Multiplex quantitative real-time reverse transcriptase PCR for F+-specific RNA coliphages: a method for use in microbial source tracking

A multi-tiered approach to assess fecal pollution in an urban watershed: Bacterial and viral indicators and sediment microbial communities

Development of effective pollution mitigation strategies require an understanding of the pollution sources and factors influencing fecal pollution loading. Fecal contamination of Turkey Creek in Gulfport, Mississippi, one of the nation's most endangered creeks, was studied through a multi-tiered approach. Over a period of approximately two years, four stations across the watershed were analyzed for nutrients, enumeration of E. coli, male-specific coliphages and bioinformatic analysis of sediment microbial communities. The results demonstrated that two stations, one adjacent to a lift station and one just upstream from the wastewater-treatment plant, were the most impacted. The station adjacent to land containing a few livestock was the least impaired. While genotyping of male-specific coliphage viruses generally revealed a mixed viral signature (human and other animals), fecal contamination at the station near the wastewater treatment plant exhibited predominant impact by municipal sewage. Fecal indicator loadings were positively associated with antecedent rainfall for three of four stations. No associations were noted between fecal indicator loadings and any of the nutrients. Taxonomic signatures of creek sediment were unique to each sample station, but the sediment microbial community did overlap somewhat following major rain events. No presence of Escherichia coli (E. coli) or enterococci were found in the sediment. At some of the stations it was evident that rainfall was not always the primary driver of fecal transport. Repeated monitoring and analysis of a variety of parameters presented in this study determined that point and non-point sources of fecal pollution varied spatially in association with treated and/or untreated sewage.

Quantitative Assessment of Microbial Pathogens and Indicators of Wastewater Treatment Performance for Safe and Sustainable Water Reuse in India

Currently, there is no data on the molecular quantification of microbial indicators of recycled water quality in India. In this study, multiple microbial pathogens and indicators of water quality were evaluated at three wastewater treatment plants located in two Indian cities (New Delhi and Jaipur) to determine the treatment performance and suitability of recycled water for safe and sustainable reuse applications. Real-time polymerase chain reaction (PCR) was used for the rapid evaluation of six human pathogens and six microbial indicators of fecal contamination. Among the microbial indicators, pepper mild mottle virus (PMMoV), F⁺RNA-GII bacteriophage, Bacteroides thetaiotamicron, and four human pathogens (Norovirus genogroups I & II, Giardia, and Campylobacter coli) were detected in all of the influent samples analyzed. This work suggests that the raw influents contain lower levels of noroviruses and adenoviruses and higher levels of Giardia compared to those reported from other geographic regions. Overall, the efficacy of the removal of microbial targets was over 93% in the final effluent samples, which is consistent with reports from across the world. PMMoV and Giardia were identified as the best microbial targets, from the microbial indicators spanning across bacteria, bacteriophages, DNA/RNA viruses, and protozoan parasites, by which to evaluate treatment performance and recycled water quality in Indian settings, as they were consistently present at high concentrations in untreated wastewater both within and across the sites. Also, they showed a strong correlation with other microbial agents in both the raw influent and in the final effluent. These findings provide valuable insights into the use of culture-independent molecular indicators that can be used to assess the microbial quality of recycled water in Indian settings. IMPORTANCE Wastewater treatment plants (WWTPs) have rapidly increased in India during the last decade. Nonetheless, there are only a few labs in India that can perform culture-based screening for microbial quality. In the last 2 years of the pandemic, India has witnessed a sharp increase in molecular biology labs. Therefore, it is evident that culture-independent real-time PCR will be increasingly used for the assessment of microbial indicators/pathogens in wastewater, especially in resource-limited settings. There is no data available on the molecular quantitation of microbial indicators from India. There is an urgent need to understand and evaluate the performance of widely used microbial indicators via molecular quantitation in Indian WWTPs. Our findings lay the groundwork for the molecular quantitation of microbial indicators in WWTPs in India. We have screened for 12 microbial targets (indicators and human pathogens) and have identified pepper mild mottle virus (PMMoV) and Giardia as the best molecular microbiological indicators in Indian settings.

Poultry litter as potential source of pathogens and other contaminants in groundwater and surface water proximal to large-scale confined poultry feeding operations

Manure from livestock production has been associated with the contamination of water resources. To date, research has primarily focused on runoff of these contaminants from animal operations into surface water, and the introduction of poultry-derived pathogenic zoonoses and other contaminants into groundwater is under-investigated. We characterized pathogens and other microbial and chemical contaminants in poultry litter, groundwater, and surface water near confined poultry feeding operations (chicken layer, turkey) at 9 locations in Iowa and one in Wisconsin from May and June 2016. Results indicate that poultry litter from large-scale poultry confined feeding operations is a likely source of environmental contamination and that groundwater is also susceptible to such poultry-derived contamination. Poultry litter, groundwater, and surface water samples had detections of viable bacteria growth (Salmonella spp., enterococci, staphylococci, lactobacilli), multi-drug resistant Salmonella DT104 flo_st and int genes, F⁺ RNA coliphage (group I and IV), antibiotic resistance genes (ARGs; bla_DHA, bla_OXA-48, bla_TEM, bla_CMY-2, tetM), phytoestrogens (biochanin A, daidzein, formononetin), and a progestin (progesterone). In addition, mcr-1 (a colistin ARG), was detected in a groundwater sample and in another groundwater sample, antibiotic resistant isolates were positive for Brevibacterium spp., a potential signature of poultry in the environment. Detectable estrogenicity was not measured in poultry litter, but was observed in 67% of the surface water samples and 22% were above the U.S. Environmental Protection Agency trigger level of 1 ng/L. The transport of microbial pathogens to groundwater was significantly greater (p < 0.001) than the transport of trace organic contaminants to groundwater in this study. In addition to viable pathogens, several clinically important ARGs were detected in litter, groundwater, and surface water, highlighting the need for additional research on sources of these contaminants in livestock dominated areas.

