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PubMed1992

Biological and biophysical characteristics of phages isolated from Clostridium botulinum type C and D strains, and physicochemical properties of the phage DNAs.

Toxin-converting phages CE beta and d-16 phi and non-converting phages CE gamma and d-1', isolated from toxigenic strains C-468 and D-CB16 of Clostridium botulinum types C and D, respectively, were characterized biologically and biophysically. DNAs isolated from these four phages were studied physicochemically. Phages CE beta, d-16 phi, CE gamma and d-1' were adsorbed to their susceptible cells at the constant rates of 1.1 x 10(-8), 3.3 x 10(-8), 1.4 x 10(-8) and 1.4 x 10(-8) ml/min, and grew after latent periods of 35, 45, 35 and 35 min at the burst sizes of 38, 85, 35 and 35, respectively. Converting phages were more susceptible than non-converting phages to physical and chemical treatments such as temperature, pH, time, UV-irradiation and organic solvents. GC% of phage DNAs were determined by melting temperature, buoyant density and HPLC analysis to be 26, 26, 29 and 29% for CE beta, d-16 phi, CE gamma and d-1' phage DNAs, respectively. The restriction digestion profiles of phage DNAs with seven endonucleases were compared by agarose gel electrophoresis, revealing that the two converting phage DNAs were similar in regard to five enzyme digestion profiles, but different in the other two enzymatic profiles. Non-converting phage DNAs produced the same restriction digestion profiles with all seven endonucleases. The molecular sizes determined from the size of restriction enzyme digestion fragments were about 110 kb for converting phage CE beta and d-16 phi DNAs and 65 kb for non-converting phage CE gamma and d-1' DNAs. Dot blot hybridization experiments revealed that DNA homology between the converting phages CE beta and d-16 phi was 50-75%, while that between non-converting phages CE gamma and d-1' was about 100%. Converting phage and non-converting phage DNAs did not hybridize at all.

Adsorption↗
PubMed2025

Exploring phage-host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics.

Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage-host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.IMPORTANCEBurkholderia cepacia complex bacteria are opportunistic pathogens inherently resistant to antibiotics, and phage therapy is a promising alternative treatment for chronically infected patients. Burkholderia bacteria are also ubiquitous in soil microbiomes. To develop improved phage therapies for pathogenic Burkholderia bacteria, or engineer phages for applications, such as microbiome editing, it's essential to know the bacterial host factors required by the phage to kill bacteria, as well as how the bacteria prevent phage infection. This work identified 65 genes involved in phage-host interactions in Burkholderia cenocepacia K56-2 and tracked their expression during infection. These findings establish a knowledge base to select and engineer phages infecting or transducing Burkholderia bacteria.

Bacteriophages↗
PubMed1976

[New lambdoid phages of Escherichia coli. II. Comparison of several genetic characteristics with lambda phages].

Functions of some newly isolated lambdoid phages and phage lambda genes were compared by their ability to interact with unrelated phages and the product of the bacterial gene gro P. 19 of 23 lambdoid phages studied interfere with prophage P2, that points out the presence of functionally active genes, essential for spi+ phenotype in their genomes. The development of 4 lambdoid phages with spi- phenotype is independent on the prophage P2 presence. Most of lambdoid phages show the reduced growth ability on the C600 groP- bacterial lawn. This indicates that they have a function similar to the gene P of phage lambda. The development of phage phi M417 in bacterial mutants groP- is not disturbed, which indicates that the gene P of phage phi M417 is different from that of the phage lambda. Newly isolated phages, that are homoimmune to phage lambda, restrict the development of T4 rII phage. The rest lambdoid phages have no rex function. The growth efficiency of lampodid phages on E. coli C cells, carrying Eco R1 plasmid, varies from 10(-6) to 10(-8) that presumbaly indicates on different amounts of restionci strites in DNA of these phages.

Coliphages↗
PubMed2002

Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages.

