Distribution of ribonucleic acid coliphages in south and east Asia

Advancing RNA phage biology through meta-omics

Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.

Shining Light on Human Gut Bacteriophages

The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as “viral dark matter.” Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform in silico phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.

Repeated pressurization as a potential cause of deterioration in virus removal by aged reverse osmosis membrane used in households

Reverse osmosis (RO) membrane is widely used for household water treatment in areas with limited access to safe drinking water; however, some studies documented deterioration in the quality of RO permeate. Repeated pressurization from intermittent operation in households is suspected to have an adverse effect on RO. This study aimed to evaluate virus removal by RO used in actual households as well as the water quality of permeate, and to elucidate the main cause of RO deterioration. We conducted a survey in households in Hanoi, Vietnam, to collect 27 membranes along with their usage history, where virus removal was investigated in laboratory. Of the used RO membranes, 22% did not show the protective level, >3 log₁₀ (99.9%) virus removal, recommended by World Health Organization. The differences in virus removal among Aichi virus, MS2 and φX-174 were <0.5 log₁₀. All membranes with estimated pressurization times of <4000 showed >3 log₁₀ virus removal, while 17% of membranes used for <3years, the manufacturers' warranty period, did not achieve the criterion. Therefore, virus removal performance may not be assured even if the users replace the membrane following the warranty period. Furthermore, more pressurized membranes exhibited significantly lower virus removal than less pressurized ones, suggesting a major role of repeated pressurization in the deterioration of RO. Coliforms were detected from 44% of the permeate of the point-of-use devices applying RO (RO-POU), raising concerns on the extrinsic contamination and regrowth of bacteria. Consequently, RO in households may deteriorate more rapidly than the manufactures' expectation due to repeated pressurization. RO in households should be replaced based on not only membrane age but also total pressurized times (i.e., 4000 times) to keep the protective level of virus removal. The deteriorated bacterial quality in RO permeate suggested the need for installing post-treatment, such as UV irradiation.

Metagenomic Analysis of Infectious F-Specific RNA Bacteriophage Strains in Wastewater Treatment and Disinfection Processes

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.

Occurrence of microbial indicators, pathogenic bacteria and viruses in tropical surface waters subject to contrasting land use

Fecal indicator bacteria, such as Escherichia coli (E.coli) and Enterococcus, have been widely used to indicate the presence of pathogens. However, the suitability of fecal indicator bacteria to represent health risks is still being challenged, particularly in tropical aquatic environments. The objective of this study is to understand the occurrence and prevalence of indicators and pathogens in areas with contrasting land use, as well as to identify the major correlations between indicators, pathogens and environmental parameters. The spatial and temporal variation of indicators and pathogens was studied to examine the distribution patterns for areas with different land use, and the impact of seasonal changes on microbial populations. A total of 234 water samples were sampled for two years from reservoirs and their tributaries, and tested for fecal indicator bacteria, coliphages, human specific markers, pathogenic bacteria and viruses. The prevalence of indicators and pathogens in reservoirs were generally low, while relatively high concentrations were observed in tributaries to varying degrees. Of the enteric viruses, norovirus GII was among the most prevalent and had the highest concentration. Although strong correlations were found between indicators, only relatively weak correlations were found between indicators and pathogens. The results in this study showed that none of the bacteria/phage indicators were universal predictors for pathogens. Inclusion of the alternative indicators, Methanobrevibacter smithii, Bacteroides and human polyomaviruses (HPyVs) to monitoring programs could help to determine whether the fecal source was human. The microbial distribution patterns allow the classification of sampling sites to different clusters and thus, help to identify sites which have poor water quality. This approach will be useful for water quality management to pinpoint factors that influence water quality and help to prioritize sites for restoration of water quality.