Occurrence of Staphylococcus spp. and investigation of fecal and animal viral contaminations in livestock, river water, and sewage from Tunisia and Romania

The objective of this study was to determine the occurrence of Staphylococcus spp., Escherichia coli, somatic coliphages, F-specific RNA bacteriophages, hepatitis E virus (HEV), and bovine enterovirus (BEV) in fecal and water samples. The occurrence of Staphylococcus spp. was investigated in treated wastewater samples collected from slaughterhouse of Tunisia. Results showed that Staphylococcus spp. were detected in the totality of collected samples with an average mean of 5.44 Log₁₀ (CFU/100 ml). Regarding fecal indicator bacteria, E. coli was detected in the totality of water samples and was more abundant in Tunisian samples than in samples collected from Romania (P < 0.05). Concerning somatic coliphages and F-specific RNA bacteriophages used as viral indicators, they were detected in all raw and treated wastewaters. Bovine enterovirus (BEV) was detected in 20.1% and 28% of bovine stool samples collected from Tunisia and Romania, respectively. BEV was also detected in 60% of porcine stool samples from Romania. BEV was absent in all treated sewage samples. HEV was detected in raw sewage and bovine fecal sample from Romania with low occurrence and none sample from Tunisia was positive. This study may give us an insight into the monitoring of water quality in Tunisia and Romania.

Preliminary Source Tracking of Male-Specific (F+) RNA Coliphage on Lettuce as a Surrogate of Enteric Viruses Using Reverse Transcription-PCR

The aim of this research was to preliminary track fecal source male-specific F+RNA coliphages including human and animals in lettuce. At first, two published virus extraction procedures of ultracentrifugation and PEG precipitation were compared using DAL assay for determining the recovery efficiency in lettuce spiked artificially with three concentrations (102, 104, 106 pfu/100 ml) of MS2 coliphage. The results showed that PEG precipitation had the highest recovery in which the recovery efficiency at the spiked level of 106 pfu/100 ml was 16.63 %. Aqueous phase obtained from the final step of PEG method was applied for enumeration of coliphage and viral RNA extraction in naturally contaminated lettuce samples (N = 30) collected from two sources (market and farm). The samples were then analyzed based on (I, II, III, and IV primer sets) using RT-PCR method. Coliphages were detected in 9 (60 %) and 12 (80 %) out of 15 market and farm samples, respectively, using DAL assay, whereas male-specific F+RNA coliphages were detected using the RT-PCR method in 9 (60 %) and 13 (86.6 %) out of 15 samples of market and farm, respectively. Based on the results, only genotype I of male-specific F+RNA coliphages was detected in lettuce samples and no sample tested was positive for other genotypes (II, III, and IV).

Field-based evaluation of a male-specific (F+) RNA coliphage concentration method

Fecal contamination of water poses a significant risk to public health due to the potential presence of pathogens, including enteric viruses. Therefore, sensitive, reliable and easy to use methods for the concentration, detection and quantification of microorganisms associated with the safety and quality of water are needed. In this study, we performed a field evaluation of an anion exchange resin-based method to concentrate male-specific (F+) RNA coliphages (FRNA), fecal indicator organisms, from diverse environmental waters that were suspected to be contaminated with feces. In this system, FRNA coliphages are adsorbed to anion exchange resin and direct nucleic acid isolation is performed, yielding a sample amenable to real-time reverse transcriptase (RT)-PCR detection. Matrix-dependent inhibition of this method was evaluated using known quantities of spiked FRNA coliphages belonging to four genogroups (GI, GII, GII and GIV). RT-PCR-based detection was successful in 97%, 72%, 85% and 98% of the samples spiked (10⁶ pfu/l) with GI, GII, GIII and GIV, respectively. Differential FRNA coliphage genogroup detection was linked to inhibitors that altered RT-PCR assay efficiency. No association between inhibition and the physicochemical properties of the water samples was apparent. Additionally, the anion exchange resin method facilitated detection of naturally present FRNA coliphages in 40 of 65 environmental water samples (61.5%), demonstrating the viability of this system to concentrate FRNA coliphages from water.

Assessing the microbial quality of a tropical watershed with an urbanization gradient using traditional and alternate fecal indicators

Urbanization affects the microbial loading into tropical streams, but its impact on water quality varies across watersheds. Rainfall in tropical environments also complicates microbial dynamics due to high seasonal and annual variations. Understanding the dynamics of fecal contamination in tropical surface waters may be further hindered by limitations from the utilization of traditional microbial indicators. We measured traditional (Enterococcus spp. and Escherichia coli), as well as alternate (enterophages and coliphages) indicators of fecal contamination in a tropical watershed in Puerto Rico during a 1-year period, and examined their relationship with rainfall events across an urbanization gradient. Enterococcus spp. and E. coli concentrations were 4 to 5 logs higher in non-urbanized or pristine sites when compared to enterophages and coliphages, suggesting that traditional fecal indicator bacteria may be natural inhabitants of pristine tropical waters. All of the tested indicators were positively correlated with rainfall and urbanization, except in the most urbanized sites, where rainfall may have had a dilution effect. The present study indicates that utilizing novel indicators of microbial water quality may improve the assessment of fecal contamination and pathogen risk for tropical watersheds.

Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR

The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at which 95% of positive samples are detected) for the entire process of waterborne pathogen detection. We began by spiking the lowest concentration that was consistently positive at the qPCR step (based on its standard curve) into each procedural step working backwards (i.e., extraction, secondary concentration, primary concentration), which established a concentration that was detectable following losses of the pathogen from processing. Using the fraction of positive replicates (n = 10) at this concentration, we selected and analyzed a second, and then third, concentration. If the fraction of positive replicates equaled 1 or 0 for two concentrations, we selected another. We calculated the LOD using probit analysis. To demonstrate our approach we determined the 95% LOD for Salmonella enterica serovar Typhimurium, adenovirus 41, and vaccine-derived poliovirus Sabin 3, which were 11, 12, and 6 genomic copies (gc) per reaction (rxn), respectively (equivalent to 1.3, 1.5, and 4.0 gc L(-1) assuming the 1500 L tap-water sample volume prescribed in EPA Method 1615). This approach limited the number of analyses required and was amenable to testing multiple genetic targets simultaneously (i.e., spiking a single sample with multiple microorganisms). An LOD determined this way can facilitate study design, guide the number of required technical replicates, aid method evaluation, and inform data interpretation.

Contribution of hydrological data to the understanding of the spatio-temporal dynamics of F-specific RNA bacteriophages in river water during rainfall-runoff events

Heavy rainfall events were previously reported to bring large amounts of microorganisms in surface water, including viruses. However, little information is available on the origin and transport of viral particles in water during such rain events. In this study, an integrative approach combining microbiological and hydrological measurements was investigated to appreciate the dynamics and origins of F-specific RNA bacteriophage fluxes during two distinct rainfall-runoff events. A high frequency sampling (automatic sampler) was set up to monitor the F-specific RNA bacteriophages fluxes at a fine temporal scale during the whole course of the rainfall-runoff events. A total of 276 rainfall-runoff samples were collected and analysed using both infectivity and RT-qPCR assays. The results highlight an increase of 2.5 log10 and 1.8 log10 of infectious F-specific RNA bacteriophage fluxes in parallel of an increase of the water flow levels for both events. Faecal pollution was characterised as being mainly from anthropic origin with a significant flux of phage particles belonging to the genogroup II. At the temporal scale, two successive distinct waves of phage pollution were established and identified through the hydrological measurements. The first arrival of phages in the water column was likely to be linked to the resuspension of riverbed sediments that was responsible for a high input of genogroup II. Surface runoff contributed further to the second input of phages, and more particularly of genogroup I. In addition, an important contribution of infectious phage particles has been highlighted. These findings imply the existence of a close relationship between the risk for human health and the viral contamination of flood water.

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California

F+ RNA coliphages (FRNA) are used to source-track fecal contamination and as surrogates for enteric pathogen persistence in the environment. However, the environmental persistence of FRNA is not clearly understood and necessitates the evaluation of the survival of prototype and environmental isolates of FRNA representing all four genogroups in surface waters from the central coast of California. Water temperature played a significant role in persistence-all prototype and environmental strains survived significantly longer at 10 °C compared to 25 °C. Similarly, the availability of host bacterium was found to be critical in FRNA survival. In the absence of E. coli F(amp), all prototypes of FRNA disappeared rapidly with a D-value (days for one log reduction) of <1.2 d from water samples incubated at 25 °C; the longest surviving prototype was SP. However, in the presence of the host, the order of persistence at 25 °C was QB>MS2>SP>GA and at 10 °C it was QB = MS2>GA>SP. Significant differences in survival were observed between prototypes and environmental isolates of FRNA. While most environmental isolates disappeared rapidly at 25 °C and in the absence of the host, members of genogroups GIII and GI persisted longer with the host compared to members of GII and GIV. Consequentially, FRNA based source tracking methods can be used to detect phages from recent fecal contamination along with those that persist longer in the environment as a result of cooler temperatures and increased host presence.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 10(6) gene copies per ml), followed by those of HF183 (8.0 × 10(5) gene copies per ml) and Enterococcus spp. (3.6 × 10(5) gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters.

Application of F⁺RNA Coliphages as Source Tracking Enteric Viruses on Parsley and Leek Using RT-PCR

The objective of this study was to identify sources of fecal contamination in leek and parsley, by using four different F(+)RNA coliphage genogroups (IV, I indicate animal fecal contamination and II, III indicate human fecal contamination). Three different concentrations (10(2), 10(4), 10(6) pfu/ml) of MS2 coliphage were inoculated on the surface of parsley and leek samples for detection of phage recovery efficiency among two methods of elution concentration (PEG-precipitation and Ultracentrifugation) by performing double agar layer (DAL) assay in three replications. Highest recovery of MS2 was observed in PEG method and in 10(6) inoculation concentration. Accordingly, the PEG method was used for washing and isolation of potentially contaminated phages of 30 collected samples (15 samples from the market and 15 samples from the farm). The final solutions of PEG method were tested for the enumeration of plaques by DAL assay. Total RNA was then extracted from recovered phages, and RT-PCR was performed by using four primer sets I, II, III, and IV. Incidence of F(+)RNA coliphages was observed in 12/15 (80 %) and 10/15 (66/6 %) of samples were obtained from farm and market, respectively, using both DAL and RT-PCR test methods. Different genotypes (I, II, and IV) of F(+)RNA coliphages were found in farm samples, while only genotype I was detected in market samples by using the primer sets. Due to the higher frequency of genotype I and IV, the absence of genotype III, and also the low frequency of genotype II, it is concluded that the contamination of vegetable (parsley and leek) in Neyshabour, Iran is most likely originated from animal sources.

