitivity (percentage true positives) of MST results in sewage and animal waste samples (21-33%) was lower than specificity (83-90%, percentage of true negatives). Next generation DNA sequencing revealed two dominant bacterial families that were common to all sample types: Ruminococcaceae and Lachnospiraceae. Five dominant phyla and 15 dominant families comprised 97% and 74%, respectively, of sequences from all fecal sources. Phyla and families not represented on the microarray are possible candidates for inclusion in subsequent array designs.

Microbial release from seeded beach sediments during wave conditions

Beach sands can sustain indigenous and introduced populations of enterococci. The objective of this study was to evaluate wave action in promoting the release of introduced bacteria. To accomplish this objective this study developed a method to assess attachment and identified conditions under which introduced bacteria are integrated into the sand. A new "shearing assay" showed that attachment of the introduced spike mimicked that of the natural sand when the spike was allowed to integrate into the sand for 24h at room temperature at a sand moisture content of 20%. Experiments in a wave flume showed that waves were capable of releasing about 60% of the total bacteria added. This suggests that for the range of wave conditions evaluated (height: 1.9-10.5 cm, period:1-2.7s), waves were incapable of releasing all of the bacteria. Further study is needed to evaluate bacteria attachment mechanisms.

Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study

Gulls were reported as sources of fecal pollution in coastal environments and potential vectors of human infections. Microbial source tracking (MST) methods were rarely tested to identify this pollution origin. This study was conducted to ascertain the source of water fecal contamination in the Berlenga Island, Portugal. A total of 169 Escherichia coli isolates from human sewage, 423 isolates from gull feces and 334 water isolates were analyzed by BOX-PCR. An average correct classification of 79.3% was achieved. When an 85% similarity cutoff was applied 24% of water isolates were present in gull feces against 2.7% detected in sewage. Jackknifing resulted in 29.3% of water isolates classified as gull, and 10.8% classified as human. Results indicate that gulls constitute a major source of water contamination in the Berlenga Island. This study validated a methodology to differentiate human and gull fecal pollution sources in a real case of a contaminated beach.

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

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

Development and application of a quantitative PCR assay targeting Catellicoccus marimammalium for assessing gull-associated fecal contamination at Lake Erie beaches

Gulls represent one of the major fecal contamination sources responsible for the degradation of water quality at Lake Erie beaches. For assessing gull-associated fecal contamination, a real-time quantitative PCR assay (qPCR) targeting 16S rRNA gene sequences from Catellicoccus marimammalium, which are abundant in gull feces, was developed and evaluated by comparing assay results with beach survey data that included gull counting, and quantifying densities of Escherichia coli and human-associated fecal markers at two Lake Erie beaches. In evaluating the specificity and sensitivity of the qPCR assay with animal and wastewater samples, C. marimammalium was detected in most gull fecal samples (80.7%), some chicken fecal samples (24.1%), but was not readily detected from other fecal samples of animals and humans, and wastewater. Among 66 Lake Erie water samples collected in 2010, C. marimammalium was frequently detected from Villa Angela (36.4%) and Headlands beaches (57.6%). C. marimammalium densities were not associated with E. coli densities or sanitary survey data. E. coli counts were likely driven by other sources, such as human, rather than gulls at the study sites. The presumption that human contamination influenced E. coli counts was supported by more frequent detection of the human-specific Bacteroides gyrB marker (gyrB) at Villa Angela (33.3%) than Headlands (6.1%). Since E. coli may not be an effective indicator for assessing gull-related fecal contamination at these beaches, where contamination sources are mixed, our novel qPCR assay can be useful for understanding fecal source contributions from gulls not explained by gull abundance or E. coli densities.

Dramatic improvements in beach water quality following gull removal

Gulls are often cited as important contributors of fecal contamination to surface waters, and some recreational beaches have used gull control measures to improve microbial water quality. In this study, gulls were chased from a Lake Michigan beach using specially trained dogs, and water quality improvements were quantified. Fecal indicator bacteria and potentially pathogenic bacteria were measured before and during gull control using culture methods and quantitative polymerase chain reaction (qPCR). Harassment by dogs was an effective method of gull control: average daily gull populations fell from 665 before to 17 during intervention; and a significant reduction in the density of a gull-associated marker was observed (p < 0.001). Enterococcus spp. and Escherichia coli densities were also significantly reduced during gull control (p < 0.001 and p = 0.012, respectively for culture methods; p = 0.012 and p = 0.034, respectively for qPCR). Linear regression results indicate that a 50% reduction in gulls was associated with a 38% and 29% decrease in Enterococcus spp. and E. coli densities, respectively. Potentially human pathogenic bacteria were detected on 64% of days prior to gull control and absent during gull intervention, a significant reduction (p = 0.005). This study demonstrates that gull removal can be a highly successful beach remedial action to improve microbial water quality.

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

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