Pepper mild mottle virus as a process indicator at drinking water treatment plants employing coagulation-sedimentation, rapid sand filtration, ozonation, and biological activated carbon treatments in Japan

To assess the potential of pepper mild mottle virus (PMMoV) as a viral process indicator, its reduction through coagulation-sedimentation (CS) and rapid sand filtration (RSF) were compared with those of Escherichia coli, previously used viral indicators, and norovirus genotype II (NoV GII; enteric virus reference pathogen) in a bench-scale experiment. PMMoV log₁₀ reductions in CS (1.96 ± 0.30) and RSF (0.26 ± 0.38) were similar to those of NoV GII (1.86 ± 0.61 and 0.28 ± 0.46). PMMoV, the most abundant viruses in the raw water, was also determined during CS, RSF, and advanced treatment processes at two full-scale drinking water treatment plants under strict turbidity management over a 13-month period. PMMoV was concentrated from large-volume water samples (10-614 L) and quantified by Taqman-based quantitative polymerase chain reaction. The PMMoV log₁₀ reduction in CS (2.38 ± 0.74, n = 13 and 2.63 ± 0.76, n = 10 each for Plant A and B) and in ozonation (1.91 ± 1.18, n = 5, Plant A) greatly contributed to the overall log₁₀ reduction. Our results suggest that PMMoV can act as a useful treatment process indicator of enteric viruses and can be used to monitor the log₁₀ reduction of individual treatment processes at drinking water treatment plants due to its high and consistent copy numbers in source water.

Hyperexpansion of RNA Bacteriophage Diversity

Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.

This study uses computational metagenomics and molecular experimentation to massively expand the known genomic and ecological diversity of RNA bacteriophages, identifying novel tropisms and genes.

Bacteriophages (viruses that infect bacteria) can alter biological processes in numerous ecosystems. While there are numerous studies describing the role of bacteriophages with DNA genomes in these processes, the role of bacteriophages with RNA genomes (RNA bacteriophages) is poorly understood. This gap in knowledge is in part because of the limited diversity of known RNA bacteriophages. Here, we begin to address the question by identifying 122 novel RNA bacteriophage partial genome sequences present in metagenomic datasets that are highly divergent from each other and previously described RNA bacteriophages. Additionally, many of these sequences contained novel properties, including novel genes, segmentation, and host range, expanding the frontiers of RNA bacteriophage genomics, evolution, and tropism. These novel RNA bacteriophage sequences were globally distributed from numerous ecological niches, including animal-associated and environmental habitats. These findings will facilitate our understanding of the role of the RNA bacteriophage in microbial communities. Furthermore, there are likely many more unrecognized RNA bacteriophages that remain to be discovered.

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

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

Analysis of Six New Genes Encoding Lysis Proteins and Coat Proteins inEscherichia coliGroup A RNA Phages

Group A RNA phages consist of four genes-maturation protein, coat protein, lysis protein and replicase genes. We analyzed six plasmids containing lysis protein genes and coat protein genes of Escherichia coli group A RNA phages and compared their amino acid sequences with the known proteins of E. coli(group A), Pseudomonas aeruginosa(PP7) RNA phages and Rg-lysis protein from Qbeta phage. The size of lysis proteins was different by the groups but the coat proteins were almost the same size among phages. The phylogenetic analysis shows that the sub-groups A-I and A-II of E. coli RNA phages were clearly dispersed into two clusters.

Rethinking the evolution of single-stranded RNA (ssRNA) bacteriophages based on genomic sequences and characterizations of two R-plasmid-dependent ssRNA phages, C-1 and Hgal1

We have sequenced and characterized two R-plasmid-dependent single-stranded RNA bacteriophages (RPD ssRNA phages), C-1 and Hagl1. Phage C-1 requires a conjugative plasmid of the IncC group, while Hgal1 requires the IncH group. Both the adsorption rate constants and one-step growth curves are determined for both phages. We also empirically confirmed the lysis function of the predicted lysis genes. Genomic sequencing and phylogenetic analyses showed that both phages belong to the Levivirus group and are most closely related to another IncP-plasmid-dependent ssRNA phage, PRR1. Furthermore, our result strongly suggests that the stereotypical bauplans of genome organization found in Levivirus and Allolevivirus predate phage specialization for conjugative plasmids, suggesting that the utilization of conjugative plasmids for cell attachment and entry comprises independent evolutionary events for these two main clades of ssRNA phages. Our result is also consistent with findings of a previous study, making the Levivirus-like genome organization ancestral and the Allolevivirus-like genome derived. To obtain a deeper insight into the evolution of ssRNA phages, more phages specializing for various conjugative plasmids and infecting different bacterial species would be needed.

