Teschoviruses as indicators of porcine fecal contamination of surface water

Atypical Viral Infections in Gastroenterology

Enteric viruses are commonly found obligate parasites in the gastrointestinal (GI) tract. These viruses usually follow a fecal-oral route of transmission and are characterized by their extraordinary stability as well as resistance in high-stress environments. Most of them cause similar symptoms including vomiting, diarrhea, and abdominal pain. In order to come in contract with mucosal surfaces, these viruses need to pass the three main lines of defense: mucus layer, innate immune defenses, and adaptive immune defenses. The following atypical gastrointestinal infections are discussed: SARS-CoV2, hantavirus, herpes simplex virus I, cytomegalovirus, and calicivirus. Dysbiosis represents any modification to the makeup of resident commensal communities from those found in healthy individuals and can cause a patient to become more susceptible to bacterial and viral infections. The interaction between bacteria, viruses, and host physiology is still not completely understood. However, with growing research on viral infections, dysbiosis, and new methods of detection, we are getting closer to understanding the nature of these viruses, their typical and atypical characteristics, long-term effects, and mechanisms of action in different organ systems.

Enteric viruses in food safety: New threats for an old problem

Foodborne diseases are one of the most serious concerns in public health. It is estimated that around 600 million cases of gastroenteritis occur worldwide each year. At present, more than 200 food-borne diseases are known, which can cause from mild gastroenteritis to syndromes with a fatal outcome, with the added possibility of chronic complications. One of the major etiological agents in foodborne diseases are the food and waterborne viruses, which are attracting a great deal of attention to researchers, food hygienists and policy makers. Several aspects differentiate these pathogens from foodborne pathogenic bacteria: their high capacity for infection and preservation in food environments, and their difficulty for a correct and sensitive detection. In recent years, different initiatives have been carried out to prioritize research in the area of viruses in food, prioritizing different aspects of their detection, epidemiology and control. There is clear evidence that the existing data on their prevalence may be underestimated due to the lack of robust methods for their sensitive detection. It is also necessary to know exactly what the incidence is in the different stages of the food production chain, and particularly in that which is dedicated to the transformation of products of animal origin. Finally, it is also necessary to calibrate the current disinfection procedures in the food industry in order to reliably establish a quantitative evaluation of the viral risk in food.

Case Report and Genomic Characterization of a Novel Porcine Nodavirus in the United States

Nodaviruses are small bisegmented RNA viruses belonging to the family Nodaviridae. Nodaviruses have been identified in different hosts, including insects, fishes, shrimps, prawns, dogs, and bats. A novel porcine nodavirus was first identified in the United States by applying next-generation sequencing on brain tissues of pigs with neurological signs, including uncontrollable shaking. RNA1 of the porcine nodavirus had the highest nucleotide identity (51.1%) to the Flock House virus, whereas its RNA2 shared the highest nucleotide identity (48%) with the RNA2 segment of caninovirus (Canine nodavirus). Genetic characterization classified porcine nodavirus as a new species under the genus Alphanodavirus. Further studies are needed to understand the pathogenicity and clinical impacts of this virus.

Nutritional, Energy and Sanitary Aspects of Swine Manure and Carcass Co-digestion

Renewable energy can assist the management of the effects of population growth and rapid economic development on the sustainability of animal husbandry. The primary aim of renewable energy is to minimize the use of fossil fuels via the creation of environmentally friendly energy products from depleted fossil fuels. Digesters that treat swine manure are extensively used in treatment systems; and inclusion of swine carcasses can increase the organic loading rate (OLR) thereby improving biogas yield and productivity on farms. However, the characteristics of the components including animal residues, proteins, lipids, remains of undigested feed items, antimicrobial drug residues, pathogenic microorganisms and nutrient contents, are complex and diverse. It is therefore necessary to manage the anaerobic process stability and digestate purification for subsequent use as fertilizer. Efficient methane recovery from residues rich in lipids is difficult because such residues are only slowly biodegradable. Pretreatment can promote solubilization of lipids and accelerate anaerobic digestion, and pretreatments can process the swine carcass before its introduction onto biodigesters. This review presents an overview of the anaerobic digestion of swine manure and carcasses. We analyze the characteristics of these residues, and we identify strategies to enhance biogas yield and process stability. We consider energy potential, co-digestion of swine manure and carcasses, physical, chemical, and biological pretreatment of biomass, sanitary aspects of swine manure and co-digestates and their recycling as fertilizers.

Two novel porcine teschovirus strains as the causative agents of encephalomyelitis in the Netherlands

Background

Porcine teschovirus (PTV) circulates among wild and domesticated pig populations without causing clinical disease, however neuroinvasive strains have caused high morbidity and mortality in the past. In recent years, several reports appeared with viral agents as a cause for neurologic signs in weanling and growing pigs among which PTV and new strains of PTV were described.

Case presentation

On two unrelated pig farms in the Netherlands the weanling pig population showed a staggering gate, which developed progressively to paresis or paralysis of the hind legs with a morbidity up to 5%. After necropsy we diagnosed a non-suppurative encephalomyelitis on both farms, which was most consistent with a viral infection. PTV was detected within the central nervous system by qPCR. From both farms PTV full-length genomes were sequenced, which clustered closely with PTV-3 (98%) or PTV-11 (85%). Other common swine viruses were excluded by qPCR and sequencing of the virus.

Conclusion

Our results show that new neuroinvasive PTV strains still emerge in pigs in the Netherlands. Further research is needed to investigate the impact of PTV and other viral agents causing encephalomyelitis within wild and domestic pig populations supported by the awareness of veterinarians.

