Статті в журналах: "Specific F-RNA bacteriophages"

1

Schaper, M., A. E. Durán, and J. Jofre. "Comparative Resistance of Phage Isolates of Four Genotypes of F-Specific RNA Bacteriophages to Various Inactivation Processes." Applied and Environmental Microbiology 68, no. 8 (August 2002): 3702–7. http://dx.doi.org/10.1128/aem.68.8.3702-3707.2002.

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ABSTRACT The effect of natural inactivation in freshwater, chlorination, ammonia, extreme pHs, temperature, and salt content on phage inactivation was evaluated on mixtures of F-specific RNA bacteriophage isolates belonging to genotypes I, II, III, and IV. The bacteriophages studied were previously but recently isolated from natural samples, characterized as F-specific RNA bacteriophages and genotyped by plaque hybridization with genotype-specific probes. Natural inactivation in river water was modeled by in situ incubation of bacteriophages inside submerged dialysis tubes. After several days bacteriophages of genotype I showed the highest persistence, which was significantly different from that of bacteriophages of genotype II, IV, or III. The pattern of resistance of phages belonging to the various genotypes to extreme pHs, ammonia, temperature, salt concentration, and chlorination was similar. In all cases, phages of genotype I showed the highest persistence, followed by the phages of genotypes II, III, and IV. The phages of genotypes III and IV were the least resistant to all treatments, and resistance of genotypes III and IV to the treatments was similar. Bacteriophages of genotype II showed intermediate resistance to some of the treatments. The resistance of four phages of genotype I to natural inactivation and chlorination did not differ significantly. These results indicate that genotypes III and IV are much more sensitive to environmental stresses and to treatments than the other genotypes, especially than genotype I. This should be taken into consideration in future studies aimed at using genotypes of F-specific RNA bacteriophages to fingerprint the origin of fecal pollution.

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Lee, J. V., S. R. Dawson, S. Ward, S. B. Surman, and K. R. Neal. "Bacteriophages are a better indicator of illness rates than bacteria amongst users of a white water course fed by a lowland river." Water Science and Technology 35, no. 11-12 (June 1, 1997): 165–70. http://dx.doi.org/10.2166/wst.1997.0728.

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An examination was made of the risk factors for gastrointestinal illness (GI) and other symptoms among canoeists and rafters using an artificial white-water canoe slalom course fed by a lowland river. The investigation was made by carrying out cohort studies of users on several days throughout one year. On each day water samples were collected for the determination of Escherichia coli, enterococci (faecal streptococci), F-specific RNA bacteriophage, sulphite reducing clostridia, culturable enteroviruses and turbidity. Of 755 questionnaires distributed, 473 (63%) were returned. The relative risks of GI and other symptoms were determined by logistic regression analyses. The variables associated with an increased risk of GI-illness were swallowing water, unintentional swimming in the course, eating and drinking before getting changed and the levels of F-specific RNA bacteriophages. Being a regular user was associated with a decreased risk of GI-illness. This study demonstrates the value of F-specific RNA bacteriophages as an index of risk from recreational use of a fresh water environment.

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Havelaar, A. H., W. M. Hogeboom, and R. Pot. "F Specific RNA Bacteriophages in Sewage: Methodology and Occurrence." Water Science and Technology 17, no. 4-5 (April 1, 1985): 645–55. http://dx.doi.org/10.2166/wst.1985.0167.

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F specific RNA (FRNA) bacteriophages are attractive models for the study of the fate of animal viruses in water treatment processes and pure cultures (MS2, f2) have frequently been used in model experiments. The use of indigenous FRNA phages has been hampered by the lack of selective enumeration methods. Usually, bacteriophages in sewage are enumerated by counting the number of plaques produced in a lawn of an Escherichia coli host strain. Both somatic and F specific phages will contribute to the count. We report the development of a simple and highly selective method, based on a specially constructed host strain of Salmonella typhimurium (WG 49, phage type 3 Nalr (F'42 lac :: Tn5)). Counts on this host strain normally originate exclusively from F specific phages, because there are only few somatic Salmonella phages in most sewage samples. FRNA phage counts from natural sewage samples using this host strain are more reliable and higher than those obtained on E. coli hosts. F specific bacteriophages were detected in all sewage samples investigated in numbers ranging from 102 − 5 × 104 pfu/ml. Data are presented on the number and types of F specific phages in mixed domestic/industrial sewage; in poultry processing wastewater and in hospital wastewater. The potential of F specific phages as water quality indicators is discussed.

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Kfir, R., P. Coubrough, and W. O. K. Grabow. "The Occurrence of Male-Specific and Somatic Bacteriophages in Polluted South African Waters." Water Science and Technology 24, no. 2 (July 1, 1991): 251–54. http://dx.doi.org/10.2166/wst.1991.0068.

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The occurrence of somatic (F') and male-specific (F') coliphages and Salmonella phages in a variety of environmental water samples was studied using different bacterial hosts. The number of plaque-forming units (pfu) of the different bacteriophages were compared and their resistance pattern to a biological treatment (humus tank) and chlorination was evaluated. The presence of the bacteriophages in shellfish was also studied. The morphology of isolate bacteriophages was examined as well as the visibility of the different plaques formed. Coliphages were found to produce larger and clearer plaques than all other bacteriophages studied. In most of the environmental water samples coliphages outnumbered all other bacteriophages, with the exception of dam water in which higher levels of F' Salmonella phages were detected. The majority of the F' Salmonella phages were shown to be RNA bacteriophages.

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Gourmelon, Michèle, Marie Paule Caprais, Raphaël Ségura, Cécile Le Mennec, Solen Lozach, Jean Yves Piriou, and Alain Rincé. "Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries." Applied and Environmental Microbiology 73, no. 15 (June 8, 2007): 4857–66. http://dx.doi.org/10.1128/aem.03003-06.

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ABSTRACT In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193′), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries, but in all sewage samples. Most detected F RNA bacteriophages were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird feces and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal, or mixed fecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing Escherichia coli or enterococcus concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers.

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Shirasaki, N., T. Matsushita, Y. Matsui, T. Urasaki, and K. Ohno. "Difference in behaviors of F-specific DNA and RNA bacteriophages during coagulation–rapid sand filtration and coagulation–microfiltration processes." Water Supply 12, no. 5 (August 1, 2012): 666–73. http://dx.doi.org/10.2166/ws.2012.041.

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Difference in behaviors of F-specific DNA and RNA bacteriophages during coagulation–rapid sand filtration and coagulation–microfiltration (MF) processes were investigated by using river water spiked with F-specific DNA bacteriophage f1 and RNA bacteriophage f2. Because the particle characteristics of f1 (filamentous) and f2 (spherical) are quite different and the surface charge of f1 in the river water was slightly more negative than that of f2, the removal ratios of f1 were approximately 1-log lower than the removal ratio of f2 after any treatment process used in the present study. This result indicates that the behaviors of the two bacteriophages during the treatment processes were different, and that the removal of f1 by the combination of coagulation and filtration processes was more difficult than that of f2. The removal ratios for f1 and f2 were approximately 3-log and 4-log, respectively, in the coagulation–rapid sand filtration process, and 6-log and 7-log, respectively, in the coagulation–MF filtration process. Therefore, as expected, the coagulation–MF process appears to be more effective than the coagulation–rapid sand filtration process for the removal of not only spherical viruses but also filamentous viruses.

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FLANNERY, JOHN, SINÉAD KEAVENEY, and WILLIAM DORÉ. "Use of FRNA Bacteriophages To Indicate the Risk of Norovirus Contamination in Irish Oysters." Journal of Food Protection 72, no. 11 (November 1, 2009): 2358–62. http://dx.doi.org/10.4315/0362-028x-72.11.2358.