Ecological basis for rational phage therapy

Understanding the mutual interactions of bacterial and phage populations in the environment of a human or animal body is essential in any attempt to influence these complex processes, particularly for rational phage therapy. Current knowledge on the impact of naturally occurring bacteriophages on the populations of their host bacteria, and their role in the homeostasis maintenance of a macro host, is still sketchy. The existing data suggest that different mechanisms stabilize phage-bacteria coexistence in different animal species or different body sites. The defining set of parameters governing phage infection includes specific physical, chemical, and biological conditions, such as pH, nutrient densities, host prevalence, relation to mucosa and other surfaces, the presence of phage inhibiting substances, etc. Phage therapy is also an ecological process that always implies three components that form a complex pattern of interactions: populations of the pathogen, the bacteriophages used as antibacterial agents, and the macroorganism. We present a review of contemporary data on natural bacteriophages occuring in human- and animal-body associated microbial communities, and analyze ecological and physiological considerations that determine the success of phage therapy in mammals.

Molecular characterization of bacteriophages for microbial source tracking in Korea

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

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.

The bacteriophages in human- and animal body-associated microbial communities

Felix d'Herelle first demonstrated, about 90 years ago, the presence of bacteriophages in human and animal body microbiota. Our comprehension of the impact of naturally occurring bacteriophages on symbiotic bacteria, and of their role in general homeostasis of macro-organism, nevertheless remains quite fragmentary. Analysis of data in various human- and animal body-associated microbial systems on phage occurrence, diversity, host specificity and dynamics, as well as host occurrence, specificity and dynamics, suggests that mechanisms which stabilize phage-bacteria coexistence are not identical for either different species or different body sites. Regulation by phage infection instead probably depends on specific physical, chemical and biological conditions, e.g. pH, nutrient densities, host prevalence, relation to mucosa and other surfaces and presence of phage inhibiting substances. In some animal species intestinal bacteriophages thus appear to exert significant selective pressure over at least some resident bacterial populations, resulting in phages playing important roles in the self-regulation of these microbial systems while at the same time contributing to maintenance of bacterial diversity (i.e. 'killing the winner'). Emerging data additionally suggest that bacteriophage particles could play roles in regulating the immune reactions of the macro-organism. Alternatively, for many systems links between phages and community characteristics have not been established.

Simple and rapid F+ coliphage culture, latex agglutination, and typing assay to detect and source track fecal contamination

Simple, rapid, and reliable fecal indicator tests are needed to better monitor and manage ambient waters and treated waters and wastes. Antibody-coated polymeric bead agglutination assays can fulfill these needs and are inexpensive and portable for nonlaboratory settings, and their reagents can be stored at ambient temperatures for months. The goal of this study was to develop, optimize, and validate a rapid microbial water quality monitoring assay using F+ coliphage culture, latex agglutination, and typing (CLAT) to detect F+ coliphage groups with antibody-coated particles. Rapid (180 min) F+ coliphage culture gave comparable results to those with the 16- to 24-h culture time used in EPA method 1601 and was amenable to CLAT assay detection. CLAT was performed on a cardboard card by mixing a drop of coliphage enrichment culture with a drop of antibody-coated polymeric beads as the detection reagent. Visual agglutination or clumping of positive samples occurred in <60 seconds. The CLAT assay had sensitivities of 96.4% (185/192 samples) and 98.2% (161/164 samples) and specificities of 100% (34/34 samples) and 97.7% (129/132 samples) for F+ RNA and DNA coliphages, respectively. CLAT successfully classified F+ RNA coliphages into serogroups typically obtained from human (groups II and III) and animal (groups I and IV) fecal sources, in similar proportions to those obtained with a nucleic acid hybridization assay. This novel group-specific antibody-based particle agglutination technique for rapid and simple detection and grouping of F+ coliphages provides a new and improved tool for monitoring the microbiological quality of drinking, recreational, shellfishing, and other waters.