Evaluation of Human- and Animal-Specific Viral Markers and Application of CrAssphage, Pepper Mild Mottle Virus, and Tobacco Mosaic Virus as Potential Fecal Pollution Markers to River Water in Japan

Five human-specific markers were detected in 59-74% of 27 human fecal-source samples collected in Yamanashi Prefecture, Japan. Similarly, potential human-specific markers, crAssphage, pepper mild mottle virus (PMMoV), and tobacco mosaic virus were detected in 96-100% of samples, with crAssphage showing the maximum concentration of 12.03 log copies/L. However, these markers were detected in 100% (3/3) of pig fecal-source samples, suggesting their applicability as general fecal pollution markers. Microbial source tracking analysis demonstrated that the rivers are contaminated by human and pig fecal sources. CrAssphage showed higher marker concentrations in river water samples than PMMoV, suggesting the preference of crAssphage to PMMoV as a marker of fecal pollution.

Teschovirus and other swine and human enteric viruses in Brazilian watersheds impacted by swine husbandry

Several emerging viral agents related to gastroenteritis are distributed in human and animal populations and may contaminate the environment due to anthropic activities. The objective of this study was to analyze the seasonal contamination by enteric virus and coliforms in water from streams in the Vale do Taquari, draining a large number of pig farms. Microbiological contamination was evidenced by the detection of total and thermotolerant coliforms, reaching their peak in December. Hepatitis E virus (HEV), Enterovirus-G (EV-G) genome, and Sapelovirus-A (SV-A) genome were not detected. On the other hand, Rotavirus (RV) was detected in 3% (1/32) of the samples, whereas Teschovirus-A (PTV) was detected in 6% (2/32). This is the first detection of PTV in environmental samples in Brazil, pointing that the virus is being shedded from swine herds to watersheds. Human mastadenovirus (HAdV) was the most frequent detected viral agent in 9.3% (3/32) with values of 2.54 × 10⁵, 7.13 × 10⁴, and 3.09 × 10⁵ genome copies/liter (gc/L). The circulation of coliforms and viral pathogens is noticeable due to anthropic activities and to the management of animal waste from the pig farming. In this way, enteric viruses can assist in monitoring the quality of watersheds and in tracking sources of contamination.

Detection of Pathogenic Viruses, Pathogen Indicators, and Fecal-Source Markers within Tanker Water and Their Sources in the Kathmandu Valley, Nepal

Tanker water is used extensively for drinking as well as domestic purposes in the Kathmandu Valley of Nepal. This study aimed to investigate water quality in terms of microbial contamination and determine sources of fecal pollution within these waters. Thirty-one samples from 17 tanker filling stations (TFSs) and 30 water tanker (WT) samples were collected during the dry and wet seasons of 2016. Escherichia coli was detected in 52% of the 31 TFS samples and even more frequently in WT samples. Of the six pathogenic viruses tested, enteroviruses, noroviruses of genogroup II (NoVs-GII), human adenoviruses (HAdVs), and group A rotaviruses were detected using quantitative PCR (qPCR) at 10, five, four, and two TFSs, respectively, whereas Aichi virus 1 and NoVs-GI were not detected at any sites. Index viruses, such as pepper mild mottle virus and tobacco mosaic virus, were detected using qPCR in 77% and 95% out of 22 samples, respectively, all of which were positive for at least one of the tested pathogenic viruses. At least one of the four human-associated markers tested (i.e., BacHum, HAdVs, and JC and BK polyomaviruses) was detected using qPCR in 39% of TFS samples. Ruminant-associated markers were detected at three stations, and pig- and chicken-associated markers were found at one station each of the suburbs. These findings indicate that water supplied by TFSs is generally of poor quality and should be improved, and proper management of WTs should be implemented.

Impact of seasonal temperature transition, alkalinity and other abiotic factors on the persistence of viruses in swine and dairy manures

Animal manures are a valued source of nutrients for crop production. They frequently do, however, contain zoonotic pathogens including a wide range of viruses. Ideally, manures would be treated prior to land application, reducing the burden of zoonotic viruses, and thus the potential for transmission to adjacent water resources or crops intended for human or animal consumption. In the present study, manure was obtained from four dairy and three swine farms. The manure was incubated anaerobically in the laboratory for 28 weeks at temperatures ranging from 4 to 25 °C, and multiple physical and chemical parameters were monitored. The abundance of various DNA and RNA viruses was measured throughout the incubation by amplifying virus-specific gene targets. A combination of statistical analyses were applied to identify whether the viruses are significantly impacted by temperature transition or affected by other abiotic factors. Temperature had no effect on the persistence of any of the viruses studied. An increase in pH of the manures during the incubation was significantly (P < 0.05) associated with decreased persistence, suggesting that pH manipulation during storage could reduce the abundance of viruses.

Molecular Identification of Enteroviruses from Cattle and Goat Feces and Environment in Thailand

The identification and characterization of viruses of the genus Enterovirus in healthy and infected livestock, including cattle and goats, have been increasing. Enterovirus E (EV-E) and Enterovirus F (EV-F) are commonly found in cattle, whereas Enterovirus G (EV-G) is found in goats. In this study, molecular and phylogenetic analyses were performed to determine the prevalence of EVs in cattle and goat feces from Kanchanaburi Province, Thailand. The presence of EVs in water samples and the feces of other animals collected from the areas surrounding cattle and goat farms was also investigated. By use of 5'-untranslated region (5' UTR) real-time reverse transcription-PCR (RT-PCR), EVs were detected in 39.5% of cattle samples, 47% of goat samples, 35.3% of water samples, and one pool of chicken feces. Phylogenetic analysis revealed the presence of EV-E and EV-F in cattle, EV-E and EV-G in goats, and EV-F in water samples and chicken feces. Analysis of enteroviral VP1 sequences from cattle revealed that the EV-E genotypes circulating in the study region were EV-E1, with a possible new genotype that is closely related to EV-E2. Analysis of enteroviral VP1 sequences from goats suggested the circulation of EV-G5 and a possible new genotype that is closely related to EV-G20. Sequence analyses also suggested that although the VP1 sequences from goats were closely related to those of EV-G, which were considered porcine enterovirus sequences, their 5' UTRs form a separated cluster with sequences of sheep and goat origin, suggesting a new classification of the ovine/caprine-specific enterovirus group.IMPORTANCE Possible new EV-E and EV-G genotypes were identified for EVs detected in this study. The EV-E viruses were also successfully isolated from MDBK cells. The goat EV sequence analysis suggested the presence of an ovine/caprine-specific EV group that is different from EV-G of porcine origin. The significance of our research is that it identifies and characterizes possible novel EVs, thereby indicating that enteroviruses in animals are continually evolving. The facts that enteroviruses can persist in the environment, contaminate it for long periods, and be transmitted between animals raise serious concerns regarding this group of viruses as emerging livestock pathogens.

