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 log₁₀ by direct RT-PCR-based method versus 0.30 log₁₀ 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.     

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 °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.     

Differential persistence of F-specific RNA phage subgroups hinders their use as single tracers for faecal source tracking in surface water

The four subgroups of F-specific RNA bacteriophages (I-IV) have been proposed as potential tracers for faecal source tracking. Groups II and III predominate in human sources while groups I and IV are most abundant in animal sources. The four subgroups of naturally occurring F-specific RNA bacteriophages were identified in different samples by plaque hybridization with genotype-specific probes and the persistence of each subgroup was evaluated. The proportions of the F-specific RNA bacteriophage subgroups were measured in wastewaters, after inactivation in surface waters or after wastewater treatment and in mixtures of wastewater of human and animal origin. Our results indicate that phage groups differ in their persistence in the environment and to different disinfecting treatments. The greater survival of subgroups I and II in treated samples hinders the interpretation of results obtained with F-specific RNA bacteriophages. The phages of subgroups III and IV were the least resistant to all treatments. These results should be considered when using genotypes of F-specific RNA as sole tracers for faecal source tracking.     

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.     

Fates of bacteriophages and bacterial indicators in the Moselle river (France)

It has been suggested that bacteriophages can provide useful information about the pathogenic microorganisms, particularly enteric viruses, present in water. This information is complementary to that obtained from bacterial indicators of faecal contamination, which would be of great value for evaluating the risks associated with the use of certain types of water. Before bacteriophages can be used as indicators of faecal contamination, we need to confirm that bacteriophages give a different response to that given by the well-known bacteria indicators and to determine what happens to bacteriophages in river water. Indeed, drinking water is often produced from river water, either by natural filtration through the soil or after undergoing various treatments. We collected 96 river water samples from six different sites between February and November 2000. The samples were analysed for three faecal indicator bacteria (thermotolerant coliforms, enterococci and spores of sulphite-reducing anaerobes) and three types of bacteriophages (somatic coliphages, F-specific phages and Bacteroides fragilis phages). The densities of thermotolerant coliforms and enterococci depended mainly on physical factors such as flow rate and water temperature. High temperature and low flow rate led to a decrease in the density of these microorganisms, especially in the absence of a major input of faecal pollution. Conversely, the densities of somatic coliphages, F-specific phages and spores of sulphite-reducing anaerobes remained constant regardless of the flow rate and temperature. The density of Bacteroides fragilis phages was too low for unambiguous determination of their fate in river water.     

Microbial quality assessment of household greywater

A monitoring program was undertaken to assess the microbial quality of greywater collected from 93 typical households in Melbourne, Australia. A total of 185 samples, comprising 75 washing machine wash, 74 washing machine rinse and 36 bathroom samples were analysed for the faecal indicator Escherichia coli. Of these, 104 were also analysed for genetic markers of pathogenic E coli and 111 for norovirus (genogroups GI and GII), enterovirus and rotavirus using RT-PCR. Enteric viruses were detected in 20 out of the 111 (18%) samples comprising 16 washing machine wash water and 4 bathroom samples. Eight (7%) samples were positive for enterovirus, twelve (11%) for norovirus genogroup GI, one (1%) for norovirus genogroup GII and another (1%) for rotavirus. Two washing machine samples contained more than one virus. Typical pathogenic E. coli were detected in 3 out of 104 (3%) samples and atypical enteropathogenic E. coli in 11 (11%) of samples. Levels of indicator E. coli were highly variable and the presence of E. coli was not associated with the presence of human enteric viruses in greywater. There was also little correlation between reported gastrointestinal illness in households and detection of pathogens in greywater.     

Release of infectious human enteric viruses by full-scale wastewater utilities

In the United States, infectious human enteric viruses are introduced daily into the environment through the discharge of treated water and the digested sludge (biosolids). In this study, a total of 30 wastewater and 6 biosolids samples were analyzed over five months (May-September 2008-2009) from five full-scale wastewater treatment plants (WWTPs) in Michigan using real-time PCR and cell culture assays. Samples were collected from four different locations at each WWTP (influent, pre-disinfection, post-disinfection and biosolids) using the 1MDS electropositive cartridge filter. Adenovirus (HAdV), enterovirus (EV) and norovirus genogroup II (NoV GGII) were detected in 100%, 67% and 10%, respectively of the wastewater samples using real-time PCR. Cytopathic effect (CPE) was present in 100% of the cell culture samples for influent, pre- and post-disinfection and biosolids with an average log concentration of 4.1 (2.9-4.7, range) 1.1 (0.0-2.3, range) and 0.5 (0.0-1.6, range) MPN/100 L and 2.1 (0.5-4.1) viruses/g, respectively. A significant log reduction in infectious viruses throughout the wastewater treatment process was observed at an average 4.2 (1.9-5.0, range) log units. A significant difference (p-value <0.05) was observed using real-time PCR data for HAdV but not for EV (p-value >0.05) removal in MBR as compared to conventional treatment. MBR treatment was able to achieve an additional 2 and 0.5 log reduction of HAdV and EV, respectively. This study has demonstrated the release of infectious enteric viruses in the final effluent and biosolids of wastewater treatment into the environment.     