Sequence variation among group III F-specific RNA coliphages from water samples and swine lagoons

Typing of F-specific RNA (FRNA) coliphages has been proposed as a useful method for distinguishing human from animal fecal contamination in environmental samples. Group II and III FRNA coliphages are generally associated with human wastes, but several exceptions have been noted. In the present study, we have genotyped and partially sequenced group III FRNA coliphage field isolates from swine lagoons in North Carolina (NC) and South Carolina (SC), along with isolates from surface waters and municipal wastewaters. Phylogenetic analysis of a region of the 5' end of the maturation protein gene revealed two genetically different group III FRNA subclusters with 36.6% sequence variation. The SC swine lagoon isolates were more closely related to group III prototype virus M11, whereas the isolates from a swine lagoon in NC, surface waters, and wastewaters grouped with prototype virus Q-beta. These results suggest that refining phage genotyping systems to discriminate M11-like phages from Q-beta-like phages would not necessarily provide greater discriminatory power in distinguishing human from animal sources of pollution. Within the group III subclusters, nucleotide sequence diversity ranged from 0% to 6.9% for M11-like strains and from 0% to 8.7% for Q-beta-like strains. It is demonstrated here that nucleotide sequencing of closely related FRNA strains can be used to help track sources of contamination in surface waters. A similar use of phage genomic sequence information to track fecal pollution promises more reliable results than phage typing by nucleic acid hybridization and may hold more potential for field applications.

Conservation of phage reference materials and water samples containing bacteriophages of enteric bacteria

The survival was determined in different conservation conditions of: somatic coliphages, F-specific RNA bacteriophages and phages infecting Bacteroides fragilis proposed as model micro-organisms for water quality control. Titres of phages of all groups either in pure culture phage suspensions or in naturally occurring phage suspensions were stable at (-70+/-10) degrees C and at (-20+/-5) degrees C when protected with glycerol. Moreover, phage analysis of stored suspensions demonstrated that their numbers were homogeneous, both between vials and within vials, and consequently they can be used as reference materials. Furthermore, changes in the storage temperature of the vials cause unpredictable changes in the numbers of bacteriophages. Consequently, phage reference materials and samples containing a quantitative number of phages must be maintained and dispatched at a constant temperature. Consequently, the results indicate that bacteriophages should be packed in dry ice during transport and storage. Finally, the number of phages in water samples stored at (5+/-3) degrees C in the dark does not decrease significantly during the first 72 h of storage. In addition, phage concentrates from natural samples obtained by adsorption-elution to cellulose nitrate filters and mixed with 10% glycerol were stable at least for 2 months at (-70+/-10) degrees C and at (-20+/-5) degrees C.

Comparative resistance of phage isolates of four genotypes of f-specific RNA bacteriophages to various inactivation processes

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.

Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain

AIMS

To assess whether the distribution of genotypes of F-specific RNA bacteriophages reflects faecal pollution of human and animal origin in water environments.

METHODS AND RESULTS

Stool samples, animal feedlot waste slurries and a wide variety of faecally polluted waters were studied in South Africa and Spain. Genotyping was performed by plaque and spot hybridization with genotype-specific probes. Only genotypes II and III were detected in human stool. Animal faeces contained predominantly, but not exclusively, genotypes I and IV. Raw hospital and municipal sewage contained mostly genotypes II and III, whereas genotypes I and II prevailed in settled sewage, secondary treated sewage and non-point diffuse effluents from developing communities. Abattoir wastewaters contained mostly genotypes I and IV. No differences were observed between the distribution of genotypes in Spain and South Africa.

CONCLUSIONS

Although the association of genotypes II and III with human excreta and I and IV with animal excreta was statistically significant, the results suggest that the association cannot be used for absolute distinction between faecal pollution of human and animal origin.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study contributes greatly to understanding the usefulness of genotypes of F-specific RNA bacteriophages in source tracking of faecal wastes.