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Male-specific (F) RNA bacteriophages have been proposed as indicators for human enteric viruses in shellfish. This study compared the use of Escherichia coli and FRNA bacteriophages to indicate the presence and level of noroviruses in Crassostrea gigas. A total of 167 samples from category A and B shellfish harvesting areas were analyzed for E. coli and FRNA bacteriophages by standard methods and for noroviruses (NoV) by using a previously described real-time PCR assay. FRNA bacteriophage and NoV levels in shellfish showed a seasonal trend and were elevated during the winter period (October through March). Conversely, E. coli levels did not reflect this seasonal trend. Categorizing samples on the basis of E. coli levels according to European Union regulatory limits failed to indicate the occurrence or level of NoV in shellfish. However, by grouping shellfish samples on the basis of FRNA bacteriophage levels a clear correlation was observed with NoV levels. The use of FRNA bacteriophages to predict the occurrence of NoV in shellfish could provide improved public health protection and should be considered when developing risk management procedures for shellfisheries.

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Schijven, J. F., W. Hoogenboezem, P. J. Nobel, G. J. Medema, and A. Stakelbeek. "Reduction of FRNA-bacteriophages and faecal indicator bacteria by dune infiltration and estimation of sticking efficiencies." Water Science and Technology 38, no. 12 (December 1, 1998): 127–31. http://dx.doi.org/10.2166/wst.1998.0521.

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A field study was performed to investigate reduction by dune infiltration and to estimate sticking efficiencies of F-specific RNA bacteriophages, total and thermotolerant coliforms, faecal streptococci and spores of sulphite-reducing clostridia. Reduction was considered as a β-binomially distributed process and a Monte Carlo simulation was applied for estimating sticking efficiencies. Reduction of F-specific RNA bacteriophages within the first 2m was 3.8 log10 and the sticking efficiency was about 0.002. The faecal indicator bacteria were removed only 0.9 log10 within 2m and sticking efficiency was 0.007. Concentrations of spores of sulphite reducing clostridia were reduced 1.9 log10 and their sticking efficiency was about 0.009.

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Daehnel, Katrin, Robin Harris, Lucinda Maddera, and Philip Silverman. "Fluorescence assays for F-pili and their application." Microbiology 151, no. 11 (November 1, 2005): 3541–48. http://dx.doi.org/10.1099/mic.0.28159-0.

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Conjugative pili are extracellular filaments elaborated by Gram-negative bacteria expressing certain type IV secretion systems. They are required at the earliest stages of conjugal DNA transfer to establish specific and secure cell–cell contacts. Conjugative pili also serve as adsorption organelles for both RNA and DNA bacteriophages. Beyond these facts, the structure, formation and function of these filaments are poorly understood. This paper describes a rapid, quantitative assay for F-pili encoded by the F plasmid type IV secretion system. The assay is based on the specific lateral adsorption of icosahedral RNA bacteriophage R17 by F-pili. Bacteriophage particles conjugated with a fluorescent dye, Alexa 488, and bound to F-pili defined filaments visible by immunofluorescence microscopy. F-pili attached to F+ cells and free F-pili were both visible by this method. For quantification, cell-bound bacteriophage were separated from free bacteriophage particles by sedimentation and released by suspending cell pellets in 0·1 % SDS. Fluorescence in cell-free supernatant fractions was measured by fluorometry. The authors present a characterization of this assay and its application to F-pilus formation by cells carrying mutations in the gene for the F-pilus subunit F-pilin. Each mutation introduced a cysteine, which F-pilin normally lacks, at a different position in its primary structure. Cysteine residues in the N-terminal domain I abolished filament formation as measured by fluorescent R17 binding. This was confirmed by measurements of DNA donor activity and filamentous DNA bacteriophage infection. With one exception (G53C), cysteines elsewhere in the F-pilin primary structure did not abolish filament formation, although some mutations differentially affected F-pilus functions.

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Vantarakis, A., D. Venieri, G. Komninou, and M. Papapetropoulou. "Hybridisation of F+ RNA coliphages detected in shellfish samples with oligonucleotide probes to assess the origin of microbiological pollution of shellfish." Water Science and Technology 54, no. 3 (August 1, 2006): 219–23. http://dx.doi.org/10.2166/wst.2006.472.

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Current measures for controlling the public health risks associated with bivalve molluscan shellfish consumption rely on the use of Escherichia coli to indicate the sanitary quality of shellfish harvesting areas. However, it has been demonstrated that E. coli is an inadequate indicator of the viral risk associated with shellfish. An alternative indicator, male-specific B+ coliphages, have been investigated as viral indicators of faecal contamination that may provide source-specific information for impacted environmental waters. This study compared the distribution of E. coli and F+ RNA bacteriophages in shellfish grown in harvesting areas of Greece and also examined the presence and proportions of the different subgroups of F+ RNA coliphages in shellfish. F+ RNA bacteriophages were present in shellfish at higher concentrations than E. coli. Elevated numbers of F+ RNA bacteriophages observed in the winter concur with the known increased viral risk associated with shellfish harvested at that time of year in Greece. The majority of F+ RNA coliphages detected in shellfish samples belonged to group IV which indicated the possible presence of animal faecal material in sample harvesting areas. Phages of groups II and III (human waste and human faecal material, respectively) were present at low levels. Finally, 8% of the phages hybridised were found to belong to group I. The presence of group IV showed seasonal distribution (more in winter, less in summer) whereas the other groups did not show any difference. Monitoring of F+ coliphage subgroups may indicate the presence and major sources of microbial inputs to surface waters; however, environmental effects on the relative occurrence of different groups need to be considered.

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Lee, Jung Eun, Mi Young Lim, Sei Yoon Kim, Sunghee Lee, Heetae Lee, Hyun-Myung Oh, Hor-Gil Hur, and GwangPyo Ko. "Molecular Characterization of Bacteriophages for Microbial Source Tracking in Korea." Applied and Environmental Microbiology 75, no. 22 (September 18, 2009): 7107–14. http://dx.doi.org/10.1128/aem.00464-09.

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ABSTRACT 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 Qβ-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.

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Havelaar, A. H., and W. M. Pot-Hogeboom. "F-Specific RNA-Bacteriophages as Model Viruses in Water Hygiene: Ecological Aspects." Water Science and Technology 20, no. 11-12 (November 1, 1988): 399–407. http://dx.doi.org/10.2166/wst.1988.0312.

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Model organisms can be used to detect the possible presence of pathogens (index-function) or to assess the performance of a treatment process (indicator-function). To evaluate the index-function of FRNA-phages their ecology was studied. These phages were shown to be absent from feces of humans, dogs, cows, horses and to occur in relatively low numbers only in feces of pigs and calves. High counts were obtained from feces of broiler chickens (103-107 pfu/g). In various types of wastewater, counts were usually between 103 and 104 pfu/ml. These high counts could not be explained by direct fecal input. Multiplication of FRNA-phages in the environment seemed unlikely because of the necessity of bacterial host-strains to bear F-pili. These are only produced at temperatures above 30°C. It was shown however, that multiplication of FRNA-phages can also occur if a host-cell pregrown at 37°C (e.g. in the warm-blooded intestine) is transferred to environmental temperatures. Hence, the presence of FRNA-phages in environmental samples is indirectly associated with fecal pollution

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Havelaar, A. H., Th J. Nieuwstad, C. C. E. Meulemans, and M. van Olphen. "F-Specific RNA Bacteriophages as Model Viruses in UV Disinfection of Wastewater." Water Science and Technology 24, no. 2 (July 1, 1991): 347–52. http://dx.doi.org/10.2166/wst.1991.0088.

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F-specific RNA (FRNA) bacteriophages can be assayed in wastewater by simple and rapid methods. Their inactivation by UV radiation follows first-order kinetics and relatively simple formulas can describe the effect of UV absorbance by wastewater and the wavelength-dependent killing efficiency of polychromatic lamps. Because the organisms can be grown in high concentrations, biological calibration of full-scale reactors requires only relatively small volumes of phage culture. Naturally occurring FRNA-phages were more resistant to UV than somatic coliphages, Escherichiacoli and faecal streptococci. The inactivation rate constant was almost equal to that of reoviruses, which underlines the suitability of FRNA-phages as a process indicator for UV inactivation of viruses. A pure culture of MS2 was inactivated at a rate which was almost twice that of naturally occurring FRNA-phages, indicating the necessity of designing reactors for practical applications on field-data rather than laboratory experiments.