The complete genomic sequence of the Lactococcus lactis virulent phage ul36 belonging to P335 lactococcal phage species was determined and analyzed. The genomic sequence of this lactococcal phage contained 36,798 bp with an overall G+C content of 35.8 mol %. Fifty-nine open reading frames (ORFs) of more than 40 codons were found. N-terminal sequencing of phage structural proteins as well as bioinformatic analysis led to the attribution of a function to 24 ORFs (41%). A lysogeny module was found within the genome of this virulent phage. The putative integrase gene seems to be the product of a horizontal transfer because it is more closely related to Streptococcus pyogenes phages than it is to L. lactis phages. Comparative genome analysis with six complete genomes of temperate P335-like phages confirmed the heterogeneity among phages of P335 species. A dUTPase gene is the only conserved gene among all P335 phages analyzed as well as the phage BK5-T. A genetic relationship between P335 phages and the phage-type of the BK5-T species was established. Thus, we proposed that phage BK5-T be included within the P335 species and thereby reducing the number of lactococcal phage species to 11.

Bacteriophages↗
PubMed2002

Evaluation of the international phage typing set and some experimental phages for typing of Listeria monocytogenes from poultry in Spain.

AIMS: The validity of the international phage set and 13 experimental phages for subtyping Listeria monocytogenes strains isolated from poultry in Spain was investigated. METHODS AND RESULTS: Ninety-six L. monocytogenes strains (52 from serogroup 1/2 and 44 from serogroup 4) were phage-typed using the international phage set, 10 experimental phages for typing serogroup 1/2 strains (seven isolated in France: 1313, 9425, 1807, 351, 881, 717 and 586-, and three from Denmark: 5775, 12682 and 6223-) and three experimental phages isolated in France for typing serogroup 4 strains (2425 A, 4286 and 197). Percentages of serogroup 1/2, serogroup 4 and total phage-typeable strains were 57.7%, 52.3% and 55.2%, respectively. Important differences in the behaviour of the phages tested were found. The typeability rate, the specificity index and the percentage of strong reactions were greater in the phages of international set than in the experimental phages. The number of phage typeable strains and the number of phage types (42) were not modified by the use of experimental phages. CONCLUSIONS: The phage set used was not effective for typing L. monocytogenes strains from poultry in Spain, because a low typeability rate was found. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggest the importance of the availability of new phages specific to a geographical area in order to improve the typeability of the system.

Abattoirs↗
PubMed2005

Human volunteers receiving Escherichia coli phage T4 orally: a safety test of phage therapy.

Fifteen healthy adult volunteers received in their drinking water a lower Escherichia coli phage T4 dose (10(3) PFU/ml), a higher phage dose (10(5) PFU/ml), and placebo. Fecal coliphage was detected in a dose-dependent way in volunteers orally exposed to phage. All volunteers receiving the higher phage dose showed fecal phage 1 day after exposure; this prevalence was only 50% in subjects receiving the lower phage dose. No fecal phage was detectable a week after a 2-day course of oral phage application. Oral phage application did not cause a decrease in total fecal E. coli counts. In addition, no substantial phage T4 replication on the commensal E. coli population was observed. No adverse events related to phage application were reported. Serum transaminase levels remained in the normal range, and neither T4 phage nor T4-specific antibodies were observed in the serum of the subjects at the end of the study. This is, to our knowledge, the first safety test in the recent English literature which has measured the bioavailability of oral phage in humans and is thus a first step to the rational evaluation of phage therapy for diarrheal diseases.

Administration, Oral↗
PubMed2002

The Phage Proteomic Tree: a genome-based taxonomy for phage.

There are approximately 10(31) phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the "Phage Proteomic Tree," which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.

Bacteriophages↗
PubMed2025

Filamentous cheater phages drive bacterial and phage populations to lower fitness.