Enteric bacteriophages as potential fecal indicators in ground beef and poultry meat

Recovery efficiencies of enteric bacteriophages (F+ RNA coliphages, somatic coliphages, and Salmonella phages) as alternative fecal indicators were determined from ground beef and chicken breast meat using amino acid eluants (glycine and threonine) and a complex eluant (3% beef extract). Levels of F+ RNA coliphages (MS2, GA, Qbeta, FI, and SP), the somatic coliphage phiX174, and three environmental isolates of Salmonella phages (isolated from raw sewage) were assayed using three respective hosts: Escherichia coli Famp, E. coli C, and Salmonella Typhimurium. When 8% polyethylene glycol and 0.1 M NaCl were used to precipitate bacteriophages eluted with five different eluants, the highest recoveries of the three phage groups were with 0.5 M threonine and 0.25 M glycine-threonine. The average recoveries of F+ RNA coliphages, somatic coliphages, and the Salmonella phages from ground beef and chicken meat were 100, 69, and 65%, respectively, with threonine (0.5 M, pH 9.0) as the eluate. Of eight market food samples tested, F+ RNA coliphages were detected in five (63%) and somatic coliphages were detected in seven (88%). The overall detection sensitivity of the method was 3 PFU/100 g of ground beef or chicken meat. Levels of bacteriophages and bacterial indicators on chicken carcass surfaces were determined at identified critical control points at a poultry plant. Through the processing steps of evisceration, washing, and chilling, the levels of F+ RNA coliphages and fecal coliforms were reduced by 1.6 and 1.9 log10 PFU or CFU/100 g, respectively. F+ RNA coliphages and perhaps other enteric bacteriophages may be effective candidate indicators for monitoring the microbiological quality of meat, poultry, and perhaps other foods during processing. The bacteriophage concentration method developed provides a simple, rapid, and practical tool for the evaluation of fecal contamination levels in ground beef and processed chicken meat.

Comparison of methods for detecting genotypes of F-specific RNA bacteriophages and fingerprinting the origin of faecal pollution in water samples

The performance of Salmonella typhimurium WG49 and Escherichia coli HS(pFamp)R was compared on detecting the different genotypes of F-specific RNA bacteriophages by plaque hybridisation. The sensitivity of this assay was also compared with the sensitivity of RT-PCR followed by Southern blotting for detecting F-specific RNA bacteriophages belonging to genotype III in water. S. typhimurium WG49 detected slightly higher numbers of F-specific RNA bacteriophages than E. coli HS(pFamp)R both in mixtures of pure culture bacteriophage suspensions and in water samples. There were no differences between the two host strains with regard to detection of the four genotypes of F-specific RNA phages both in mixtures of pure culture bacteriophage suspensions and in environmental samples. In urban sewage samples, the host strains detected genotypes II and III as the predominant F-RNA bacteriophages. Plaque transfer to a N(+) hybond membrane and posterior hybridisation was easier using S. thyphimurium WG49 as the host strain. The efficiency of detection in sewage of genotype III F-specific RNA bacteriophages by RT-PCR was inferior to that of plaque hybridisation with the assay conditions described below. Hybridisation of plaques obtained on WG49 seems to be the most sensitive method to study the distribution of genotypes of F-specific RNA bacteriophages in water samples.

Genotyping male-specific RNA coliphages by hybridization with oligonucleotide probes

F-specific (F+) RNA coliphages are prevalent in sewage and other fecal wastes of humans and animals. There are four antigenically distinct serogroups of F+ RNA coliphages, and those predominating in humans (groups II and III) differ from those predominating in animals (groups I and IV). Hence, it may be possible to distinguish between human and animal wastes by serotyping F+ RNA coliphage isolates. Because serotyping is laborious and requires scarce antiserum reagents, we investigated genotyping using synthetic oligonucleotide probes as an alternative approach to distinguishing the four groups of F+ RNA coliphages. Oligoprobes I, II, III, IV, A, and B were selected to detect group I, II, III, IV, I plus II, and III plus IV phages, respectively. Methods for phage transfer from zones of lysis on a host cell lawn to candidate membrane filters and fixation of genomic nucleic acid on the membranes were optimized. The oligoprobes, which were end labeled with digoxigenin, were applied in DNA-RNA hybridization, and hybrids were observed by colorimetric, immunoenzymatic detection. Of 203 isolates of F+ RNA coliphages from environmental samples of water, wastes, and shellfish, 99.5 and 96.6% could be classified into each group by serotyping and genotyping, respectively. Probes A and B correctly identified 100% of the isolates. On the basis of these results, this method for genotyping F+ RNA coliphages appears to be practical and reliable for typing isolates in field samples.