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Bourrouet, A., J. Garcia, R. Mujeriego, and G. Peñuelas. "Faecal bacteria and bacteriophage inactivation in a full-scale UV disinfection system used for wastewater reclamation." Water Science and Technology 43, no. 10 (May 1, 2001): 187–94. http://dx.doi.org/10.2166/wst.2001.0616.

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A study was carried out to compare the inactivation of faecal bacteria and one type of bacteriophage in a full-scale UV disinfection system. The system is part of a water reclamation facility for effluent reuse in golf course and agricultural irrigation. Influent and effluent samples were taken over two sampling periods (three consecutive days in July and one day in August), with three different UV doses applied each day (ranging from 10 to 40 mW.s/cm2 and 20 to 80 mW.s/cm2 in July and August, respectively). Effluent samples were also taken from a chlorine disinfection channel (5 mg Cl2/L dose) operating in parallel to the UV system. Total coliforms (TC), faecal coliforms (FC), faecal streptoccoci (FS) and somatic coliphages (SC) were measured in each sample. F-specific RNA bacteriophages and bacteriophages of Bacteroides fragilis were also measured one day in July. The decay ratio observed for all the microorganisms was similar when UV doses applied were low (July), ranging from 1.15 to 1.25 log-units. This suggests that bacterial indicators may be suitable for virus inactivation control when low UV doses are applied; however, such low doses are inadequate to achieve effluent quality requirements for unrestricted irrigation. At higher UV doses (August), decay ratios for TC and FC were 3.1 and 2.8 log-units respectively, indicating that they were more susceptible to UV exposure than SC and FS, with decay ratios of 2.6 and 1.0 log-units, respectively. Nevertheless, these higher doses were also inadequate to achieve water quality requirements for unrestricted irrigation. The decay ratio of SC during chlorine disinfection was clearly lower than that of the other microorganisms. Bacteriophages of Bacteroides fragilis were more resistant to UV disinfection than SC and F-specific RNA. In fact, bacteriophages of Bacteroides fragilis were not affected during UV exposure. A UV dose ranging from 40 to 80 mW.s/cm2 marks the borderline beyond which inactivation rates of SC are clearly lower than those of bacterial indicators.

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Sinton, Lester W., Rochelle K. Finlay, and Philippa A. Lynch. "Sunlight Inactivation of Fecal Bacteriophages and Bacteria in Sewage-Polluted Seawater." Applied and Environmental Microbiology 65, no. 8 (August 1, 1999): 3605–13. http://dx.doi.org/10.1128/aem.65.8.3605-3613.1999.

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ABSTRACT Sunlight inactivation rates of somatic coliphages, F-specific RNA bacteriophages (F-RNA phages), and fecal coliforms were compared in seven summer and three winter survival experiments. Experiments were conducted outdoors, using 300-liter 2% (vol/vol) sewage-seawater mixtures held in open-top chambers. Dark inactivation rates (kD s), measured from exponential survival curves in enclosed (control) chambers, were higher in summer (temperature range: 14 to 20°C) than in winter (temperature range: 8 to 10°C). Winter kD s were highest for fecal coliforms and lowest for F-RNA phages but were the same or similar for all three indicators in summer. Sunlight inactivation rates (kS ), as a function of cumulative global solar radiation (insolation), were all higher than thekD s with a consistentkS ranking (from greatest to least) as follows: fecal coliforms, F-RNA phages, and somatic coliphages. Phage inactivation was exponential, but bacterial curves typically exhibited a shoulder. Phages from raw sewage exhibitedkS s similar to those from waste stabilization pond effluent, but raw sewage fecal coliforms were inactivated faster than pond effluent fecal coliforms. In an experiment which included F-DNA phages and Bacteroides fragilis phages, thekS ranking (from greatest to least) was as follows: fecal coliforms, F-RNA phages, B. fragilis phages, F-DNA phages, and somatic coliphages. In a 2-day experiment which included enterococci, the initial concentration ranking (from greatest to least: fecal coliforms, enterococci, F-RNA phages, and somatic coliphages) was reversed during sunlight exposure, with only the phages remaining detectable by the end of day 2. Inactivation rates under different optical filters decreased with the increase in spectral cutoff wavelength (50% light transmission) and indicated that F-RNA phages and fecal coliforms are more susceptible than somatic coliphages to longer solar wavelengths, which predominate in seawater. The consistently superior survival of somatic coliphages in our experiments suggests that they warrant further consideration as fecal, and possibly viral, indicators in marine waters.

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Guan, D., R. D. Joerger, K. E. Kniel, K. R. Calci, D. T. Hicks, L. F. Pivarnik, and D. G. Hoover. "Effect of high hydrostatic pressure on four genotypes of F-specific RNA bacteriophages." Journal of Applied Microbiology 102, no. 1 (January 2007): 51–56. http://dx.doi.org/10.1111/j.1365-2672.2006.03064.x.

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Niemi, R. M., A. Kytövaara, J. Pääkkönen, and K. Lahti. "Removal of F-specific RNA bacteriophages in artificial recharge of groundwater - a field study." Water Science and Technology 50, no. 1 (July 1, 2004): 155–58. http://dx.doi.org/10.2166/wst.2004.0046.

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Artificial recharge of groundwater offers a semi-natural means to produce raw water for drinking-water plants. Surface water works are increasingly being replaced by artificial groundwater works in Finland. Two municipalities, one serving 30,000 and the other 170,000 inhabitants, have considered filtering river water through eskers for the production of potable water. In this study the removal of bacteriophages during infiltration of river water was estimated, for the evaluation of treatment adequacy in a field study. A 5-m-deep column of sand was constructed and used to mimic the percolating phase in infiltration. An artificial esker was constructed on the riverbank by isolating a 2-m-wide, 2-m-deep and 18-m-long bed of coarse sand with plastic. The sand bed represented the saturated zone. River water was pumped at a rate of 40 L/h to the sand column. The river water was spiked with F+ specific RNA phage MS2 by adding phage suspension during one week at an average concentration of 4.3 × 109 PFU/mL. Samples for phage assays were taken during one month, from four sampling sites, on the basis of detention time as estimated by a tracer experiment with sodium chloride. The median count of MS2 for percolated water was 2.4 × 105 PFU/mL, representing a 96.7% reduction. During the passage of 6 m in the saturated zone, a further reduction of 98.5% occurred. During the passage from 6 m to 12 m the additional reduction was 99.97%. The overall reduction was between 6 and 7 log10 units. The removal of MS2 phages was rather efficient, although the esker material was coarse, mainly sandy, gravel.

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Havelaar, A. H., M. van Olphen, and Y. C. Drost. "F-specific RNA bacteriophages are adequate model organisms for enteric viruses in fresh water." Applied and Environmental Microbiology 59, no. 9 (1993): 2956–62. http://dx.doi.org/10.1128/aem.59.9.2956-2962.1993.

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Mauffret, Aourell, Marie-Paule Caprais, and Michèle Gourmelon. "Relevance of Bacteroidales and F-Specific RNA Bacteriophages for Efficient Fecal Contamination Tracking at the Level of a Catchment in France." Applied and Environmental Microbiology 78, no. 15 (May 18, 2012): 5143–52. http://dx.doi.org/10.1128/aem.00315-12.

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ABSTRACTThe relevance of three host-associatedBacteroidalesmarkers (HF183, Rum2Bac, and Pig2Bac) and four F-specific RNA bacteriophage genogroups (FRNAPH I to IV) as microbial source tracking markers was assessed at the level of a catchment (Daoulas, France). They were monitored together with fecal indicators (Escherichia coliand enterococci) and chemophysical parameters (rainfall, temperature, salinity, pH, and turbidity) by monthly sampling over 2 years (n= 240 water samples) and one specific sampling following an accidental pig manure spillage (n= 5 samples). During the 2-year regular monitoring, levels ofE. coli, enterococci, total F-specific RNA bacteriophages, and the generalBacteroidalesmarker AllBac were strongly correlated with one another and with Rum2Bac (r= 0.37 to 0.50,P< 0.0001). Their correlations with HF183 and FRNAPH I and II were lower (r= 0.21 to 0.29,P< 0.001 toP< 0.0001), and HF183 and enterococci were associated rather than correlated (Fisher's exact test,P< 0.01). Rum2Bac and HF183 enabled 73% of water samples that had ≥2.7 log10most probably number (MPN) ofE. coli/100 ml to be classified. FRNAPH I and II enabled 33% of samples at this contamination level to be classified. FRNAPH I and II complemented the water sample classification obtained with the twoBacteroidalesmarkers by an additional 8%. Pig2Bac and FRNAPH III and IV were observed in a small number of samples (n= 0 to 4 of 245). The present study validates Rum2Bac and HF183 as relevant tools to trace fecal contamination originating from ruminant or human waste, respectively, at the level of a whole catchment.