Evaluation of FRNA coliphages as indicators of human enteric viruses in a tropical urban freshwater catchment

This study aimed to evaluate the relationship between FRNA coliphages (FRNA GI to GIV) and human enteric viruses (human adenoviruses, HAdV, astroviruses, AstV, noroviruses, NoV, and rotaviruses, RoV) in a tropical urban freshwater catchment. Positive associations between human-specific coliphages and human viral pathogens substantiate their use as viral indicators and in microbial source tracking. Reverse transcription qPCR was used to measure the concentrations of viruses and FRNA coliphages in concentrated water samples. Environmental water samples were also analyzed for male-specific (F+) and somatic (Som) coliphages using plaque assay. The most abundant enteric virus was NoV (55%) followed by HAdV (33%), RoV (33%), and AstV (23%), while the most abundant FRNA genogroup was GI (85%) followed by GII (48%), GIV (8%) and GIII (7%). Concentrations of human-specific coliphages FRNA GII were positively correlated with NoV, HAdV, RoV, AstV, F+ and Som (τ = 0.5 to 0.3, P < 0.05) while concentrations of animal-specific coliphages FRNA GI were negatively correlated with HAdV and RoV (τ = -0.2, P < 0.05). This study demonstrates statistical relationships between human-specific coliphages and a suite of human enteric viruses in the environment.

U.S. Recreational Water Quality Criteria: A Vision for the Future

This manuscript evaluates the U.S. Recreational Water Quality Criteria (RWQC) of 2012, based upon discussions during a conference held 11-13 March 2013, in Honolulu, Hawaii. The RWQC of 2012 did not meet expectations among the research community because key recommended studies were not completed, new data to assess risks to bathers exposed to non-point sources of fecal indicator bacteria (FIB) were not developed, and the 2012 RWQC did not show marked improvements in strategies for assessing health risks for bathers using all types of recreational waters. The development of the 2012 RWQC was limited in scope because the epidemiologic studies at beach sites were restricted to beaches with point sources of pollution and water samples were monitored for only enterococci. The vision for the future is development of effective RWQC guidelines based on epidemiologic and quantitative microbial risk assessment (QMRA) studies for sewage specific markers, as well as human enteric pathogens so that health risks for bathers at all recreational waters can be determined. The 2012 RWQC introduced a program for states and tribes to develop site-specific water quality criteria, and in theory this approach can be used to address the limitations associated with the measurements of the traditional FIB.

Occurrence of bacteriophages infecting Aeromonas, Enterobacter, and Klebsiella in water and association with contamination sources in Thailand

The co-residence of bacteriophages and their bacterial hosts in humans, animals, and environmental sources directed the use of bacteriophages to track the origins of the pathogenic bacteria that can be found in contaminated water. The objective of this study was to enumerate bacteriophages of Aeromonas caviae (AecaKS148), Enterobacter sp. (EnspKS513), and Klebsiella pneumoniae (KlpnKS648) in water and evaluate their association with contamination sources (human vs. animals). Bacterial host strains were isolated from untreated wastewater in Bangkok, Thailand. A double-layer agar technique was used to detect bacteriophages. All three bacteriophages were detected in polluted canal samples, with likely contamination from human wastewater, whereas none was found in non-polluted river samples. AecaKS148 was found to be associated with human fecal sources, while EnspKS513 and KlpnKS648 seemed to be equally prevalent in both human and animal fecal sources. Both bacteriophages were also present in polluted canals that could receive contamination from other fecal sources or the environment. In conclusion, all three bacteriophages were successfully monitored in Bangkok, Thailand. This study provided an example of bacteriophages for potential use as source identifiers of pathogen contamination. The results from this study will assist in controlling sources of pathogen contamination, especially in developing countries.

Development and evaluation of a culture-independent method for source determination of fecal wastes in surface and storm waters using reverse transcriptase-PCR detection of FRNA coliphage genogroup gene sequences

A method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for detecting interferences in RNA recovery and analysis, was developed for the direct, culture-independent detection of genetic markers from FRNA coliphage genogroups I, II & IV in water samples. Results were obtained from an initial evaluation of the performance of this method in analyses of waste water, ambient surface water and stormwater drain and outfall samples from predominantly urban locations. The evaluation also included a comparison of the occurrence of the FRNA genetic markers with genetic markers from general and human-related bacterial fecal indicators determined by current or pending EPA-validated qPCR methods. Strong associations were observed between the occurrence of the putatively human related FRNA genogroup II marker and the densities of the bacterial markers in the stormwater drain and outfall samples. However fewer samples were positive for FRNA coliphage compared to either the general bacterial fecal indicator or the human-related bacterial fecal indicator markers particularly for ambient water samples. Together, these methods show promise as complementary tools for the identification of contaminated storm water drainage systems as well as the determination of human and non-human sources of contamination.

Enzyme treatment reverse transcription-PCR to differentiate infectious and inactivated F-specific RNA phages

F-specific (F+) RNA phages are recommended as indicators of fecal contamination and the presence of enteric viruses and as viral surrogates to elucidate the resistance of viruses to adverse conditions or to assess the effectiveness of inactivating processes. Reverse transcription (RT)-PCR methods have been used to detect, quantify, or identify subgroups of F+ RNA phages. However, these methods may overestimate the infectivity of F+ RNA phages in test samples, since the presence of both infectious and inactivated phages (or naked RNA) can lead to positive RT-PCR signals. In this study, we evaluated the ability of an enzyme treatment (ET) with proteinase K and RNase A prior to RNA extraction, followed by RT-PCR, to differentiate infectious and inactivated F+ RNA phages. The results indicated that ET RT-PCR reduced, but did not completely eliminate, false-positive signals encountered with RT-PCR alone. The two-step ET RT-PCR, in which the enzymes were added sequentially, was more effective at reducing false-positive signals than the one-step ET RT-PCR, which involved addition of both enzymes together. Despite its inability to completely eliminate false-positive signals, ET RT-PCR gave more reliable information on the infectivity of F+ RNA phages. Thus, the method is better than RT-PCR alone for detecting F+ RNA phages as indicators to assess the risk of fecal contamination by enteric pathogens or to evaluate the effectiveness of virus-inactivating processes.