Bacteriophages for incompatibility group H plasmids: morphological and growth characteristics

Two independently isolated temperature-sensitive bacteriophage that are specific for enterobacterial hosts harboring HI and HII plasmids were characterized to determine if any identifiable differences existed between them. The traits examined included adsorption pattern of phage to H pili, bacteriophage size, sensitivity to chloroform, RNA strandedness, reaction with F-specific antiphage serum, virion protein pattern, temperature range of lytic ability, and plaque morphology. No differences between the phages were observed for any of the features analyzed. Ecological questions on the origin and maintenance of temperature-sensitive phages are discussed.

Complete nucleotide sequence of the group I RNA bacteriophage fr

We report the complete nucleotide sequence of the group I RNA bacteriophage fr. The entire genome consists of 3575 nucleotides, six nucleotides more than the only other sequenced group I representative, MS2. The greatest divergence between these phages occurs in the 5' terminal region of the A gene, while the lysis-replicase gene overlap, the coat gene and the central region of the replicase gene are highly conserved. Overall sequence homology between fr and MS2 is 77%. Here, we present a general comparison between the two phages. In the accompanying paper we use phylogenetic sequence comparison between MS2 and fr to deduce the secondary structure at the 3' untranslated region.

F-specific RNA bacteriophages and sensitive host strains in faeces and wastewater of human and animal origin

Faeces of humans, pigs, cattle and chickens were investigated for the presence of somatic coliphages, F-specific bacteriophages and Escherichia coli strains sensitive to infection by F-specific phages. Attention was given to the possible effect of age and use of antibiotics on the prevalence of the FRNA phages and sensitive E. coli strains. Somatic coliphages were often detected in high numbers in all types of faeces. In contrast, FRNA phages were rarely detected in faeces from humans and cattle but more often in faeces from pigs and adult chickens. Samples from young chickens (with or without antibiotics) were consistently positive for FRNA phages (up to 3 x 10(6) pfu/g). F-specific RNA phages were found in substantial numbers (greater than 10(3) pfu/ml) in a variety of wastewaters: domestic, hospital, slaughterhouses and occasionally in 'grey water'. Their origin in wastewater was not clear. Strains from faeces usually belonged to serogroups I and IV. These types were also found in wastewater, as were group II and III strains. Serogroup II phages were abundant in wastewater of human origin but rare in faeces. Escherichia coli strains sensitive to infection by F-specific phages were common in faeces (overall 290/1081: 27%). No strains with fully depressed F-pilus synthesis were detected among the sensitive strains. It is concluded that the occurrence of F-specific RNA bacteriophages in water points to sewage pollution rather than faecal pollution; the mechanism of replication of these organisms in wastewater is not understood.

Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP

We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through protein contains 330 amino acids and the replicase beta-subunit contains 575 amino acids. SP is 59 nucleotides longer than Q beta. We have analyzed both sequence and structural conservation between SP and Q beta and shown that the sequences for the coat and central region of the replicase are strongly conserved between the two genomes. We also show that the S and M replicase binding sites of Q beta are strongly conserved in SP. Interestingly, the base composition of SP and Q beta differ significantly from one another, and most of the differences can be accounted for by a strong preponderance of U in the third position of each codon of Q beta relative to SP. We also compare conserved hairpins associated with potential coat protein and replicase binding sites.

Bacteriophages and indicator bacteria in human and animal faeces

In an attempt to explain the presence of F-specific (RNA) bacteriophages in waste-water, faecal material from humans and a variety of animals was examined. The phages were detected in appreciable numbers only in faeces from pigs, broiler chickens, sheep and calves but not from dogs, cows, horses and humans. Parallel examinations for somatic coliphages, thermotolerant coliforms, faecal streptococci and spores of sulphite-reducing clostridia revealed the consistent presence of these organisms in all types of samples, albeit in variable numbers. The number of F-specific bacteriophages was related to the total number of somatic coliphages, but phage counts were unrelated to bacterial counts. F-specific RNA phages were grouped by serotyping and all animal isolates were found to belong to either group I (MS2 subtype) or IV (four different subtypes). Among the group IV isolates, most belonged to well-known subtypes SP (24 isolates) or FI (18 isolates) but five isolates were related to phage ID2 and one isolate was a new subtype. In contrast with animal isolates, 19 isolates from hospital wastewater belonged to serogroups II or III.