F-specific RNA coliphages: occurrence,types, and survival in natural waters

A small, well-defined watershed was investigated over a 2-year period to determine the prevalence of F-specific RNA coliphage (F + RNA) serotypes as indicators of animal fecal contamination. Sampling sites collected runoff from areas of urban and agricultural land use patterns. F-specific coliphages were concentrated from 2-L freshwater samples by polyethylene glycol precipitation, isolated using the double agar layer (DAL) method, confirmed as F + RNA by RNAse suppression, and serotyped. A subset of serotyped F + RNA were confirmed by genotyping. To determine relative survival, 10 confirmed F + RNA field isolates and 5 prototypic F + RNA were spiked into surface water and incubated at 25 degrees C for 36 days. F-specific coliphage isolation was strongly associated with rainfall events and was infrequent from primarily animal impacted surface waters. Field isolates were predoffiinantly Type I F + RNA (81%) and raw sewage isolates were predominantly Type III F + RNA (57%). Genotyping from either the watershed or raw sewage samples never positively identified Type IV F + RNA. Results from laboratory studies showed that F + RNA differ in their survival in water and that Type IV strains were the least persistent. Type III F + RNA were found to be reliably related to the release of uncontrolled human fecal material in the watershed, but the results of this study suggest that further study is required before utilizing for fecal source identification in natural waters.     

Detection and molecular characterization of noroviruses from five sewage treatment plants in central Italy

Noroviruses (NoVs) are the most frequent etiological agents of non-bacterial gastroenteritis. These viruses are transmitted through the fecal-oral route, leading to high viral loads in sewages. The objective of this paper was to study the environmental occurrence of the most prevalent NoV strains in different wastewater treatment plants. In addition, molecular characterization of the isolated strains was performed. Two different PCR-based methods were carried out and a novel strategy was used to verify the level of RT-PCR inhibition.From May to September 2007, a total of 97 inflow and outflow samples were collected from five wastewater treatment plants in central Italy. We detected NoV by nested PCR in 96.9% of influent samples: 89.1% contained both genogroups; 4.7% contained only GI and 3.1% only GII. In effluents, we detected NoV in 78.8% of samples: 30.3% contained both genogroups, and 48.5% contained only GI. The major genotypes detected by sequencing analyses were GI/2, GI/5, GII/b, GII/4 and GII/6.This work confirms the wide circulation of NoVs in Italy with a predominance of GI strains, and the widespread distribution of NoV variants in both raw and treated wastewater.     

The genetic diversity of human noroviruses detected in river water in Korea

We studied the genetic diversity of human noroviruses in river waters by RT-nested PCR and phylogenetic analysis. During 2002-2003, water samples were collected from four rivers in Gyeonggi Province, South Korea. Among the 58 samples, 32 (55.2%) and 26 (44.8%) showed positive results with noroviruses belonging to genogroups I (GI) and II (GII), respectively. The phylogenetic analysis grouped 8 and 7 genotypes in GI and GII, respectively. The major types were GI/1, GI/13, and GII/15, and GI/1 and GI/3 were temporarily distributed. Most GI- and GII-grouped strains were closely related to the reference strains from neighboring countries, China and Japan, and GII/4-related strains had similar sequences to strains recognized as worldwide epidemic outbreaks. The strains circulating between countries are of particular concern to the outbreaks of noroviral diseases in Korea and must be periodically monitored in the natural environments.     