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Blanch, Anicet R., Lluï¿½s Belanche-Muï¿½oz, Xavier Bonjoch, James Ebdon, Christophe Gantzer, Francisco Lucena, Jakob Ottoson, et al. "Integrated Analysis of Established and Novel Microbial and Chemical Methods for Microbial Source Tracking." Applied and Environmental Microbiology 72, no. 9 (September 2006): 5915–26. http://dx.doi.org/10.1128/aem.02453-05.

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ABSTRACT Several microbes and chemicals have been considered as potential tracers to identify fecal sources in the environment. However, to date, no one approach has been shown to accurately identify the origins of fecal pollution in aquatic environments. In this multilaboratory study, different microbial and chemical indicators were analyzed in order to distinguish human fecal sources from nonhuman fecal sources using wastewaters and slurries from diverse geographical areas within Europe. Twenty-six parameters, which were later combined to form derived variables for statistical analyses, were obtained by performing methods that were achievable in all the participant laboratories: enumeration of fecal coliform bacteria, enterococci, clostridia, somatic coliphages, F-specific RNA phages, bacteriophages infecting Bacteroides fragilis RYC2056 and Bacteroides thetaiotaomicron GA17, and total and sorbitol-fermenting bifidobacteria; genotyping of F-specific RNA phages; biochemical phenotyping of fecal coliform bacteria and enterococci using miniaturized tests; specific detection of Bifidobacterium adolescentis and Bifidobacterium dentium; and measurement of four fecal sterols. A number of potentially useful source indicators were detected (bacteriophages infecting B. thetaiotaomicron, certain genotypes of F-specific bacteriophages, sorbitol-fermenting bifidobacteria, 24-ethylcoprostanol, and epycoprostanol), although no one source identifier alone provided 100% correct classification of the fecal source. Subsequently, 38 variables (both single and derived) were defined from the measured microbial and chemical parameters in order to find the best subset of variables to develop predictive models using the lowest possible number of measured parameters. To this end, several statistical or machine learning methods were evaluated and provided two successful predictive models based on just two variables, giving 100% correct classification: the ratio of the densities of somatic coliphages and phages infecting Bacteroides thetaiotaomicron to the density of somatic coliphages and the ratio of the densities of fecal coliform bacteria and phages infecting Bacteroides thetaiotaomicron to the density of fecal coliform bacteria. Other models with high rates of correct classification were developed, but in these cases, higher numbers of variables were required.

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Blanch, Anicet R., Luis Belanche-Muñoz, Xavier Bonjoch, James Ebdon, Christophe Gantzer, Francisco Lucena, Jakob Ottoson, et al. "Tracking the origin of faecal pollution in surface water: an ongoing project within the European Union research programme." Journal of Water and Health 2, no. 4 (December 1, 2004): 249–60. http://dx.doi.org/10.2166/wh.2004.0022.

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The objectives of this study are to generate knowledge about methods to track the sources of faecal pollution in surface waters, with the aim of having one or a few easy procedures applicable to different geographic areas in Europe. For this, a first field study using already proposed methods (genotypes of F-specific RNA bacteriophages, bacteriophages infecting Bacteroides fragilis, phenotypes of faecal coliforms and enterococci, and sterols) has been done in five areas representing a wide array of conditions in Europe. The present faecal indicators (faecal coliforms, enterococci, sulfite reducing clostridia and somatic coliphages) have also been included in this first field study. At the same time some emerging methods have been settled or adapted to water samples and assayed in a limited number of samples. The results of this first field study indicate that no single parameter alone is able to discriminate the sources, human or non-human, of faecal pollution, but that a ‘basket’ of 4 or 5 parameters, which includes one of the present faecal indicators, will do so. In addition, numerical analysis of the data shows that this ‘basket’ will allow the successful building of predictive models. Both the statistical analyses and the studied predictive models indicate that genotype II of F-specific RNA bacteriophages, the coprostanol and the ratio coprostanol: coprostanol+epicoprostanol are, out of the studied parameters, those with a greater discriminating power. Either because unsuccessful adaptation of the methods to water samples or because the preliminary assays in water samples indicated low discriminating capability, only three (sorbitol-fermenting bifidobacteria, some species of bifidobacteria detected by PCR with specific primers and phages infecting Bacteroidestethaiotaomicron) of the newly assayed methods have been considered for a second field study, which is currently underway. Expectations are that these new tools will minimize the number of parameters in the ‘basket’, or at least minimize the difficulty in assaying them.

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Myrmel, M., E. M. M. Berg, E. Rimstad, and B. Grinde. "Detection of Enteric Viruses in Shellfish from the Norwegian Coast." Applied and Environmental Microbiology 70, no. 5 (May 2004): 2678–84. http://dx.doi.org/10.1128/aem.70.5.2678-2684.2004.

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ABSTRACT Common blue mussels (Mytilus edulis), horse mussels (Modiolus modiolus), and flat oysters (Ostrea edulis) obtained from various harvesting and commercial production sites along the Norwegian coast were screened for the presence of norovirus by a real-time reverse transcription (RT)-nested PCR assay and for possible indicators of fecal contamination, i.e., for F-specific RNA bacteriophages (F-RNA phages) by plaque assay and for human adenoviruses and human circoviruses by nested PCR assay. The aims were to obtain relevant information for assessing the risk of transmission of enteric viruses by shellfish and to investigate the potential of various indicator viruses in routine screening. Noroviruses were detected in 6.8% of the samples, and the indicators were detected in 23.8% (F-RNA phages), 18.6% (adenoviruses), and 8.0% (circoviruses) of the samples. A seasonal variation was observed, with the exception of circoviruses, with more positive samples in the winter. A positive correlation was found between F-RNA phages and noroviruses. However, F-RNA phages were present in only 43% of the norovirus-positive samples. The results show that mussels from the Norwegian coast can constitute a risk of infection with enteric viruses and that routine testing of samples may be justified. Advantages and disadvantages of various options for screening are discussed.

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Hartard, C., S. Banas, J. Loutreul, A. Rincé, F. Benoit, N. Boudaud, and C. Gantzer. "Relevance of F-Specific RNA Bacteriophages in Assessing Human Norovirus Risk in Shellfish and Environmental Waters." Applied and Environmental Microbiology 82, no. 18 (July 15, 2016): 5709–19. http://dx.doi.org/10.1128/aem.01528-16.