Distribution of RNA coliphages in Senegal, Ghana, and Madagascar

The distribution patterns of RNA coliphages (phages) in Senegal, Ghana, and Madagascar were investigated by collecting sewage samples from domestic drainage in November, 1980. In Senegal, among 65 sewage samples collected mainly from Dakar and its vicinity, 14 (22%) contained RNA phages (16 strains). By serological analysis, 13 of 16 strains were found to belong to group III. This is consistent with the distribution pattern of RNA coliphages in tropical and subtropical regions of Asia. In Ghana, however, among 106 samples collected from Accra, Suhum, and their vicinities, only seven (7%) contained RNA phages (seven strains) (groups I, II, and III [1:3:3]). In Madagascar, among 124 samples collected from Antananarivo, Moramanga, and their vicinities, seven (6%) contained RNA phages (seven strains) (groups I, II, III, and IV [1:1:1:4]). In spite of the low isolation frequency, it can be said that Madagascar appears to have a unique distribution pattern (abundance of group IV phages) which differs from that of any other countries we have examined. The generality of the distribution pattern of RNA phages in the tropical region (abundance of group III phages) was thus verified at least in Senegal.

Distribution of ribonucleic acid coliphages in raw sewage from treatment plants in Japan

To determine the transmission cycle of ribonucleic acid (RNA) coliphages in their natural habitats, we investigated the distribution patterns of RNA phages in raw sewage collected from treatment plants in various localities in Japan. Most of the sewage samples contained group II and III phages. Samples from treatment plants in Sapporo, Tokyo, and Toyama contained appreciable amounts of group I phages in addition to the group II and III phages. As a whole, raw sewage from treatment plants in Japan contained RNA phages of the three groups in the ratio 1:2:5, group I/II/III. Based on the distribution patterns of RNA phages in sewage from domestic drainage in Japan proper (group II/III, 3:1), in animal feces and sewage from slaughter houses (mostly group I), and in human feces (group II/III, 1:1), it can be reasonably said that group I phages tend to be introduced from animal sources and group II and III phages tend to be introduced from human sources. Raw sewage from treatment plants in Japan consists mainly of human feces, sewage from domestic drainage, and industrial wastewater, and, in part, from slaughter houses. In fact, sewage from slaughter houses together with that from human sources flowed into the treatment plants of Tokyo as far as we could confirm.

Distribution of ribonucleic acid coliphages in Korea

To determine the geographical distribution of ribonucleic acid (RNA) coliphages in Korea, we collected sewage samples from domestic drainage in densely populated urban areas in July through August, 1979. Of 132 samples, 74 (56%) contained RNA phages (106 strains). They were classified into groups I, II and III (4:47:55) by serological analysis. Based on previous data for Japan (groups II and III [3:11]) and Southeast Asia (mostly group III), the distribution pattern of RNA phages in Korea was of an intermediate type between those of Japan and Southeast Asia.

Distribution of ribonucleic acid coliphages in animals

To determine the distribution pattern of ribonucleic acid (RNA) coliphages (classified by serological groups I through IV) in animal sources, we isolated RNA phages from (i) feces samples from domestic animals (cows, pigs, horses, and fowls), some other animals in a zoological garden, and humans, (ii) the gastrointestinal contents of cows and pigs, and (iii) sewage samples from treatment plants in slaughter houses. These samples were then analyzed serologically. The concentration of RNA phages in the first and second kinds of material was fairly low (10 to 10(3) plaque-forming units per original phage sample), whereas that in the third kind of material was fairly high (10(3) to 10(5) plaque-forming units per original phage sample). Concerning the group types of the RNA phages in the first and second kinds of material, human feces contained RNA phages of groups II and III almost equally, the gastrointestinal contents of pigs included those of groups I and II equally, and the feces or gastrointestinal contents of other mammals other than humans and pigs had those of group I exclusively. In the third type of material we found mostly group I phages with a minor fraction of group II phages. Thus, the prominent features of the distribution pattern of RNA phages are the predominance of groups III and II in humans and the predominance of group I in animals.