Microbial indicators and pathogens: removal, relationships and predictive capabilities in water reclamation facilities

Four water reclamation facilities in north-eastern Spain were monitored over 2 years to determine the occurrence and concentrations of a set of microbial indicators (total coliforms, Escherichia coli, enterococci, spores of sulphite reducing clostridia, somatic coliphages, F-specific RNA phages, phages infecting Bacteroides fragilis strain RYC2056 and phages infecting Bacteroides tethaiotaomicron strain GA-17), and two selected pathogens (cytopathogenic enteroviruses and viable Cryptosporidium oocysts). The indicator (survival) and index (presence) functions of the various indicators tested were evaluated through the wastewater treatments. The inactivation pattern of all groups of bacteriophages tested was closer to the inactivation of enteroviruses than to the inactivation of the conventional bacterial indicators tested. The inactivation of sulfite reducing clostridia spores and bacteriophages more closely approximates the reduction of viable Cryptosporidium than do the conventional bacterial indicators. We observed neither index functions nor a predictive relationship between any of microbial indicators and viable Cryptosporidium oocysts. In contrast, several regression models (r > 0.6) and discriminant functions (67-88% well classified samples) based mostly on numbers of bacteriophages were able to predict both the presence and concentrations of enteroviruses. A combination of both bacterial and bacteriophage indicators seem to be the best choice for ensuring the microbial quality of reclaimed water.     

Real-time PCR detection of adenoviruses, polyomaviruses, and torque teno viruses in river water in Japan

The prevalence of DNA viruses in water from the Tamagawa River, Japan was quantitatively surveyed for 6 months, from April to September 2003. A total of 18 river water samples were subjected to virus concentration method using an electronegative membrane, followed by DNA extraction and direct quantitative real-time polymerase chain reaction (qPCR) for DNA viruses. Adenoviruses of serotypes 40 and 41 were detected most frequently in the river water samples tested (61.1%), at a concentration ranging from 3.16 × 10³ to 1.38 × 10⁵ copies/l, followed by JC polyomaviruses (11.1%) and torque teno viruses (5.6%). No sample was positive for BK polyomaviruses. In addition, for selective detection of virus particles, adenoviruses 40 and 41 were tested with qPCR combined with an immunomagnetic separation technique; they were detected in only 16.7% of the samples, showing a concentration ranging from 7.42 × 10² to 4.24 × 10⁴ copies/l. This study is significant since it is the first study to demonstrate the prevalence of polyomaviruses in water samples in Japan and to use immunomagnetic separation qPCR to detect adenovirus particles in aquatic environments.     

Occurrence and levels of indicator bacteriophages in bathing waters throughout Europe

Somatic coliphages, F-specific RNA bacteriophages, bacteriophages infecting Bacteroides fragilis, Escherichia coli and enterococci were counted in bathing waters in the late spring and summer. We tested fresh and marine bathing waters from North, South, East and West Europe expected to contain between 100 and 500 E. coli per 100 ml, although wider ranges were sometimes found. Bacteriophages were counted after concentration, since a preliminary study proved that this step was necessary to obtain positive counts. During monitoring, a first-line quality control with reference materials for bacteria and bacteriophages was performed by all the laboratories participating in the study. The same microbes were also counted in raw sewage samples from various areas in Europe, where the bacterial indicators and the three groups of bacteriophages were detected in roughly the same numbers. All groups of bacteriophages were detected in both fresh and marine bathing waters throughout Europe. Reliable and complete results from 147 samples showed that for log-transformed values, E. coli and bacteriophages were slightly correlated. However, the slope of the regression line changed according to E. coli concentration and the correlation diminished when this concentration was close to zero per 100 ml. The ratios between E. coli and phages in bathing waters differed significantly from those in sewage. The relative amounts of bacteriophages, mainly somatic coliphages and phages infecting Bact. fragilis RYC2056, increased in bathing waters with low E. coli concentration, especially in seawater samples containing <100 E. coli per 100 ml. The relationship of bacteriophages with respect to enterococci paralleled that of bacteriophages with respect to E. coli. Somatic coliphages and bacteriophages infecting Bact. fragilis are useful to predict the presence of some pathogens with the same origin as present bacterial indicators but with higher survival rates.     

Occurrence of polycyclic aromatic hydrocarbons in water and sediment samples from KwaZulu Natal Province,South Africa

Solid‐phase extraction (SPE) and ultrasonic extraction (UE) techniques followed by Gas Chromatography‐Mass Spectrometry (GC‐MS) have been modified for qualitative and quantitative analysis of polycyclic aromatic hydrocarbons (PAHs) in water and sediment samples. Percentage recoveries of PAHs ranged from 85 to 121% in water and 82 to 117% in sediment samples. The limits of detection (LOD) and limits of quantification (LOQ) ranged from 0.02 to 0.2 and 0.05 to 0.5 µg/L for SPE while for UE, they were between 0.008–0.09 and 0.02–0.30 µg/kg, respectively. The concentration levels of PAHs (naphthalene, acenaphthene, acenaphthylene, fluorine, anthracene, phenanthrene and pyrene) detected in water samples were 0.071–2.7, 2.0–10.4 and 2.5–3.5 µg/L in wastewater, river water, and dam water, respectively. In sediment samples, concentration levels of PAHs were between 2.8–42.0 and 2.8–3.9 µg/kg, in river and dam sediment, respectively.     