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ABSTRACTHuman noroviruses (HuNoVs) are the main cause of shellfish-borne gastroenteritis outbreaks. In the absence of routine technical approaches allowing infectious particles to be detected, this viral pathogen is currently targeted by genome research, leading to difficult interpretations. In this study, we investigated the potential of F-specific RNA bacteriophages (FRNAPH) as fecal and viral contamination indicators in shellfish and water from a local harvesting area. FRNAPH were also used as microbial source tracking tools. Constraints imposed by detection limits are illustrated here by the detection of infectious FRNAPH in several samples in the absence of FRNAPH genomes. The opposite situation was also observed, likely explained by the persistence of the genomes being greater than infectivity. Similar considerations may be applied to HuNoVs, suggesting that HuNoV genome targeting is of limited relevance in assessing infectious risks. While FRNAPH did not provide any benefits compared toEscherichia colias fecal pollution indicators in water, novel observations were made in shellfish: contrary toE. coli, a seasonal trend of infectious FRNAPH concentrations was observed. These concentrations were higher than those found in water, confirming bioaccumulation in shellfish. This study also underlines a relationship between the presence of HuNoV genomes and those of human-specific FRNAPH subgroup II (FRNAPH-II) in shellfish collected throughout Europe. Further research should be undertaken to evaluate FRNAPH potential as an indicator of the presence of infectious HuNoVs. To this end, shellfish involved in HuNoV-caused gastroenteritis outbreaks should be analyzed for the presence of infectious FRNAPH-II.IMPORTANCEThis work provides new data about the use of F-specific RNA phages (FRNAPH) as a tool for evaluating fecal or viral contamination, especially in shellfish. In our case study, FRNAPH did not provide any benefits compared toE. colias fecal pollution indicators in water but were found to be very useful in shellfish. Their concentrations in shellfish were higher than those found in the surrounding water, confirming bioaccumulation. This study also underlines a relationship between the presence of human norovirus genomes (HuNoVs) and those of FRNAPH subgroup II (FRNAPH-II). Considering that the two virus types have similar behaviors and since FRNAPH infectivity can be investigated, the specific detection of infectious FRNAPH-II could be regarded as an indication of the presence of infectious HuNoVs. The contribution of infectious human FRNAPH targeting for assessing the viral risk associated with HuNoVs in shellfish should thus be investigated.

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Lee, Suwa, and Shigemura. "Metagenomic Analysis of Infectious F-Specific RNA Bacteriophage Strains in Wastewater Treatment and Disinfection Processes." Pathogens 8, no. 4 (November 3, 2019): 217. http://dx.doi.org/10.3390/pathogens8040217.

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F-specific RNA bacteriophages (FRNAPHs) can be used to indicate water contamination and the fate of viruses in wastewater treatment plants (WWTPs). However, the occurrence of FRNAPH strains in WWTPs is relatively unknown, whereas FRNAPH genotypes (GI–GIV) are well documented. This study investigated the diversity of infectious FRNAPH strains in wastewater treatment and disinfection processes using cell culture combined with next-generation sequencing (integrated culture–NGS (IC–NGS)). A total of 32 infectious strains belonging to FRNAPH GI (nine strains), GI-JS (two strains), GII (nine strains), GIII (seven strains), and GIV (five strains) were detected in wastewater samples. The strains of FRNAPH GI and GII exhibited greater resistance to wastewater treatment than those of GIII. The IC–NGS results in the disinfected samples successfully reflected the infectivity of FRNAPHs by evaluating the relationship between IC–NGS results and the integrated culture–reverse-transcription polymerase chain reaction combined with the most probable number assay, which can detect infectious FRNAPH genotypes. The diversity of infectious FRNAPH strains in the disinfected samples indicates that certain strains are more resistant to chlorine (DL52, GI-JS; T72, GII) and ultraviolet (T72, GII) disinfection. It is possible that investigating these disinfectant-resistant strains could reveal effective mechanisms of viral disinfection.

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Simonet, Julien, and Christophe Gantzer. "Inactivation of Poliovirus 1 and F-Specific RNA Phages and Degradation of Their Genomes by UV Irradiation at 254 Nanometers." Applied and Environmental Microbiology 72, no. 12 (October 13, 2006): 7671–77. http://dx.doi.org/10.1128/aem.01106-06.

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ABSTRACT Several models (animal caliciviruses, poliovirus 1 [PV1], and F-specific RNA bacteriophages) are usually used to predict inactivation of nonculturable viruses. For the same UV fluence, viral inactivation observed in the literature varies from 0 to 5 logs according to the models and the methods (infectivity versus molecular biology). The lack of knowledge concerning the mechanisms of inactivation due to UV prevents us from selecting the best model. In this context, determining if viral genome degradation may explain the loss of infectivity under UV radiation becomes essential. Thus, four virus models (PV1 and three F-specific RNA phages: MS2, GA, and Qβ) were exposed to UV radiation from 0 to 150 mJ · cm−2. PV1 is the least-resistant virus, while MS2 and GA phages are the most resistant, with phage Qβ having an intermediate sensitivity; respectively, 6-log, 2.3-log, 2.5-log, and 4-log decreases for 50 mJ · cm−2. In parallel, analysis of RNA degradation demonstrated that this phenomenon depends on the fragment size for PV1 as well as for MS2. Long fragments (above 2,000 bases) for PV1 and MS2 fell rapidly to the background level (>1.3-log decrease) for 20 mJ · cm−2 and 60 mJ · cm− 2, respectively. Nevertheless, the size of the viral RNA is not the only factor affecting UV-induced RNA degradation, since viral RNA was more rapidly degraded in PV1 than in the MS2 phage with a similar size. Finally, extrapolation of inactivation and UV-induced RNA degradation kinetics highlights that genome degradation could fully explain UV-induced viral inactivation.

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SETIYAWAN, Ahmad S., Toshiro YAMADA, Joni A. FAJRI, Fusheng LI, Denny HELARD, Akihiro HORIO, Ming Huang, and Toshiyuki KAWAGUCHI. "SPATIALAND TEMPORAL VARIATION IN CONCENTRATION OF F-SPECIFIC RNA BACTERIOPHAGES IN AN OPEN CHANNEL RECEIVING JOHKASOU EFFLUENTS." Journal of Japan Society of Civil Engineers, Ser. G (Environmental Research) 69, no. 7 (2013): III_667—III_678. http://dx.doi.org/10.2208/jscejer.69.iii_667.

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Havelaar, A. H., W. M. Pot-Hogeboom, K. Furuse, R. Pot, and M. P. Hormann. "F-specific RNA bacteriophages and sensitive host strains in faeces and wastewater of human and animal origin." Journal of Applied Bacteriology 69, no. 1 (July 1990): 30–37. http://dx.doi.org/10.1111/j.1365-2672.1990.tb02908.x.

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McAlister, Victor, Chao Zou, Robert H. Winslow, and Gail E. Christie. "Purification and In Vitro Characterization of the Serratia marcescens NucC Protein, a Zinc-Binding Transcription Factor Homologous to P2 Ogr." Journal of Bacteriology 185, no. 6 (March 15, 2003): 1808–16. http://dx.doi.org/10.1128/jb.185.6.1808-1816.2003.

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ABSTRACT NucC is structurally and functionally homologous to a family of prokaryotic zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. Characterization of these proteins in vitro has been hampered by their relative insolubility and tendency to aggregate. We report here the successful purification of soluble, active, wild-type NucC protein. Purified NucC exhibits site-specific binding to a conserved DNA sequence that is located upstream of NucC-dependent Serratia marcescens promoters and the late promoters of P2-related phages. This sequence is sufficient for binding of NucC in vitro. NucC binding to the S. marcescens nuclease promoter P nucA and to the sequence upstream of the P2 late promoter P F is accompanied by DNA bending. NucC protects about 25 nucleotides of the P F upstream region from DNase I digestion, and RNA polymerase protects the promoter region only in the presence of NucC. Template DNA, RNA polymerase holoenzyme, and purified NucC are the only macromolecular components required for transcription from P F in vitro.

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Martínez-Carreras, Núria, Leslie Ogorzaly, Cécile Walczak, Christophe Merlin, Emmanuelle Montargès-Pelletier, Christophe Gantzer, Jean-François Iffly, Henry-Michel Cauchie, and Christophe Hissler. "F-Specific RNA Bacteriophage Transport in Stream Water: Hydro-Meteorological Controls and Association with Suspended Solids." Water 13, no. 16 (August 18, 2021): 2250. http://dx.doi.org/10.3390/w13162250.

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F-specific RNA bacteriophages (FRNAPHs) are commonly used as indicators of faecal and viral contamination in waters. Once they enter surface waters, the exact role of suspended solids, sediments and hydro-meteorological factors in their fluvial fate and transport is poorly understood, and long-term studies (e.g., over years) are lacking. In this study, FRNAPH concentrations and genogroup distribution were measured in the Orne River (France) during two years at weekly intervals, and during four storm runoff events. Hydro-meteorological driving factors were investigated at both time scales. FRNAPH concentrations and genogroups at different depths of a riverbank sediment core were also examined to better discriminate the origin of the faecal pollution. During low flows, the FRNAPH and the suspended solid transport were decoupled and the FRNAPH concentrations were mainly correlated with the air and water temperature. During storm runoff events, the FRNAPH concentrations only showed a significant correlation with conductivity, turbidity and water discharge. Despite the uncertainty of the predictions, multi parameter regression models using hydro-meteorological variables were suitable to predict log transformed FRNAPHs’ concentrations at low flows with a standard error of 0.46. Model performance using the storm runoff events dataset was low. This study highlights different driving factors at low flows and during storm runoff events, and the need to measure at both time scales to better understand phage transport dynamics in surface water.