Water quality indicators: bacteria, coliphages, enteric viruses

Water quality through the presence of pathogenic enteric microorganisms may affect human health. Coliform bacteria, Escherichia coli and coliphages are normally used as indicators of water quality. However, the presence of above-mentioned indicators do not always suggest the presence of human enteric viruses. It is important to study human enteric viruses in water. Human enteric viruses can tolerate fluctuating environmental conditions and survive in the environment for long periods of time becoming causal agents of diarrhoeal diseases. Therefore, the potential of human pathogenic viruses as significant indicators of water quality is emerging. Human Adenoviruses and other viruses have been proposed as suitable indices for the effective identification of such organisms of human origin contaminating water systems. This article reports on the recent developments in the management of water quality specifically focusing on human enteric viruses as indicators.

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

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

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

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

Application of Molecular Beacons in Real-Time PCR

Real-time PCR or quantitative PCR (QPCR) is a powerful technique that allows measurement of PCR product while the amplification reaction proceeds. It incorporates the fluorescent element into conventional PCR as the calculation standard to provide a quantitative result. In this sense, fluorescent chemistry is the key component in QPCR. Till now, two types of fluorescent chemistries have been adopted in the QPCR systems: one is nonspecific probe and the other is specific. As a brilliant invention by Kramer et al. in 1996, molecular beacon is naturally suited as the reporting element in real-time PCR and has been adapted for many molecular biology applications. In this chapter, we briefly introduce the working principle of QPCR and overview different fluorescent chemistries, and then we focus on the applications of molecular beacons-like gene expression study, single-nucleotide polymorphisms and mutation detection, and pathogenic detection.

Molecular Approach to Microbiological Examination of Water Quality in the Grand Bay National Estuarine Research Reserve (NERR) in Mississippi, USA

Grand Bay National Estuarine Research Reserve (NERR) is an important ecosystem in the Mississippi Gulf Coast. It serves as important nursery areas for juveniles of many species of fish. The bay is also used for fishing, crabbing, oyster togging, boating as well as recreation. Like in other aquatic environments, this bay may be contaminated by microorganisms including pathogenic bacteria. The objective of this study was to evaluate the microbiological quality of water in the Grand Bay NERR and determine the levels and potential source(s) of human fecal pollution. To achieve this goal, water samples were collected aseptically every month in Bayou Heron, Bayou Cumbest, Point Aux Chenes Bay and Bangs Lake. Enterococci were concentrated from water samples by membrane filtration according to the methodology outlined in USEPA Method 1600. After incubation, DNA was extracted from bacteria colonies on the membrane filters by using QIAamp DNA extraction kit. Water samples were also tested for the presence of traditional indicator bacteria including: heterotrophic plate count, total coliforms, fecal coliforms, and Enterococcus bacteria. The marker esp gene was detected in one site of Bayou Cumbest, an area where human populations reside. Data from this study indicates higher concentrations of indicator bacteria compared to the recommended acceptable levels. Presence of esp marker and high numbers of indicator bacteria suggest a public health concern for shellfish and water contact activities. Hence, control strategies should be developed and implemented to prevent further contamination of the Grand bay NERR waters.

Relationship of human-associated microbial source tracking markers with Enterococci in Gulf of Mexico waters

Human and ecosystem health can be damaged by fecal contamination of recreational waters. Microbial source tracking (MST) can be used to specifically detect domestic sewage containing human waste, thereby informing both risk assessment and remediation strategies. Previously, an inter-laboratory collaboration developed standardized PCR methods for a bacterial, an archaeal, and a viral indicator of human sewage. Here we present results for two subsequent years of field testing in fresh and salt water by five laboratories across the U.S. Gulf Coast (two in Florida and one each in Mississippi, Louisiana and Texas) using common standard operating procedures (SOPs) developed previously. Culturable enterococci were enumerated by membrane filtration, and PCR was used to detect three MST markers targeting domestic sewage: human-associated Bacteroides (HF183), Methanobrevibacter smithii and human polyomaviruses BK and JC (HPyVs). Detection of sewage markers in surface waters was significantly associated with higher enterococci levels and with exceedance of the recreational water quality standard in four or three regions, respectively. Sewage markers were frequently co-detected in single samples, e.g., M. smithii and HF183 were co-detected in 81% of Louisiana samples, and HPyVs and M. smithii were co-detected in over 40% of southwest Florida and Mississippi samples. This study demonstrates the robustness and inter-laboratory transferability of these three markers for the detection of pollution from domestic sewage in the waters impacting the Gulf of Mexico over a coastal range of over 1000 miles.

Escherichia coli in the Environment: Implications for Water Quality and Human Health

Escherichia coli is naturally present in the intestinal tracts of warm-blooded animals. Since E. coli is released into the environment through deposition of fecal material, this bacterium is widely used as an indicator of fecal contamination of waterways. Recently, research efforts have been directed towards the identification of potential sources of fecal contamination impacting waterways and beaches. This is often referred to as microbial source tracking. However, recent studies have reported that E. coli can become "naturalized" to soil, sand, sediments, and algae in tropical, subtropical, and temperate environments. This phenomenon raises issues concerning the continued use of this bacterium as an indicator of fecal contamination. In this review, we discuss the relationship between E. coli and fecal pollution and the use of this bacterium as an indicator of fecal contamination in freshwater systems. We also discuss recent studies showing that E. coli can become an active member of natural microbial communities in the environment, and how this bacterium is being used for microbial source tracking. We also discuss the impact of environmentally-"naturalized" E. coli populations on water quality.

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.