Co-Infection by Waterborne Enteric Viruses in Children with Gastroenteritis in Nepal

Enteric viruses are highly contagious and a major cause of waterborne gastroenteritis in children younger than five years of age in developing world. This study examined the prevalence of enteric virus infection in children with gastroenteritis to identify risk factors for co-infections. In total, 107 stool samples were collected from patients with acute gastroenteritis along with samples of their household drinking water and other possible contamination sources, such as food and hand. The presence of major gastroenteritis-causing enteric virus species (group A rotaviruses, enteroviruses, adenoviruses, and noroviruses of genogroup I) in stool and water samples was examined using quantitative polymerase chain reaction. Among the 107 stool samples tested, 103 (96%) samples contained at least one of the four tested enteric viruses, and the combination of group A rotaviruses and enteroviruses was the most common co-infection (52%, n = 54/103). At least one viral agent was detected in 16 (16%) of 103 drinking water samples. Identical enteric viruses were detected in both the stool and water samples taken from the same patients in 13% of cases (n = 13/103). Group A rotaviruses were most frequently found in children suffering from acute diarrhea. No socio-demographic and clinical factors were associated with the risk of co-infection compared with mono-infection. These less commonly diagnosed viral etiological agents in hospitals are highly prevalent in patients with acute gastroenteritis.

Hepatitis E Virus: A New Foodborne Zoonotic Concern

Hepatitis E virus (HEV) is an enteric nonenveloped single-stranded RNA virus. Among the mammalian lineages, four genotypes are associated to human infection: genogroups 1 and 2 infect only humans and are mainly found in developing countries, while genogroups 3 and 4 are zoonotic, being found in a variety of animal species including pigs, and are autochthonous in developed countries. HEV infection can result in liver damage and with genotypes 1 and 2 symptoms can be particularly severe in pregnant women, with a high lethality ratio. Several cases of foodborne transmission of hepatitis E have been reported, often involving consumption of meat, especially raw or undercooked. Information is lacking on the exact extent of foodborne transmission of HEV.

Potential Approaches to Assess the Infectivity of Hepatitis E Virus in Pork Products: A Review

The zoonotic transmission of hepatitis E, caused by the hepatitis E virus (HEV), is an emerging issue. HEV appears common in pigs (although infected pigs do not show clinical signs), and evidence suggests that a number of hepatitis E cases have been associated with the consumption of undercooked pork meat and products. Little information is available on whether cooking can eliminate HEV, since there is currently no robust method for measuring its infectivity. HEV infectivity can be clearly demonstrated by monitoring for signs of infection (e.g., shedding of virus) in an animal model. However, this approach has several disadvantages, such as lack of reproducibility and unsuitability for performing large numbers of tests, high costs, and not least ethical considerations. Growth in cell culture can unambiguously show that a virus is infectious and has the potential for replication, without the disadvantages of using animals. Large numbers of tests can also be performed, which can make the results more amenable to statistical interpretation. However, no HEV cell culture system has been shown to be applicable to all HEV strains, none has been standardized, and few studies have demonstrated their use for measurement of HEV infectivity in food samples. Nonetheless, cell culture remains the most promising approach, and the main recommendation of this review is that there should be an extensive research effort to develop and validate a cell culture-based method for assessing HEV infectivity in pork products. Systems comprising promising cell lines and HEV strains which can grow well in cell culture should be tested to select an assay for effective and reliable measurement of HEV infectivity over a wide range of virus concentrations. The assay should then be harnessed to a procedure which can extract HEV from pork products, to produce a method suitable for further use. The method can then be used to determine the effect of heat or other elimination processes on HEV in pork meat and products, or to assess whether HEV detected in any surveyed foodstuffs is infectious and therefore poses a risk to public health.

Development of Polioencephalomyelitis in Cesarean-Derived Colostrum-Deprived Pigs Following Experimental Inoculation with Either Teschovirus A Serotype 2 or Serotype 11

Teschovirus encephalomyelitis is a sporadic disease associated with Teschovirus A (PTV) serotype 1 and, less frequently, other serotypes. In recent years, the number of cases submitted to the Iowa State University Veterinary Diagnostic Laboratory with a history of posterior paresis has increased. Submission histories from various regions of the United States suggest a trend for clinical disease to persist in herds and affect a wider age-range of pigs than historically reported. Polioencephalitis and/or myelitis was consistently present and PTV was detected in affected neural tissue by PCR in a portion of cases. Sequencing from two clinical cases identified PTV-2 and PTV-11. To assess neuropathogenicity of these isolates, 5-week-old cesarean derived and colostrum-deprived pigs were assigned to three groups: negative control (n = 4), PTV-2-inoculated (n = 7), and PTV-11-inoculated (n = 7). Three PTV-2-inoculated pigs developed mild incoordination of the hind limbs, one of which progressed to posterior ataxia. While all PTV-11-inoculated pigs showed severe neurological signs consistent with Teschovirus encephalomyelitis, no evidences of neurological signs were observed in sham-inoculated animals. All PTV-2- and PTV-11-inoculated pigs had microscopic lesions consistent with Teschovirus encephalomyelitis. To our knowledge, this is the first description of PTV-11 and experimental study demonstrating the neuropathogenicity of PTV-11 in the United States.

Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers

Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively.

IMPORTANCE

Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.

F-coliphages, porcine adenovirus and porcine teschovirus as potential indicator viruses of fecal contamination for pork carcass processing

There are concerns about the zoonotic transmission of viruses through undercooked pork products. There is a lack of information on suitable indicator viruses for fecal contamination with pathogenic enteric viruses in the meat processing chain. The study compared the incidence and levels of contamination of hog carcasses with F-coliphages, porcine teschovirus (PTV), and porcine adenovirus (PAdV) at different stages of the dressing process to assess their potential as indicator viruses of fecal contamination. One hundred swab samples (200cm²) were collected from random sites on hog carcasses at 4 different stages of the dressing process and from retail pork over the span of a year from 2 pork processing plants (500/plant). Viable F-coliphages, PAdV DNA and PTV RNA were each detected on ≥99% of the incoming carcasses at both plants and were traceable through the pork processing chain. Significant correlations were observed between viable F-coliphages and PAdV DNA and between F-coliphages and PTV RNA but not between PAdV DNA and PTV RNA at the various stages of pork processing. Detection of viable F-coliphages was more sensitive than genomic copies of PAdV and PTV at low levels of contamination, making F-coliphages a preferred indicator in the pork slaughter process as it also provides an indication of infectivity. For plant A, F-RNA coliphages were detected in 25%, 63%, and 21% of carcass swabs after pasteurization, evisceration, and retail pork products, respectively. For plant B, F-coliphages were detected in 33%, 25%, and 13% of carcass swabs after skinning, evisceration, and retail pork samples, respectively. Viable F-RNA coliphages were genotyped. Viable F-RNA GII and GIII were generally not detected at the earlier stages of the slaughter process but they were detected on 13% of carcasses after evisceration and 2% of retail pork samples at plant A, which raises concerns of potential food handler contamination during pork processing. Consumers could be at risk when consuming undercooked meat contaminated with pathogenic enteric viruses.

Genes Indicative of Zoonotic and Swine Pathogens Are Persistent in Stream Water and Sediment following a Swine Manure Spill

Manure spills into streams are relatively frequent, but no studies have characterized stream contamination with zoonotic and veterinary pathogens, or fecal chemicals, following a spill. We tested stream water and sediment over 25 days and downstream for 7.6 km for the following: fecal indicator bacteria (FIB), the fecal indicator chemicals cholesterol and coprostanol, 20 genes for zoonotic and swine-specific bacterial pathogens by presence/absence PCR for viable cells, one swine-specific Escherichia coli toxin gene (STII gene) by quantitative PCR (qPCR), and nine human and animal viruses by qPCR or reverse transcription-qPCR. Twelve days postspill, and 4.2 km downstream, water concentrations of FIB, cholesterol, and coprostanol were 1 to 2 orders of magnitude greater than those detected before, or above, the spill, and genes indicating viable zoonotic or swine-infectious Escherichia coli were detected in water or sediment. STII gene levels increased from undetectable before or above the spill to 10(5) copies/100 ml of water 12 days postspill. Thirteen of 14 water (8/9 sediment) samples had viable STII-carrying cells postspill. Eighteen days postspill, porcine adenovirus and teschovirus were detected 5.6 km downstream. FIB concentrations (per gram [wet weight]) in sediment were greater than in water, and sediment was a continuous reservoir of genes and chemicals postspill. Constituent concentrations were much lower, and detections less frequent, in a runoff event (200 days postspill) following manure application, although the swine-associated STII and stx2e genes were detected. Manure spills are an underappreciated pathway for livestock-derived contaminants to enter streams, with persistent environmental outcomes and the potential for human and veterinary health consequences.

Comparison of ZetaPlus 60S and nitrocellulose membrane filters for the simultaneous concentration of F-RNA coliphages, porcine teschovirus and porcine adenovirus from river water

Increasing attention is being paid to the impact of agricultural activities on water quality to understand the impact on public health. F-RNA coliphages have been proposed as viral indicators of fecal contamination while porcine teschovirus (PTV) and porcine adenovirus (PAdV) are proposed indicators of fecal contamination of swine origin. Viruses and coliphages are present in water in very low concentrations and must be concentrated to permit their detection. There is little information comparing the effectiveness of the methods for concentrating F-RNA coliphages with concentration methods for other viruses and vice versa. The objective of this study was to compare 5 current published methods for recovering F-RNA coliphages, PTV and PAdV from river water samples concentrated by electronegative nitrocellulose membrane filters (methods A and B) or electropositive Zeta Plus 60S filters (methods C-E). Method A is used routinely for the detection of coliphages (Méndez et al., 2004) and method C (Brassard et al., 2005) is the official method in Health Canada's compendium for the detection of viruses in bottled mineral or spring water. When river water was inoculated with stocks of F-RNA MS2, PAdV, and PTV to final concentrations of 1×10(6) PFU/100 mL, 1×10(5) gc/100 mL and 3×10(5) gc/100 mL, respectively, a significantly higher recovery for each virus was consistently obtained for method A with recoveries of 52% for MS2, 95% for PAdV, and 1.5% for PTV. When method A was compared with method C for the detection of F-coliphages, PAdV and PTV in river water samples, viruses were detected with higher frequencies and at higher mean numbers with method A than with method C. With method A, F-coliphages were detected in 11/12 samples (5-154 PFU/100 mL), PTV in 12/12 samples (397-10,951 gc/100 mL), PAdV in 1/12 samples (15 gc/100 mL), and F-RNA GIII in 1/12 samples (750 gc/100 mL) while F-RNA genotypes I, II, and IV were not detected by qRT-PCR.