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Mocé-Llivina, Laura, Francisco Lucena, and Juan Jofre. "Enteroviruses and Bacteriophages in Bathing Waters." Applied and Environmental Microbiology 71, no. 11 (November 2005): 6838–44. http://dx.doi.org/10.1128/aem.71.11.6838-6844.2005.

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ABSTRACT A new procedure for detecting and counting enteroviruses based on the VIRADEN method applied to 10 liters of seawater was examined. It improved the efficiency of detection by taking into account both the number of positive isolations and numbers found with traditional methods. It was then used to quantify viruses in bathing waters. A number of bacterial indicators and bacteriophages were also tested. Cultivable enteroviruses were detected in 55% of the samples, most of which complied with bacteriological criteria. In contrast, viral genomes were only detected in 20% of the samples by reverse transcription-PCR. Somatic coliphages outnumbered all other indicators. F-specific RNA phages were detected in only 15% of the samples, whereas phages infecting Bacteroides thetaiotaomicron were detected in 70% of samples. A numerical relationship between the numbers of enteroviruses and the numbers of enterococci and somatic coliphages was observed. In situ inactivation experiments showed that viruses persisted significantly longer than the bacterial indicators. Only somatic coliphages and bacteriophages infecting Bacteroides persisted longer than the viruses. These results explain the numbers of enteroviruses and indicators in bathing waters attending the numbers usually found in sewage in the area. Somatic coliphages show a very good potential to predict the risk of viruses being present in bathing waters.

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Chung, H., L. A. Jaykus, G. Lovelace, and M. D. Sobsey. "Bacteriophages and bacteria as indicators of enteric viruses in oysters and their harvest waters." Water Science and Technology 38, no. 12 (December 1, 1998): 37–44. http://dx.doi.org/10.2166/wst.1998.0494.

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Reliable indicators are needed to detect enteric virus contamination of bivalve molluscan shellfish and their harvest waters. Concentrations of male-specific (F+) coliphages, Bacteroides fragilis phages, Salmonella phages and several indicator bacteria in wastewater, estuarine receiving water and its oysters were examined for their ability to predict the presence and levels of faecal contamination and enteric viruses in oysters. Enteric viruses in oysters were detected by cell culture and RT-PCR methods. F+ coliphages, Salmonella phages, B fragilis phages and faecal indicator bacteria (faecal coliforms, E coli, enterococci and Clostridium perfringens) were generally positively associated and were highest in raw sewage and progressively lower in sewage effluent and in receiving waters at increasing distance from the wastewater discharge. Indicator levels in oysters were highest for F+ coliphages and C perfringens. One F+ RNA coliphage serotype (Group II) predominated in the wastewater, receiving water and oysters. Human enteric viruses were detected in 17/31 oyster samples. The levels of most indicators in oysters and water were higher when oysters were enteric virus-positive and lower when oysters were enteric virus-negative. F+ coliphages and C perfringens were the only indicators significantly associated with the presence of enteric viruses in oysters. F+ coliphages and their serotypes are promising indicators of human enteric virus contamination in oysters and their harvest waters.

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Dika, C., M. H. Ly-Chatain, G. Francius, J. F. L. Duval, and C. Gantzer. "Non-DLVO adhesion of F-specific RNA bacteriophages to abiotic surfaces: Importance of surface roughness, hydrophobic and electrostatic interactions." Colloids and Surfaces A: Physicochemical and Engineering Aspects 435 (October 2013): 178–87. http://dx.doi.org/10.1016/j.colsurfa.2013.02.045.

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Mocé-Llivina, Laura, Maite Muniesa, Hugo Pimenta-Vale, Francisco Lucena, and Juan Jofre. "Survival of Bacterial Indicator Species and Bacteriophages after Thermal Treatment of Sludge and Sewage." Applied and Environmental Microbiology 69, no. 3 (March 2003): 1452–56. http://dx.doi.org/10.1128/aem.69.3.1452-1456.2003.

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ABSTRACT The inactivation of naturally occurring bacterial indicators and bacteriophages by thermal treatment of a dewatered sludge and raw sewage was studied. The sludge was heated at 80°C, and the sewage was heated at 60°C. In both cases phages were significantly more resistant to thermal inactivation than bacterial indicators, with the exception of spores of sulfite-reducing clostridia. Somatic coliphages and phages infecting Bacteroides fragilis were significantly more resistant than F-specific RNA phages. Similar trends were observed in sludge and sewage. The effects of thermal treatment on various phages belonging to the three groups mentioned above and on various enteroviruses added to sewage were also studied. The results revealed that the variability in the resistance of phages agreed with the data obtained with the naturally occurring populations and that the phages that were studied were more resistant to heat treatment than the enteroviruses that were studied. The phages survived significantly better than Salmonella choleraesuis, and the extents of inactivation indicated that naturally occurring bacteriophages can be used to monitor the inactivation of Escherichia coli and Salmonella.

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Lee, Suntae, Mamoru Suwa, and Hiroyuki Shigemura. "Occurrence and reduction of F-specific RNA bacteriophage genotypes as indicators of human norovirus at a wastewater treatment plant." Journal of Water and Health 17, no. 1 (December 13, 2018): 50–62. http://dx.doi.org/10.2166/wh.2018.367.

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Abstract F-specific RNA bacteriophages (FRNAPHs) have been suggested as good indicators of the presence of human enteric viruses in water treatment facilities. The occurrence and reduction of norovirus (NoV) and FRNAPH genotypes in wastewater treatment plants (WWTPs) have been well studied; however, the relationship between these genotypes in WWTPs has not been fully elucidated. Thus, we aimed to investigate the occurrence and reduction of FRNAPH genotypes in an attempt to identify NoV indicators in a WWTP via a 1-year survey. All FRNAPH and NoV genotypes were detected in WWTP influents at high rates (71–100%), including the infectious FRNAPH genotype IV (GIV), which has been rarely detected in previous studies. The reductions of FRNAPH GII and NoV GII during wastewater treatment indicated a relationship between the two (r = 0.69, P < 0.01), and the mean values were not significantly different. These results suggested that FRNAPH GII could be used as an appropriate indicator of NoV GII during wastewater treatment. FRNAPH GI was also found to be an appropriate indicator of viral reduction because of its high resistance to wastewater treatment compared with the other FRNAPH and NoV genotypes; therefore, it can be considered as a worst-case scenario organism.

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Capizzi-Banas, Sandrine, Mélissa Palos Ladeiro, Fanny Bastien, Isabelle Bonnard, Nicolas Boudaud, Christophe Gantzer, and Alain Geffard. "The Utility of Dreissena polymorpha for Assessing the Viral Contamination of Rivers by Measuring the Accumulation of F-Specific RNA Bacteriophages." Water 13, no. 7 (March 26, 2021): 904. http://dx.doi.org/10.3390/w13070904.