The impact of temperature on the inactivation of enteric viruses in food and water: a review

Temperature is considered as the major factor determining virus inactivation in the environment. Food industries, therefore, widely apply temperature as virus inactivating parameter. This review encompasses an overview of viral inactivation and virus genome degradation data from published literature as well as a statistical analysis and the development of empirical formulae to predict virus inactivation. A total of 658 data (time to obtain a first log(10) reduction) were collected from 76 published studies with 563 data on virus infectivity and 95 data on genome degradation. Linear model fitting was applied to analyse the effects of temperature, virus species, detection method (cell culture or molecular methods), matrix (simple or complex) and temperature category (<50 and ≥50°C). As expected, virus inactivation was found to be faster at temperatures ≥50°C than at temperatures <50°C, but there was also a significant temperature-matrix effect. Virus inactivation appeared to occur faster in complex than in simple matrices. In general, bacteriophages PRD1 and PhiX174 appeared to be highly persistent whatever the matrix or the temperature, which makes them useful indicators for virus inactivation studies. The virus genome was shown to be more resistant than infectious virus. Simple empirical formulas were developed that can be used to predict virus inactivation and genome degradation for untested temperatures, time points or even virus strains.

Genogroup distribution of F-specific coliphages in wastewater and river water in the Kofu basin in Japan

AIMS

To determine the genogroup distribution of F-specific coliphages in aquatic environments using the plaque isolation procedure combined with genogroup-specific real-time PCR.

METHODS AND RESULTS

Thirty water samples were collected from a wastewater treatment plant and a river in the Kofu basin in Japan on fine weather days. F-specific coliphages were detected in all tested samples, 187 (82%) of 227 phage plaques isolated were classified into one of the 4 F-specific RNA (F-RNA) coliphage genogroups and 24 (11%) plaques were F-specific DNA coliphages. Human genogroups II and III F-RNA coliphages were more abundant in raw sewage than animal genogroups I and IV, excluding one sample that was suspected to be heavily contaminated with sporadic heavy animal faeces. The secondary-treated sewage samples were highly contaminated with genogroup I F-RNA coliphages, probably because of different behaviours among the coliphage genogroups during wastewater treatment. The river water samples were expected to be mainly contaminated with human faeces, independent of rainfall effects.

CONCLUSIONS

A wide range of F-specific coliphage genogroups were successfully identified in wastewater and river water samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results clearly show the usefulness of the genogroup-specific real-time PCR for determining the genogroups of F-specific coliphages present in aquatic environments.

Evaluation of the nifH gene marker of Methanobrevibacter smithii for the detection of sewage pollution in environmental waters in Southeast Queensland, Australia

This study aimed at evaluating the host-specificity and -sensitivity of the nifH gene marker of Methanobrevibacter smithii by screening 272 fecal and wastewater samples from 11 animal species including humans in Southeast Queensland (SEQ), Australia. In addition, environmental water samples (n = 21) were collected during the dry and wet weather conditions and tested for the presence of the nifH marker along with other sewage-associated markers, namely, enterococci surface protein (esp) found in Enterococci faecium, Bacteroides HF183, adenoviruses (AVs), and polyomaviruses (PVs). The overall host-specificity of the nifH marker to differentiate between human and animal feces was 0.96 (maximum value of 1), while the overall sensitivity of this marker in human sourced feces and wastewater was 0.81 (maximum value of 1). Among the 21 environmental water samples tested, 2 (10%), 3 (14%), 12 (57%), 6 (29%), and 6 (29%) were positive for the nifH, esp, HF183, AVs and PVs markers, respectively. The prevalence of the nifH marker in environmental water samples, however, was low compared to other markers, suggesting that the use of this marker alone may not be sensitive enough to detect fecal pollution in environmental waters. The nifH marker, however, appears to be sewage-specific in SEQ, Australia, and therefore, it is recommended that this marker should be used as an additional marker in combination with the HF183 or viral markers such as AVs or PVs for accurate and sensitive detection of fecal pollution in SEQ waterways.

Effects of ionic strength on bacteriophage MS2 behavior and their implications for the assessment of virus retention by ultrafiltration membranes

Bacteriophage MS2 is widely used as a surrogate to estimate pathogenic virus elimination by membrane filtration processes used in water treatment. Given that this water technology may be conducted with different types of waters, we focused on investigating the effects of ionic strength on MS2 behavior. For this, MS2 was analyzed while suspended in solutions of various ionic strengths, first in a batch experiment and second during membrane ultrafiltration, and quantified using (i) quantitative reverse transcriptase PCR (qRT-PCR), which detects the total number of viral genomes, (ii) qRT-PCR without the RNA extraction step, which reflects only particles with a broken capsid (free RNA), and (iii) the PFU method, which detects only infectious viruses. At the beginning of the batch experiments using solutions containing small amounts of salts, losses of MS2 infectivity (90%) and broken particles (20%) were observed; these proportions did not change during filtration. In contrast, in high-ionic-strength solutions, bacteriophage kept its biological activity under static conditions, but it quickly lost its infectivity during the filtration process. Increasing the ionic strength decreased both the inactivation and the capsid breakup in the feed suspension and increased the loss of infectivity in the filtration retentate, while the numbers of MS2 genomes were identical in both experiments. In conclusion, the effects of ionic strength on MS2 behavior may significantly distort the results of membrane filtration processes, and therefore, the combination of classical and molecular methods used here is useful for an effective validation of the retention efficiency of ultrafiltration membranes.

Occurrence, survival, and persistence of human adenoviruses and F-specific RNA phages in raw groundwater

Detection of specific genetic markers can rapidly identify the presence of enteric viruses in groundwater. However, comparison of stability characteristics between genetic and infectivity markers is necessary to better interpret molecular data. Human adenovirus serotype 2 (HAdV2), in conjunction with MS2 phages or GA phages, was spiked into raw groundwater microcosms. Viral stability was periodically assessed by both infectivity and real-time PCR methods. The results of this yearlong study suggest that adenoviruses have the most stable persistence profile and an ability to survive for a long time in groundwater. According to a linear regression model, infectivity reductions of HAdV2 ranged from 0.0076 log(10)/day (4°C) to 0.0279 log(10)/day (20°C) and were significantly lower than those observed for phages. No adenoviral genome degradation was observed at 4°C, and the reduction was estimated at 0.0036 log(10)/day at 20°C. Occurrence study showed that DNA of human adenoviruses could be observed in groundwater from a confined aquifer (7 of the 60 samples were positive by real-time PCR), while no fecal indicators were detected. In agreement with the persistence of genetic markers, the presence of adenoviral DNA in groundwater may be misleading in term of health risk, especially in the absence of information on the infective status.