Multiple models of porcine teschovirus pathogenesis in endemically infected pigs

Porcine teschoviruses (PTVs) belong to the genus Teschovirus within the family Picornaviridae. PTVs are universal contaminants in pig herds in endemic and multi-infection status. To further the understanding of PTV pathogenesis in endemically infected pigs, a set of samples was studied by real time reverse transcription PCR (qRT-PCR) to quantitate viral loads in tissues and by in situ hybridization (ISH) to locate PTV signals in target cells, both targeting the 5'-NTR. cRNA of PTV-1 and PTV-7, in vitro transcribed from cloned fragments of 5'-NTR of 2 viruses, was used to construct standard curves and to run parallel in qRT-PCR, which had detection limits of 10(1) copies/per reaction, with a linearity in between 10(1) and 10(7) copies/per reaction and correlation coefficients of 0.997-0.9988. The qRT-PCR specifically amplified RNA from PTV-1 to -11, while excluding those of Sapelovirus, PEV-9 and PEV-10. Inguinal lymph node (LN) had the highest viral load of all (assuming 100%), followed by ileac LN (89-91%), tonsil (66-68%), ileum (59-60%), spleen (38-40%), and kidney (30-31%), with the least in brain (22.9%) of the inguinal LN. The 22.9% load in brain was higher than that anticipated from a simple fecal-oral-viremia operative model. The results suggested in addition that intranasal infection and retrograding axonal infection from the tonsils were equally operative and significant. ISH revealed PTV signals in a wider variety of tissue cell types than before. PTV signals were noted most impressively in neurons of the cerebral cortex and hippocampus and in the dark zone of the germinal center and adjacent paracortex of regional LN. Multiple operative models indicated that PTVs seemed to have no difficulty invading the brain. The key to whether encephalitis would ensue resided in the animal's immune status and topographic differences of neurons' susceptibilities to PTVs. When common co-infected agents are present, as is typical in the field, PTVs may synergize in causing diseases.

Application of enteric viruses for fecal pollution source tracking in environmental waters

Microbial source tracking (MST) tools are used to identify sources of fecal pollution for accurately assessing public health risk and implementing best management practices (BMPs). This review focuses on the potential of enteric viruses for MST applications. Following host infection, enteric viruses replicate and are excreted in high numbers in the hosts' feces and urine. Due to the specificity in host infection, enteric viruses have been considered one of the most accurate library-independent culture-independent MST tools. In an assessment of molecular viral assays based on sensitivity, specificity and the density of the target virus in fecal-impacted samples, human adenovirus and human polyomavirus were found to be the most promising human-specific viral markers. However, more research is needed to identify promising viral markers for livestock because of cross-reactions that were observed among livestock species or the limited number of samples tested for specificity. Other viral indicators of fecal origin, F+ RNA coliphage and pepper mild mottle virus, have also been proposed as potential targets for developing MST markers. Enhancing the utility of enteric viruses for MST applications through next generation sequencing (NGS) and virus concentration technology is discussed in the latter part of this review. The massive sequence databases generated by shotgun and gene-targeted metagenomics enable more efficient and reliable design of MST assays. Finally, recent studies revealed that alternative virus concentration methodologies may be more cost-effective than standard technologies such as 1MDS; however, improvements in the recovery efficiency and consistency are still needed. Overall, developments in metagenomic information combined with efficient concentration methodologies, as well as high host-specificity, make enteric viruses a promising tool in MST applications.

Virus hazards from food, water and other contaminated environments

Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run-offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the Caliciviridae, Adenoviridae, Hepeviridae, Picornaviridae and Reoviridae. Sampling methods and strategies, first-choice detection methods and evaluation criteria are reviewed.

Virus hazards from food, water and other contaminated environments

Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run‐offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the Caliciviridae, Adenoviridae, Hepeviridae, Picornaviridae and Reoviridae. Sampling methods and strategies, first‐choice detection methods and evaluation criteria are reviewed.

Virus hazards from food, water and the environment, their reservoirs and routes of transmission; Sampling methods and sampling strategies thereof, including the first choice test methods, and criteria for data evaluation are described.

Evaluation of a fluorogenic real-time reverse transcription-polymerase chain reaction method for the specific detection of all known serotypes of porcine teschoviruses

Performance of a real-time reverse-transcription polymerase chain reaction method for the rapid, simple and reliable detection of porcine teschovirus (PTV) was assessed. The method was based on the use of a set of oligonucleotides consisting of two specific primers and a fluorogenic TaqMan-MGB probe. Reverse transcription and PCR reactions were performed sequentially in one step. As a result the whole procedure was simple and rapid, taking less than 3h for completion. The method reacted in a dose-dependent manner with prototype strains for the eleven known PTV serotypes (PTV1-11), with higher analytical sensitivity than other gel-based RT-PCR methods described, which were performed in parallel to allow for a comparison. The assay did not cross-react with other related viruses or porcine viruses tested. The diagnostic performance of the method was analyzed using a panel of field samples consisting of pig fecal and pig slurry samples. As a conclusion, this technique is adequate and convenient for porcine teschovirus detection, both for diagnosis as well as in environmental investigations.

Molecular characterization and phylogenetic analysis of VP1 of porcine enteric picornaviruses isolates in Italy

Porcine enterovirus (PEV), Porcine Teschovirus and Porcine sapelovirus, belonging to the family Picornaviridae, are ubiquitous and mainly cause asymptomatic infections in pigs. In this study, a total of 40 Italian porcine picornavirus isolates were characterized by sequencing the capsid VP1-encoding gene. This procedure turned out to be a useful diagnostic tool for the molecular identification of porcine enterovirus, teschovirus and sapelovirus strains and for the study of molecular epidemiology and evolution of these viruses confirming the possibility of correlating virus genotype to serotype.