Seasonal change and fate of coliphages infected to Escherichia coli O157:H7 in a wastewater treatment plant

Seasonal change of virulent phage infected to two E. coli O157:H7 strains (O:157-phage) in the influent of a domestic wastewater treatment plant in the central part of Japan and fate of O:157-phage in the plant were monitored almost monthly from March 2001 to February 2002. Coliphage infected to nonpathogenic E. coli O157:H7 ATCC43888 (43888-phage) was detected for 1 year. On the other hand, phage infected to pathogenic E. coli O157:H7 EDL933 (EDL-phage) was detected intermittently. Concentration of EDL-phage was almost one-tenth of that of 43888-phage. The progressive decrease in phage concentration with the treatment steps was observed. No phage was detected in the supernatant from the secondary settling tank and effluent. PCR amplification of the Stx 2 gene that encodes Shiga toxin (Stx) was observed when O:157-phage concentration in the influent was high x10(3) PFU/ml order. Concentration and percentage of suspended O:157-phage decreased with the progress of the wastewater treatment. 933W phage, which encodes Stx 2 gene, was more fragile and sensitive to chlorination than T4 phage. However, addition of 0.02 mg/l chlorine, in conformance with the required concentration of the plant, did not affect the viability of T4 and 933 W phages. On the other hand, 1mg/l chlorine inactivated the 933 W phage significantly.     

Specificity and sensitivity evaluation of novel and existing Bacteroidales and Bifidobacteria-specific PCR assays on feces and sewage samples and their application for microbial source tracking in Ireland

Three novel ruminant-specific PCR assays, an existing ruminant-specific PCR assay and five existing human-specific PCR assays, which target 16S rDNA from Bacteroidales or Bifidobacteria, were evaluated. The assays were tested on DNA extracted from ruminant (n = 74), human (n = 59) and non-ruminant animal (n = 44) sewage/fecal samples collected in Ireland. The three novel PCR assays compared favourably to the existing ruminant-specific assay, exhibiting sensitivities of 91-100% and specificities of 95-100% as compared to a sensitivity of 95% and specificity of 94%, for the existing ruminant-specific assay. Of the five human-specific PCR assays, the assay targeting the Bifidobacterium catenulatum group was the most promising, exhibiting a sensitivity of 100% (with human sewage samples) and a specificity of 87%. When tested on rural water samples that were naturally contaminated by ruminant feces, the three novel PCR assays tested positive with a much greater percentage (52-87%) of samples than the existing ruminant-specific assay (17%). These novel ruminant-specific assays show promise for microbial source tracking and merit further field testing and specificity evaluation.     

Quantification of anaerobic ammonium-oxidizing bacteria in enrichment cultures by real-time PCR

The anaerobic ammonium-oxidizing (ANAMMOX) bacteria were enriched from a rotating disk reactor (RDR) biofilm in semi-batch cultures. Based on fluorescence in situ hybridization (FISH) analysis, this enrichment led to a relative population size of 36% ANAMMOX bacteria. Phylogenetic analysis revealed that all the detected clones were related to the previously reported ANAMMOX bacteria, Candidatus Brocadia anammoxidans (AF375994), with 92% sequence similarity. Furthermore, we successfully developed a real-time polymerase chain reaction (PCR) assay to quantify populations of ANAMMOX bacteria in the enrichment cultures. For this real-time PCR assay, PCR primer sets targeting 16S ribosomal RNA genes of ANAMMOX bacteria were designed and used. The quantification range of this assay was 6 orders of magnitude, from 8.9x10(1) to 8.9x10(6) copies per PCR, corresponding to the detection limit of 3.6x10(3) target copies mL(-1). A significant correlation was found between the increase in copy numbers of 16S rRNA gene of ANAMMOX bacteria and the increase in nitrogen removal rates in the enrichment cultures. Quantifying ANAMMOX bacterial populations in the enrichment culture made it possible to estimate the doubling time of the enriched ANAMMOX bacteria to be 3.6 to 5.4 days. The real-time PCR assay gave comparable population sizes in the enrichment cultures with the FISH results. These results suggest that the real-time PCR assay developed in this study is useful and reliable for quantifying the populations of ANAMMOX bacteria in environmental and engineering samples.