Improved strategies and optimization of calibration models for real-time PCR absolute quantification

Real-time PCR absolute quantification applications are becoming more common in the recreational and drinking water quality industries. Many methods rely on the use of standard curves to make estimates of DNA target concentrations in unknown samples. Traditional absolute quantification approaches dictate that a standard curve must accompany each experimental run. However, the generation of a standard curve for each qPCR experiment set-up can be expensive and time consuming, especially for studies with large numbers of unknown samples. As a result, many researchers have adopted a master calibration strategy where a single curve is derived from DNA standard measurements generated from multiple instrument runs. However, a master curve can inflate uncertainty associated with intercept and slope parameters and decrease the accuracy of unknown sample DNA target concentration estimates. Here we report two alternative strategies termed 'pooled' and 'mixed' for the generation of calibration equations from absolute standard curves which can help reduce the cost and time of laboratory testing, as well as the uncertainty in calibration model parameter estimates. In this study, four different strategies for generating calibration models were compared based on a series of repeated experiments for two different qPCR assays using a Monte Carlo Markov Chain method. The hierarchical Bayesian approach allowed for the comparison of uncertainty in intercept and slope model parameters and the optimization of experiment design. Data suggests that the 'pooled' model can reduce uncertainty in both slope and intercept parameter estimates compared to the traditional single curve approach. In addition, the 'mixed' model achieved uncertainty estimates similar to the 'single' model while increasing the number of available reaction wells per instrument run.

Evaluating sewage-associated JCV and BKV polyomaviruses for sourcing human fecal pollution in a coastal river in Southeast Queensland, Australia

In this study, the host-sensitivity and host-specificity of JC virus (JCV) and BK virus (BKV) polyomaviruses were evaluated by testing wastewater and fecal samples from nine host groups in Southeast Queensland, Australia. The JCV and BKV polyomaviruses were detected in 63 human wastewater samples collected from primary and secondary effluent, suggesting high sensitivity of these viruses in human wastewater. In the 81 animal wastewater and fecal samples tested, 80 were polymerase chain reaction (PCR) negative for the JCV and BKV markers. Only one sample (out of 81 animal wastewater and fecal samples) from pig wastewater was positive. Nonetheless, the overall host-specificity of these viruses to differentiate between human and animal wastewater and fecal samples was 0.99. To our knowledge, this is the first study in Australia that reports on the high specificity of JCV and BKV polyomaviruses. To evaluate the field application of these viral markers for detecting human fecal pollution, 20 environmental samples were collected from a coastal river. In the 20 samples tested, 15% (3/20) and 70% (14/20) samples exceeded the regulatory guidelines for Escherichia coli and enterococci levels for marine waters. In all, five (25%) samples were PCR positive for JCV and BKV, indicating the presence of human fecal pollution in the coastal river investigated. The results suggest that JCV and BKV detection using PCR could be a useful tool for identifying human-sourced fecal pollution in coastal waters.

Evaluation of positively charged alumina nanofibre cartridge filters for the primary concentration of noroviruses, adenoviruses and male-specific coliphages from seawater

AIM

To evaluate the electropositive, alumina nanofibre (NanoCeram) cartridge filter as a primary concentration method for recovering adenovirus, norovirus and male-specific coliphages from natural seawater.

METHODS AND RESULTS

Viruses were concentrated from 40 l of natural seawater using a NanoCeram cartridge filter and eluted from the filter either by soaking the filter in eluent or by recirculating the eluent continuously through the filter using a peristaltic pump. The elution solution consisted of 3% beef extract and 0.1 mol l(-1) of glycine. The method using a peristaltic pump was more effective in removing the viruses from the filter. High recoveries of norovirus and male-specific coliphages (>96%) but not adenovirus (<3%) were observed from seawater. High adsorption to the filter was observed for adenovirus and male-specific coliphages (>98%). The adsorption and recovery of adenovirus and male-specific coliphages were also determined for fresh finished water and source water.

CONCLUSION

The NanoCeram cartridge filter was an effective primary concentration method for the concentration of norovirus and male-specific coliphages from natural seawater, but not for adenovirus, in spite of the high adsorption of adenovirus to the filter.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that NanoCeram cartridge filter is an effective primary method for concentrating noroviruses and male-specific coliphages from seawater, thereby simplifying collection and processing of water samples for virus recovery.

Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution

There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches are most suitable for field applications can be difficult because each assay targets a different gene, in many cases from different microorganisms, leading to variation in assay performance. We describe a performance evaluation of seven end-point PCR and real-time quantitative PCR (qPCR) assays reported to be associated with either ruminant or bovine feces. Each assay was tested against a reference collection of DNA extracts from 247 individual bovine fecal samples representing 11 different populations and 175 fecal DNA extracts from 24 different animal species. Bovine-associated genetic markers were broadly distributed among individual bovine samples ranging from 39 to 93%. Specificity levels of the assays spanned 47.4% to 100%. End-point PCR sensitivity also varied between assays and among different bovine populations. For qPCR assays, the abundance of each host-associated genetic marker was measured within each bovine population and compared to results of a qPCR assay targeting 16S rRNA gene sequences from Bacteroidales. Experiments indicate large discrepancies in the performance of bovine-associated assays across different bovine populations. Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest.