A Survey of Porcine Picornaviruses and Adenoviruses in Fecal Samples in Spain

In the course of an epidemiologic surveillance program for swine diseases carried out in Spain, 206 cytopathic viruses were isolated from 600 porcine fecal samples between 2004 and 2005. The virus isolates were examined using reverse transcription polymerase chain reaction (RT-PCR) methods specific for different types of porcine picornaviruses, including members of the Teschovirus, Enterovirus, and Sapelovirus genera, and PCR for porcine adenoviruses. Of the 206 isolates, 97 (47%) were identified as teschoviruses, 18 (9%) as sapeloviruses, and 7 (3%) as porcine adenoviruses. Neither Porcine enterovirus B nor Swine vesicular disease virus was found among the isolates. The present study confirms that teschoviruses are highly prevalent in porcine fecal samples, at least in Spain. It also reveals that these viruses commonly circulate among apparently healthy pigs.

Development of microbial and chemical MST tools to identify the origin of the faecal pollution in bathing and shellfish harvesting waters in France

The microbiological quality of coastal or river waters can be affected by faecal pollution from human or animal sources. An efficient MST (Microbial Source Tracking) toolbox consisting of several host-specific markers would therefore be valuable for identifying the origin of the faecal pollution in the environment and thus for effective resource management and remediation. In this multidisciplinary study, after having tested some MST markers on faecal samples, we compared a selection of 17 parameters corresponding to chemical (steroid ratios, caffeine, and synthetic compounds), bacterial (host-specific Bacteroidales, Lactobacillus amylovorus and Bifidobacterium adolescentis) and viral (genotypes I-IV of F-specific bacteriophages, FRNAPH) markers on environmental water samples (n = 33; wastewater, runoff and river waters) with variable Escherichia coli concentrations. Eleven microbial and chemical parameters were finally chosen for our MST toolbox, based on their specificity for particular pollution sources represented by our samples and their detection in river waters impacted by human or animal pollution; these were: the human-specific chemical compounds caffeine, TCEP (tri(2-chloroethyl)phosphate) and benzophenone; the ratios of sitostanol/coprostanol and coprostanol/(coprostanol+24-ethylcopstanol); real-time PCR (Polymerase Chain Reaction) human-specific (HF183 and B. adolescentis), pig-specific (Pig-2-Bac and L. amylovorus) and ruminant-specific (Rum-2-Bac) markers; and human FRNAPH genogroup II.

Molecular detection of pathogens in water--the pros and cons of molecular techniques

Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed.

Viral multiplex quantitative PCR assays for tracking sources of fecal contamination

Human and animal fecal pollution of the environment presents a risk to human health because of the presence of pathogenic viruses and bacteria. To distinguish between human and animal sources of pollution, we designed specific real-time reverse transcription (RT)-PCR assays for human and animal enteric viruses, including norovirus genogroups I, II, and III; porcine adenovirus types 3 and 5; ovine adenovirus; atadenovirus; and human adenovirus species C and F, which are excreted by infected humans, pigs, cattle, sheep, deer, and goats, and for the detection of F+ RNA bacteriophage genogroups I to IV, which are associated with human and animal wastes. The sensitivity of this viral toolbox (VTB) was tested against 10-fold dilution series of DNA plasmids that carry the target sequences of the respective viruses and was shown to detect at least 10 plasmid copies for each assay. A panel of human and animal enteric and respiratory viruses showed these assays to be highly sensitive and specific to their respective targets. The VTB was used to detect viruses in fecal and environmental samples, including raw sewage and biosolids from municipal sewage treatment plants, abattoir sewage, and fecally contaminated shellfish and river water, which were likely to contain animal or human viruses.

Use of a Bacteroides thetaiotaomicron-specific alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water

AIMS

The aims of this work were to develop a quantitative test, based on Bacteroides thetaiotaomicron, for human faecal pollution in water and to evaluate test performance.

METHODS AND RESULTS

qPCR primers, based on the complete genomic sequence of B. thetaiotaomicron VPI 5482, were designed and tested. The single-copy putative mannanase homologue, alpha-1-6 mannanase, was selected as the particular target and sequences within this gene chosen as the qPCR primers by Blast search for specificity to B. thetaiotaomicron. The average concentration of B. thetaiotaomicron in human faeces was 1.39 x 10(8) cells per gram faeces and the detection limit was 9.3 B. thetaiotaomicron copies per qPCR procedure. Comparison of B. thetaiotaomicron content in sewage vs pooled nonhuman faecal samples indicated that the current assay is specific for sewage.

CONCLUSION

The subject assay is potentially useful for quantification of sewage pollution in water.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteroides-associated markers, proposed for faecal source tracking, have exclusively been based on gene sequences related to generally classified and uncultured bacteria. However, genes associated with host-microbe interaction have been suggested as more specific markers. The present assay targets such a gene of B. thetaiotaomicron which is considered to be a symbiont in the human gut.