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River water that receives treated wastewater can be contaminated by pathogens including enteric viruses due to fecal pollution, which may represent an important public health hazard. There is a great diversity of enteric viruses and fecal bacteriophages, especially F-specific RNA bacteriophages (FRNAPHs), are commonly proposed as indicators of viral pollution due to a variety of characteristics such as their structural similarities to the main enteric viruses, their high concentrations in raw wastewater and their environmental survival rate, which is better than other cultivable enteric viruses. However, evaluating the viral contamination of water on the basis of FRNAPH concentration levels continues to present a challenge. This is because the quality of detection is strongly dependent on the quantity of viral particles, high spatio-temporal variabilities and the physico-chemical conditions of the water during sampling. To overcome these limitations, the present study aims to evaluate whether the bivalve mollusk Dreissena polymorpha (zebra mussel) could be considered a suitable experimental model for assessing the viral contamination of rivers. In order to determine this, the capacity of D. polymorpha to accumulate FRNAPHs and assimilate them into their soft tissue was studied. This provided a proof of concept for the use of D. polymorpha to evaluate the viral contamination of surface water. Two experiments were conducted: (1) an in situ experiment to confirm that zebra mussels naturally accumulated FRNAPHs and (2) a laboratory experiment to determine the accumulation and depuration kinetics of FRNAPHs in D. polymorpha tissue. The study highlights the capacity of the mussels to accumulate infectious FRNAPHs both on a laboratory scale under controlled conditions as well as in situ at different sites that are representative of different bodies of water. An analysis of the mussels’ soft tissue showed that they were capable of reflecting the water’s contamination level very quickly (within less than 24 h). Moreover, the soft tissue retained the viral load much longer than the water due to a low depuration rate. The analysis of FRNAPH concentrations in mussels exposed in situ suggested that there were differences in contamination levels between sites. These preliminary results underline the potential utility of zebra mussels in assessing viral contamination by measuring the accumulation of FRNAPHs in their tissue. This may ultimately enable stakeholders to use zebra mussels as a means of monitoring viral pollution in surface water.

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Formiga-Cruz, M., A. K. Allard, A. C. Conden-Hansson, K. Henshilwood, B. E. Hernroth, J. Jofre, D. N. Lees, et al. "Evaluation of Potential Indicators of Viral Contamination in Shellfish and Their Applicability to Diverse Geographical Areas." Applied and Environmental Microbiology 69, no. 3 (March 2003): 1556–63. http://dx.doi.org/10.1128/aem.69.3.1556-1563.2003.

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ABSTRACT The distribution of the concentration of potential indicators of fecal viral pollution in shellfish was analyzed under diverse conditions over 18 months in diverse geographical areas. These microorganisms have been evaluated in relation to contamination by human viral pathogens detected in parallel in the analyzed shellfish samples. Thus, significant shellfish-growing areas from diverse countries in the north and south of Europe (Greece, Spain, Sweden, and the United Kingdom) were defined and studied by analyzing different physicochemical parameters in the water and the levels of Escherichia coli, F-specific RNA bacteriophages, and phages infecting Bacteroides fragilis strain RYC2056 in the shellfish produced, before and after depuration treatments. A total of 475 shellfish samples were studied, and the results were statistically analyzed. According to statistical analysis, the presence of human viruses seems to be related to the presence of all potential indicators in the heavily contaminated areas, where E. coli would probably be suitable as a fecal indicator. The F-RNA phages, which are present in higher numbers in Northern Europe, seem to be significantly related to the presence of viral contamination in shellfish, with a very weak predictive value for hepatitis A virus, human adenovirus, and enterovirus and a stronger one for Norwalk-like virus. However, it is important to note that shellfish produced in A or clean B areas can sporadically contain human viruses even in the absence of E. coli or F-RNA phages. The data presented here will be useful in defining microbiological parameters for improving the sanitary control of shellfish consumed raw or barely cooked.

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Hartard, C., R. Rivet, S. Banas, and C. Gantzer. "Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins." Applied and Environmental Microbiology 81, no. 18 (July 10, 2015): 6505–15. http://dx.doi.org/10.1128/aem.01905-15.

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ABSTRACTF-specific RNA bacteriophages (FRNAPH) have been widely studied as tools for evaluating fecal or viral pollution in water. It has also been proposed that they can be used to differentiate human from animal fecal contamination. While FRNAPH subgroup I (FRNAPH-I) and FRNAPH-IV are often associated with animal pollution, FRNAPH-II and -III prevail in human wastewater. However, this distribution is not absolute, and variable survival rates in these subgroups lead to misinterpretation of the original distribution. In this context, we studied FRNAPH distribution in urban wastewater and animal feces/wastewater. To increase the specificity, we partially sequenced the genomes of phages of urban and animal origins. The persistence of the genomes and infectivity were also studied, over time in wastewater and during treatment, for each subgroup. FRNAPH-I genome sequences did not show any specific urban or animal clusters to allow development of molecular tools for differentiation. They were the most resistant and as such may be used as fecal or viral indicators. FRNAPH-II's low prevalence and low sequence variability in animal stools, combined with specific clusters formed by urban strains, allowed differentiation between urban and animal pollution by using a specific reverse transcription-PCR (RT-PCR) method. The subgroup's resistance over time was comparable to that of FRNAPH-I, but its surface properties allowed higher elimination rates during activated-sludge treatment. FRNAPH-III's low sequence variability in animal wastewater and specific cluster formation by urban strains also allowed differentiation by using a specific RT-PCR method. Nevertheless, its low resistance restricted it to being used only for recent urban pollution detection. FRNAPH-IV was too rare to be used.

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Schaper, Melanie, and Joan Jofre. "Comparison of methods for detecting genotypes of F-specific RNA bacteriophages and fingerprinting the origin of faecal pollution in water samples." Journal of Virological Methods 89, no. 1-2 (September 2000): 1–10. http://dx.doi.org/10.1016/s0166-0934(00)00171-3.

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Hartard, Cédric, Sandrine Banas, Romain Rivet, Nicolas Boudaud, and Christophe Gantzer. "Rapid and sensitive method to assess human viral pollution in shellfish using infectious F-specific RNA bacteriophages: Application to marketed products." Food Microbiology 63 (May 2017): 248–54. http://dx.doi.org/10.1016/j.fm.2016.12.002.

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da Silva, Diogo Trajano Gomes, James Ebdon, Daniel Dancer, Craig Baker-Austin, and Huw Taylor. "A Longitudinal Study of Bacteriophages as Indicators of Norovirus Contamination of Mussels (Mytilus edulis) and Their Overlying Waters." Pollutants 2, no. 1 (March 1, 2022): 66–81. http://dx.doi.org/10.3390/pollutants2010008.

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Sewage pollution leads to the contamination of bivalve shellfish by pathogenic microorganisms. Bacterial indicators support the management of risks associated with the consumption of shellfish; however, they often fail to indicate adequately the potential hazard to human health posed by certain human enteric viruses. Bacteriophages have been proposed as alternative indicators that may more effectively predict the presence of enteric viral pathogens. This study explored the relationships between bacterial indicators (Escherichia coli (E. coli), faecal coliforms (FC) and intestinal enterococci (IE)), phages (somatic (SOMPH), F-specific RNA (F + PH) and human-specific Bacteroides GB-124 phages (GB124PH)) and Norovirus (NoV) (GI/GII) in mussels (Mytilus edulis) and their overlying waters. The bioaccumulation of these indicators and Norovirus in shellfish matrices (e.g., flesh, digestive gland) was investigated bimonthly over a 12-month period in an English estuary. The findings revealed a marked seasonality in the distribution of all organisms, with the highest levels occurring during the autumn/winter months. The levels of all phages in shellfish and their overlying waters correlated better with the levels of Norovirus than with those of bacterial indicators. Somatic coliphages were the indicator that exhibited the strongest correlations with NoV (rho = 0.929). This study suggests that relatively low-cost culture-based phage enumeration appears to offer a more accurate indication of the likely presence of Norovirus in mussels than traditional bacterial indicators.

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Fauvel, Blandine, Christophe Gantzer, Henry-Michel Cauchie, and Leslie Ogorzaly. "In Situ Dynamics of F-Specific RNA Bacteriophages in a Small River: New Way to Assess Viral Propagation in Water Quality Studies." Food and Environmental Virology 9, no. 1 (October 22, 2016): 89–102. http://dx.doi.org/10.1007/s12560-016-9266-0.

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Schaper, M., J. Jofre, M. Uys, and W. O. K. Grabow. "Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain." Journal of Applied Microbiology 92, no. 4 (April 2002): 657–67. http://dx.doi.org/10.1046/j.1365-2672.2002.01600.x.