Occurrence and persistence of enteroviruses, noroviruses and F-specific RNA phages in natural wastewater biofilms

Enteroviruses and noroviruses are pathogenic viruses excreted by infected individuals. Discharged in wastewaters, some of these viruses can be captured by biofilms. In the present study, we assessed the occurrence and persistence of these viruses in wastewaters and in corresponding biofilms. Natural wastewaters and biofilms were analyzed monthly from January to July using real-time RT-PCR. Enterovirus RNA was detected in wastewater in June while norovirus RNA was detected from January to March. In contrast, biofilm analysis revealed the presence of both enterovirus and norovirus genomes throughout the study period. For instance, enterovirus and norovirus genogroups (GG) I and II were detected in 50, 46 and 37% of the biofilm samples, respectively (n=24). In a laboratory experiment, persistence of norovirus GGI RNA (quantified using molecular techniques) and F-specific bacteriophages (quantified using both culture and molecular techniques) was assessed in wastewater and corresponding naturally-contaminated biofilms at both 4 and 20 degrees C. The concentrations of viral genomes (norovirus GGI and F-specific RNA phage) were very stable in biofilms. Indeed, no significant decrease was observed during the persistence experiment that lasted 49 days. Furthermore, regardless of our experimental conditions, viral genome and infectious F-specific bacteriophages persisted longer in biofilm than in wastewater. According to our results, wastewater biofilms may contribute to the persistence and dispersal of pathogenic viruses outside of epidemic periods.

Molecular characterization of bacteriophages for microbial source tracking in Korea

We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

A reverse transcription-PCR assay to distinguish the four genogroups of male-specific (F+) RNA coliphages

Goals of reducing fecal contamination in recreational, drinking, shellfishing and other waters and accurately assessing risk from exposure can best be attained if tools to distinguish between sources of pollution are available. The male-specific RNA coliphage (FRNA) genogroups display a trend of source specificity. Reverse transcription-PCR (RT-PCR) can be effectively used for genotyping if specific primer sets are designed to be capable of identifying all members within each genogroup. In this study genogroup-specific primer sets were designed using a minimum of 5 to a maximum of 10 complete phage genome sequences from strains in each genogroup. With these primers and employing a heat-release procedure that eliminated the need for RNA purification an RT-PCR method for genotype identification of FRNA phages was developed. The four genogroup-specific primer sets generated discrete PCR amplicon sizes from a variety of environmental FRNA phage strains. Limits of detection, cross-reactivity and/or non-specific binding to strains from other genogroups were evaluated.

Relationship between F-specific RNA phage genogroups, faecal pollution indicators and human adenoviruses in river water

Recent studies have shown the increasing interest of F-specific RNA phage genotyping to identify major sources of faecal contamination in waters. This study, conducted in a river located in an urbanized watershed with recognized anthropogenic influences, was aimed at evaluating the relevance of direct phage genotyping by real-time RT-PCR. One hundred percent of positive results were obtained with a 5 mL aliquot of river water (n=31). Phage distribution was modified after cultivation, since the ratio of the two most abundant genogroups (II and I) reached 1.51 log(10) by direct RT-PCR-based method versus 0.30 log(10) after cultivation (n=8). For the first time, positive correlations between the concentrations of genogroup II, bacterial indicators and human adenoviruses were observed, which may indicate a human faecal pollution. No correlation between genogroups II and I has been revealed. The concentration of genogroup I was only correlated with water turbidity, suggesting an animal pollution coming from upstream after rainfall events. Among the microbiological parameters studied, only genogroup II/genogroup I ratio shows variations occurring in the major sources of faecal pollution.

Escherichia coli populations in Great Lakes waterfowl exhibit spatial stability and temporal shifting

Populations of Escherichia coli from juvenile and adult ring-billed gulls, juvenile common terns, and adult Canada geese were sampled over 6 years at five locations on Lake Superior (Duluth, MN, and Wisconsin) and Lake Michigan (Wisconsin, Illinois, and Indiana) to determine the extent of spatial and temporal variability in E. coli strains. Strain identity was determined using horizontal fluorophore-enhanced repetitive element palindromic DNA fingerprinting. Multivariate statistics were used to determine if spatial or temporal changes in E. coli populations occurred in waterfowl species. Pairwise multivariate analyses of variance revealed that E. coli populations of adult gulls from three regions of Lake Michigan and the Wisconsin shore of Lake Superior were similar to one another but different from an E. coli population of gulls from the Duluth region of Lake Superior. Juvenile and adult gulls from the Duluth area harbored different E. coli populations. The E. coli strains from juvenile gulls, however, were similar to those found in juvenile terns obtained from the same island rookery. Temporal changes in E. coli populations from several waterfowl species were also demonstrated for this site. Although portions of source tracking databases might be successfully used in other geographic regions, it is clear that juvenile birds should not be the sole source of E. coli strains used for source tracking databases, and multiple-year libraries should be constructed in order to identify the potential sources of E. coli in the environment.

Detection and characterization of F+ RNA bacteriophages in water and shellfish: application of a multiplex real-time reverse transcription PCR

Genotyping of F+ RNA bacteriophages has been used to distinguish between human and animal contributions to contaminated water and food. There are four genetically distinct genogroups of F+ RNA bacteriophages. Genogroups I and IV predominate in animal wastes and genogroups II and III in wastes of human origin. In this study, a multiplex real-time RT-PCR-based method was developed to detect and genotype F+ RNA bacteriophages. The assay was shown to be broadly reactive against a wide spectrum of F+ RNA bacteriophage strains, including MS2, GA, Q beta, MX1, SP and FI, and was able to detect and genotype F+ RNA bacteriophages in shellfish and river water. The assay is highly sensitive, with detection limits <10 PFU/reaction and <10 copies/reaction of the target sequences carried in plasmids, respectively. The applications of this assay include F+ RNA semi-quantitation and microbial source tracking.