Molecular indicators used in the development of predictive models for microbial source tracking

A number of chemical, microbial, and eukaryotic indicators have been proposed as indicators of fecal pollution sources in water bodies. No single one of the indicators tested to date has been able to determine the source of fecal pollution in water. However, the combined use of different indicators has been demonstrated to be the best way of defining predictive models suitable for determining fecal pollution sources. Molecular methods are promising tools that could complement standard microbiological water analysis. In this study, the feasibility of some proposed molecular indicators for microbial source tracking (MST) was compared (names of markers are in parentheses): host-specific Bacteroidetes (HF134, HF183, CF128, and CF193), Bifidobacterium adolescentis (ADO), Bifidobacterium dentium (DEN), the gene esp of Enterococcus faecium, and host-specific mitochondrial DNA associated with humans, cattle, and pigs (Humito, Bomito, and Pomito, respectively). None of the individual molecular markers tested enabled 100% source identification. They should be combined with other markers to raise sensitivity and specificity and increase the number of sources that are identified. MST predictive models using only these molecular markers were developed. The models were evaluated by considering the lowest number of molecular indicators needed to obtain the highest rate of identification of fecal sources. The combined use of three molecular markers (ADO, Bomito, and Pomito) enabled correct identification of 75.7% of the samples, with differentiation between human, swine, bovine, and poultry sources. Discrimination between human and nonhuman fecal pollution was possible using two markers: ADO and Pomito (84.6% correct identification). The percentage of correct identification increased with the number of markers analyzed. The best predictive model for distinguishing human from nonhuman fecal sources was based on 5 molecular markers (HF134, ADO, DEN, Bomito, and Pomito) and provided 90.1% correct classification.

Quantitative PCR assays to survey the bovine adenovirus levels in environmental samples

AIMS

Previous studies suggested bovine adenoviruses (BAdVs) could be used as cattle faecal indicators. The main aim of this study was to survey the levels of BAdV in environmental samples using quantitative polymerase chain reaction (qPCR).

METHODS AND RESULTS

Two qPCR assays were developed to identify and quantify BAdVs in environmental samples. BAdVs were detected in all dairy manure, and in most cases, the sample concentrations were around 10(3)-10(4) copies ml(-1). Farm tile drainage samples were also detected, but the concentrations were about 1-3 log(10) lower than the BAdV concentrations in the manure samples. The genome equivalent copy (GEC) levels of BAdV and the phage forming unit (PFU) levels of somatic phage in manure samples were comparable. Four of twenty individual cattle faeces were positive with concentrations similar to that found in the manure samples. Sequencing results confirmed the presence of BAdV in the environmental samples, and phylogenetic analysis indicated that BAdV 2 and 4 were the most prevalent serotypes in all the manure samples tested. The qPCR assays developed in this study showed higher sensitivity in detecting BAdV 1 and 2 than the previous published nested assay.

CONCLUSION

The high levels of BAdV in the environmental samples may suggest it could be used for bovine faecal indicator. The significant levels of BAdV in the drainage samples may indicate the potential of surface water pollution by the manure applied to farm fields.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study that reports the quantitative level of BAdV in environmental samples. These results could be useful when it comes to determining whether BAdV could be utilized as a bovine faecal indicator.

Selective inhibitors of picornavirus replication

Picornaviruses cover a large family of pathogens that have a major impact on human but also on veterinary health. Although most infections in man subside mildly or asymptomatically, picornaviruses can also be responsible for severe, potentially life-threatening disease. To date, no therapy has been approved for the treatment of picornavirus infections. However, efforts to develop an antiviral that is effective in treating picornavirus-associated diseases are ongoing. In 2007, Schering-Plough, under license of ViroPharma, completed a phase II clinical trial with Pleconaril, a drug that was originally rejected by the FDA after a New Drug Application in 2001. Rupintrivir, a rhinovirus protease inhibitor developed at Pfizer, reached clinical trials but was recently halted from further development. Finally, Biota's HRV drug BTA-798 is scheduled for phase II trials in 2008. Several key steps in the picornaviral replication cycle, involving structural as well as non-structural proteins, have been identified as valuable targets for inhibition. The current review aims to highlight the most important developments during the past decades in the search for antivirals against picornaviruses.

Assessment of the 16S-23S rDNA intergenic spacer region in Enterococcus spp. for microbial source tracking

A new library-based microbial source tracking (MST) approach intended for initial application in the coastal waters of Virginia was evaluated. Host-origin isolates of Enterococcus spp. were collected from beaches and the surrounding tidewater region of Virginia and used to construct a library based on the pattern of DNA band lengths produced by the amplification of the 16S-23S rDNA intergenic spacer (IGS) region, and subsequent digestion with MboI. Initial results from small host-origin libraries (64 and 200 total isolates) with discriminant analysis (DA) and logistic regression (LR) yielded high average rates of correct classification (ARCC) for a four-source classification split (birds, dogs, sewage, and wildlife), with ARCCs ranging from 83 to 100%. However, the poor results obtained when classification was attempted on a non-library validation set (VS, ARCCs of 47 and 48%, respectively, using DA and LR) demonstrated that a library of 200 isolates was insufficient to adequately represent the diversity of the enterococci in the sampled region. An increase in the library size to 1029 total isolates was accompanied by a reduction in the ARCC of the library to 42.7% with DA and 45.7% with LR, plus similarly poor results obtained from the VS. The low correct classification rates generated by the larger known-source library were unsuitable for field application. Many reported MST methods have been based on results obtained using small host-origin libraries without external validation. Our results indicate that such an approach can be very misleading, and that larger libraries and external validation is essential for the confirmation of preliminary results.

F+ RNA coliphage typing for microbial source tracking in surface waters

AIMS

The utility of coliphages to detect and track faecal pollution was evaluated using South Carolina surface waters that exceeded State faecal coliform standards.

METHODS AND RESULTS

Coliphages were isolated from 117 surface water samples by single agar layer (SAL) and enrichment presence/absence (EP/A) methods. Confirmed F+ RNA coliphages were typed for microbial source tracking using a library-independent approach. Concentrations of somatic coliphages using 37 and 44.5 degrees C incubation temperatures were found to be significantly different and the higher temperature may be more specific for faecal contamination. The EP/A technique detected coliphages infecting Escherichia coli Famp in 38 (66%) of the 58 surface water samples negative for F+ coliphages by the SAL method. However, coliphages isolated by EP/A were found to be less representative of coliphage diversity within a sample. Among the 2939 coliphage isolates tested from surface water and known source samples, 813 (28%) were found to be F+ RNA. The majority (94%) of surface water F+ RNA coliphage isolates typed as group I. Group II and/or III viruses were identified from 14 surface water stations, the majority of which were downstream of wastewater discharges. These sites were likely contaminated by human-source faecal pollution.