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Moreno, B., F. Goñi, O. Fernandez, J. A. Martínez, and M. Astigarraga. "The disinfection of wastewater by ultraviolet light." Water Science and Technology 35, no. 11-12 (June 1, 1997): 233–35. http://dx.doi.org/10.2166/wst.1997.0739.

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The aim of this study, carried out over four months at a pilot wastewater treatment facility, was to evaluate ultraviolet treatment of final effluent discharged into bathing waters in coastal zones. Minimum disinfection values were fixed with a target limit of 103cfu/100mL for faecal coliforms (FC) in line with the present and proposed European Directive on bathing water quality. Disinfection performance with different sources of water was studied and the disinfectant capacity with other indicator microorganisms was also checked. The target limit was reached using doses around 30mW.s/cm2. Results of this study suggest that the applied UV dose is influenced by transmittance and the microbiological load. The most sensitive indicators were faecal coliforms, the specific F-RNA bacteriophages being the most resistant. From the results obtained in these experiments, UV treated water is suitable for being discharged into bathing zones, being an alternative to submarine discharges, avoiding high investment and maintenance costs.

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Fauvel, Blandine, Leslie Ogorzaly, Henry-Michel Cauchie, and Christophe Gantzer. "Interactions of infectious F-specific RNA bacteriophages with suspended matter and sediment: Towards an understanding of FRNAPH distribution in a river water system." Science of The Total Environment 574 (January 2017): 960–68. http://dx.doi.org/10.1016/j.scitotenv.2016.09.115.

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Schaper, Melanie, and Joan Jofre. "Corrigendum to “Comparison of methods for detecting genotypes of F-specific RNA bacteriophages and fingerprinting the origin of faecal pollution in water samples”." Journal of Virological Methods 98, no. 2 (November 2001): 171. http://dx.doi.org/10.1016/s0166-0934(01)00362-7.

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Fauvel, Blandine, Henry-Michel Cauchie, Christophe Gantzer, and Leslie Ogorzaly. "Contribution of hydrological data to the understanding of the spatio-temporal dynamics of F-specific RNA bacteriophages in river water during rainfall-runoff events." Water Research 94 (May 2016): 328–40. http://dx.doi.org/10.1016/j.watres.2016.02.057.

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47

Hernroth, Bodil E., Ann-Christine Conden-Hansson, Ann-Sofi Rehnstam-Holm, Rosina Girones, and Annika K. Allard. "Environmental Factors Influencing Human Viral Pathogens and Their Potential Indicator Organisms in the Blue Mussel, Mytilus edulis: the First Scandinavian Report." Applied and Environmental Microbiology 68, no. 9 (September 2002): 4523–33. http://dx.doi.org/10.1128/aem.68.9.4523-4533.2002.

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ABSTRACT This study was carried out in order to investigate human enteric virus contaminants in mussels from three sites on the west coast of Sweden, representing a gradient of anthropogenic influence. Mussels were sampled monthly during the period from February 2000 to July 2001 and analyzed for adeno-, entero-, Norwalk-like, and hepatitis A viruses as well as the potential viral indicator organisms somatic coliphages, F-specific RNA bacteriophages, bacteriophages infecting Bacteroides fragilis, and Escherichia coli. The influence of environmental factors such as water temperature, salinity, and land runoff on the occurrence of these microbes was also included in this study. Enteric viruses were found in 50 to 60% of the mussel samples, and there were no pronounced differences between the samples from the three sites. E. coli counts exceeded the limit for category A for shellfish sanitary safety in 40% of the samples from the sites situated in fjords. However, at the site in the outer archipelago, this limit was exceeded only once, in March 2001, when extremely high levels of atypical indole-negative strains of E. coli were registered at all three sites. The environmental factors influenced the occurrence of viruses and phages differently, and therefore, it was hard to find a coexistence between them. This study shows that, for risk assessment, separate modeling should be done for every specific area, with special emphasis on environmental factors such as temperature and land runoff. The present standard for human fecal contamination, E. coli, seems to be an acceptable indicator of only local sanitary contamination; it is not a reliable indicator of viral contaminants in mussels. To protect consumers and get verification of “clean” mussels, it seems necessary to analyze for viruses as well. The use of a molecular index of the human contamination of Swedish shellfish underscores the need for reference laboratories with high-technology facilities.

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Havelaar, A. H., M. van Olphen, and J. F. Schijven. "Removal and inactivation of viruses by drinking water treatment processes under full scale conditions." Water Science and Technology 31, no. 5-6 (March 1, 1995): 55–62. http://dx.doi.org/10.2166/wst.1995.0559.

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Risk-based evaluations of the hygienic quality of drinking water require accurate data on removal and inactivation of pathogens by different steps of the treatment chain. The continuing trend to reduce chemical disinfection leads to an increased interest in the effect of other processes, based on physical removal or biological inactivation. This study reports data on the removal and inactivation of entero- and reoviruses by three such processes. For comparison, data on a variety of model organisms are also reported. All studies were carried out in the winter period because the concentration of viruses is then at its maximum, and the reducing capacities of the processes are at their minima. Storage in three reservoirs in series (average detention time 7 months) reduced the concentration of enteroviruses by a factor of 400-1,000, river bank filtration was highly effective, reducing enteroviruses by a factor of at least 10,000. The effect of coagulation/flocculation/sedimentation/filtration processes was highly variable, and was better when rapid sand filtration was included. The removal of F-specific RNA bacteriophages most closely followed that of viruses in these three processes.

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von Bonsdorff, C. H., L. Maunula, R. M. Niemi, R. Rimhanen-Finne, M. L. Hänninen, and K. Lahti. "Hygienic risk assessment by monitoring pathogens in municipal sewage." Water Supply 2, no. 3 (July 1, 2002): 23–28. http://dx.doi.org/10.2166/ws.2002.0081.

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The purpose of this study was to monitor the levels of human enteric viruses and enteric protozoa and to relate their presence to the microbes used as hygienic quality indicators in domestic sewage from a small community in Finland during a period of one year. Genome-based sensitive detection methods for the pathogens selected (astro- and Norwalk-like viruses, Giardia and Cryptosporidium) have become available only recently and thus no earlier data was available. The effluent sewage is delivered into a river that serves as raw water for a larger town and the pathogens therefore constitute a health risk. The results showed that all the monitored pathogens could be detected, and that enteric viruses were present at considerable concentrations in sewage. High concentrations of astrovirus in raw sewage were observed during a diarrhea epidemic in the local day-care centre. The presence of viruses did not correlate with the monitored bacterial indicators of faecal contamination (coliforms, E. coli and enterococci) or with bacteriophages (somatic coliphages, F-specific RNA phages and B. fragilis phages). Giardia cysts and Cryptosporidium oocysts were detected from one sample (1/10) each.

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Ibarluzea, Jesús M., Belén Moreno, Elena Serrano, Karmele Larburu, María J. Maiztegi, Asunción Yarzabal, and Loreto Santa Marina. "Somatic coliphages and bacterial indicators of bathing water quality in the beaches of Gipuzkoa, Spain." Journal of Water and Health 5, no. 3 (March 1, 2007): 417–26. http://dx.doi.org/10.2166/wh.2007.037.

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Monitoring the quality of the bathing waters of Gipuzkoa (the Basque Country, Spain) makes it possible to assess the suitability of its 15 beaches for bathing throughout each season. In 1998, the parameters E. coli, somatic coliphages (SOMCPH) and F-specific RNA bacteriophages (FRNAPH) were incorporated into the bathing water quality monitoring system. This enabled the study of the link between bacterial and viral indicators as well as the analysis of the ratios between both types of indicators in waters with different levels of pollution. Although bacterial indicators (total coliforms (TC) and faecal coliforms (FC)) and enterococci showed a strong correlation between them, the correlations between the viral indicators and between the viral and bacterial indicators were weaker, though significant in all cases. The ratio between SOMCPH and E. coli indicates that at low levels of bacterial pollution (E coli <100 MPN/100 ml) SOMCPH outnumber E coli. In contrast, at higher levels of pollution (E coli >100 MPN/100 ml), SOMCPH numbers are lower than those of E-coli. The data reveal the presence of viral indicators in waters classified as suitable for bathing by the European Directive and alert us to their suitability.

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