Recovery of coliphages from wastewater effluents and polluted lake water by the magnetite-organic flocculation method

A magnetite-organic flocculation method was developed for the concentration of coliphages from wastewater effluents and polluted lake water. A high percent (68 to 100%) recovery of coliphages from sewage effluents was achieved by this procedure. Coliphage recovery from Lake Alice, a sewage-contaminated lake, showed phage concentrations ranging from 2.3 X 10(2) to 1.9 X 10(3) plaque-forming units per liter. This method is simple and inexpensive and may be carried out under field conditions.

Concentration of coliphages from large volumes of water and wastewater

Membrane filter adsorption-elution technology has been extensively used for the concentration and detection of animal viruses from large volumes of water. This study describes the development of positively charged microporous filters (Zeta Plus) for the concentration of coliphages from large volumes of water and wastewater. Four different coliphages were studied: MS-2, phi X174, T2, and T4. Positively charged microporous filters were found to efficiently adsorb these coliphages from tap water, sewage, and lake water at neutral pH. Adsorbed viruses were eluted with a 1:1 mixture of 8% beef extract and 1 M sodium chloride at pH 9. Using this method, coliphages could be concentrated from 17-liter volumes of tap water with recoveries ranging from 34 to 100%. Coliphages occurring naturally in raw and secondarily treated sewage were recovered with average efficiencies of 56.5 and 55.0%, respectively. This method should be useful in isolation of rare phages, the ecology of phages in natural waters, and the evaluation of water quality.

Continuous survey of the distribution of RNA coliphages in Japan

In order to demonstrate the stability and continuity of RNA coliphages (phages) in their natural habitats, we investigated the amount and group types of RNA phages in sewage samples collected continuously from domestic drainage in Japan proper and islands in the seas adjacent to Japan (abbreviated simply as islands, hereafter) over a 5-yr period from 1973 to 1977. It was found that the frequencies of isolation of RNA phages were fairly high and constant. The group types of RNA phages isolated were also stable in the three cities. Choshi, Niigata, and Toyama in Japan proper. The average for the three cities was group II:III = 3:1. The investigation in islands revealed that the frequencies of isolation of RNA phages were fairly high as in the case of the above three cities in Japan proper and the group types of RNA phages isolated were also stable. That is to say, group II phages were predominant on Rishiri Island, Rebun I., Iki I., and Tsushima I., which are located relatively near to mainland Japan, while group III phages were predominant on Amamiohshima I., mainland Okinawa, Ishigakijima I., and Iriomotejima I., which are located south of Kyushu. It can thus be said that the RNA phages in the domestic drainage of Japan proper and islands remained more or less stable over at least the 5-yr period, and an apparent difference in the geographical distribution of RNA phages in Japan exists between Kyushu and Amamiohshima I.

Propagation of ribonucleic acid coliphages in gnotobiotic mice

To clarify the propagation cycle of bacteriophages in their natural habitats, we tested whether animals could support ribonucleic acid (RNA) phage propagation in their intestines, using germfree mice as the test animal. Propagation of four different antigenic types of RNA phages was tested. No detectable propagation or colonization of RNA phages was observed either in germfree mice or in gnotobiotic mice infected with the F- strain of Escherichia coli. Propagation or colonization was observed when RNA phages were orally introduced into gnotobiotic mice harboring the F+ or F' strain of E. coli. These results were consistent with data for in vitro propagation experiments. Fecal titers of phages were monitored over 24 to 98 days and were found to vary from 10(5) to 10(11) plaque-forming units per g of feces. Streptomycin administration gradually led to the disappearance of bacteria and, concomitantly, the RNA phages. Phages recovered from gnotobiotic mice feces included some of novel antigenic types. The bacterial isolates recovered from gnotobiotic mice harboring F+ bacteria included the original F+ strain, strains which had become F-, and some which had become inefficient hosts for the propagation of RNA phages.