CONCLUSIONS

The results suggest that faecal contamination in surface waters can be detected and source identifications aided by coliphage analyses.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study supports the premise that coliphage typing can provide useful, but not absolute, information to distinguish human from animal sources of faecal pollution. Furthermore, the comparison of coliphage isolation methods detailed in this study should provide valuable information to those wishing to incorporate coliphage detection into water quality assessments.

Fecal source tracking, the indicator paradigm, and managing water quality

Fecal source tracking is used because standard methods of measuring fecal contamination in water by enumerating fecal indicator bacteria (FIB) do not identify the sources of the contamination. This paper presents a critical review of source tracking with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), when methods are applicable, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper discusses the broader question of whether fecal source tracking and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many fecal source-tracking methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the "real" answer is not known, so their comparative performance and accuracy cannot be assessed. For source tracking to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB in legislation, monitoring has concentrated on FIB and lost sight of pathogens. A more rational approach to regulating water quality would start with available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with targeted fecal source tracking to control them. Baseline monitoring of indicators would become just one tool among many.

Determining sources of fecal bacteria in waterways

The microbiological contamination of waterways by pathogenic microbes has been, and is still, a persistent public safety concern in the United States and in most countries of the world. As most enteric pathogens are transmitted through the fecal-oral route, fecal pollution is generally regarded as the major contributor of pathogens to waterways. Fecal pollution of waterways can originate from wastewater treatment facilities, septic tanks, domestic- and wild-animal feces, and pets. Because enteric pathogens are derived from human or animal sources, techniques capable of identifying and apportioning fecal sources have been intensively investigated for use in remediation efforts and to satisfy regulatory concerns. Pollution of human origin is of the most concern, since human feces is more likely to contain human-specific enteric pathogens. Fecal indicator bacteria have been used successfully as the primary tool for microbiologically based risk assessment. However measurement of fecal indicator bacteria does not define what pathogens are present, or define the sources of these bacteria. Microbial source tracking (MST) methods that have the ability to differentiate among sources of fecal pollution are currently under development. These methods will ultimately be useful for risk assessment purposes and to aid regulatory agencies in developing strategies to remediate microbiologically impaired waterways.

Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents

Multiplex real-time PCR amplifying fecal mitochondrial DNA (mtDNA) combined with rapid, crude DNA preparations are promising additions to surface water source tracking methods. Amplification of eukaryotic mitochondrial DNA identifies the fecal source directly and can be used in conjunction with other intestinal microbial methods to characterize effluents. Species-specific primers and dual-labeled probes for human, swine, and bovine NADH dehydrogenase subunit 5 (ND5) genes were created for multiplex real-time PCR in feces and effluent slurries. The linear range of the multiplex assay was 10(2)-10(7) mtDNA copies for human, bovine, and swine effluent in combination (equal volumes). PCR amplification efficiencies for bovine, human, and swine mtDNA when assayed in combination were 93, 107, and 92% respectively. Linear regression correlation coefficients (r2) were 0.99 for all standard curves except for human mtDNA in combination (r2 = 0.95). Multiplex amplification of bovine, human, and swine mtDNA (ND5) exhibited no cross-reactions between the effluents from three species of interest. Also, no cross-reactions were observed with effluents of other vertebrates: sheep, goat, horse, dog, cat, Canada goose, broiler, layer, turkey, and tilapia. Performed as a blind test, the PCR operator was able to correctly identify all but two effluent challenge samples (10/12 or 83% correct) with no false positives (22/22 or 100% correct). The multiplex assay had a tendency to detect the species of highest mtDNA concentration only. Better detection of all three species in a combination of human, bovine, and swine effluents was accomplished by running each real-time PCR primer/ probe set singly. Real-time PCR detection limit was calculated as 2.0 x 10(6) mitochondrial copies or 0.2 g of human feces per 100 mL effluent. Some carry-over mtDNA PCR signal from consumed beef, but not pork, was found in feces of human volunteers.

High-throughput and quantitative procedure for determining sources of Escherichia coli in waterways by using host-specific DNA marker genes

Escherichia coli is currently used as an indicator of fecal pollution and to assess water quality. While several genotypic techniques have been used to determine potential sources of fecal bacteria impacting waterways and beaches, they do not allow for the rapid analysis of a large number of samples in a relatively short period of time. Here we report that gene probes identified by Hamilton and colleagues (M. J. Hamilton, T. Yan, and M. J. Sadowsky, Appl. Environ. Microbiol. 72:4012-4019, 2006) were useful for the development of a high-throughput and quantitative macroarray hybridization system to determine numbers of E. coli bacteria originating from geese/ducks. The procedure we developed, using a QBot robot for picking and arraying of colonies, allowed us to simultaneously analyze up to 20,736 E. coli colonies from water samples, with minimal time and human input. Statistically significant results were obtained by analyzing 700 E. coli colonies per water sample, allowing for the analysis of approximately 30 sites per macroarray. Macroarray hybridization studies done on E. coli collected from water samples obtained from two urban Minnesota lakes and one rural South Carolina lake indicated that geese/ducks contributed up to 51% of the fecal bacteria in the urban lake water samples, and the level was below the detection limit in the rural lake water sample. This technique, coupled with the use of other host source-specific gene probes, holds great promise as a new quantitative microbial source tracking tool to rapidly determine the origins of E. coli in waterways and on beaches.