Many bacteria carry phage genome(s) in their chromosome, which intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages called Pf that establish chronic infections and do not require host lysis to spread. However, spontaneous mutations in the Pf repressor gene (pf5r) can allow extreme phage production that slows bacterial growth and increases cell death, violating an apparent détente between bacterium and phage. We observed this paradoxical outcome in an evolution experiment with P. aeruginosa in media simulating nutrients from the cystic fibrosis airway. Bacteria containing pf5r mutant phage grow to a lower density but directly outcompete their ancestor and convert them into pf5r mutants via phage superinfection. Reduced fitness therefore spreads throughout the bacterial population, driven by weaponized Pf. Yet high intracellular phage replication facilitates another evolutionary conflict: "cheater miniphages" lacking capsid genes and the superinfection exclusion gene (pfsE) invade populations of full-length phages within cells. Although bacteria containing both full-length phages and miniphages are most immune to superinfection by limiting the Pf receptor, this hybrid vigor is extremely unstable, as a classic Tragedy of the Commons scenario ensues that causes complete prophage loss. The entire cycle - from phage hyperactivation to miniphage invasion to prophage loss - can occur within 24h, showcasing rapid coevolution between bacteria and their filamentous phages. This study demonstrates that P. aeruginosa, and potentially many other bacterial species that carry filamentous prophages, risk being exploited by these phages in a runaway process that reduces fitness of both host and virus.

Inoviridae↗
PubMedDate not supplied

The comparative virulence for chicks of Salmonella enteritidis phage type 4 isolates and isolates of phage types commonly found in poultry in the United States.

Phage type 4 Salmonella enteritidis has been associated with morbidity and mortality in broiler chickens in the United Kingdom. The recent isolation of this phage type from poultry in the United States has raised concerns about whether the current regulatory approach to S. enteritidis should be modified to consider phage type 4 differently from other phage types. The present study assessed and compared the virulence of phage type 4 S. enteritidis isolates, S. enteritidis isolates of other phage types, and an S. pullorum isolate in both single-comb white leghorn and white Plymouth Rock chicks. The mean incidence of severe illness or death following oral inoculation with phage type 4 S. enteritidis was significantly lower than the incidence associated with S. pullorum inoculation in both lines of chicks. Nevertheless, some individual phage type 4 S. enteritidis isolates caused severe effects at a frequency similar to that of S. pullorum in single-comb white leghorn chicks. In general, severe morbidity or mortality following infection with S. enteritidis isolates of all phage types tested occurred more often in single-comb white leghorn chicks than in white Plymouth Rock chicks. The mean frequency at which chicks were severely affected following inoculation with phage type 4 isolates was significantly higher than the mean for isolates of other phage types. However, in both lines of chicks, some significant differences in virulence were apparent within the set of phage type 4 strains tested. The observed virulence for chicks of recent U.S. poultry isolates of phage type 4 S. enteritidis was similar to that of earlier isolates from various sources, including poultry isolates from the United Kingdom.

Animals↗
PubMed2004

Models of phage growth and their applicability to phage therapy.

Phage therapy is complicated by the self-replicating nature of phage. It is difficult to extrapolate from in vitro phage growth data to in vivo expectations, difficult to interpret in vivo data and difficult to generalize from one in vivo situation to another. Various generic models of phage growth have been used as the theoretical basis for understanding the kinetics of phage therapy. Here, we have experimentally tested the efficacy of such simple models to predict, qualitatively and quantitatively, the growth of phage and the phage proliferation threshold in vitro. Naturally occurring, antibiotic-resistant bacteria were used to measure the growth of phage in vivo. In homogenous, in vitro environments, the models were predictive of T4 phage growth on Escherichia coli RR1. However, the models were not able to predict growth of T4 phage or K1-5 phage in the more complex environment of the rat's digestive tract. To explore fully the kinetics of phage therapy, more complex models need to be devised. We suggest that it may be necessary to consider and model the interactions between phage growth parameters and bacterial growth parameters.

Animals↗
PubMed1976

[New lambdoid Escherichia coli phages. I. Isolation, group immunity and recombination with lambda phage].

550 bacterial strains were isolated from sewage. 69 of them were lysogenic by phages active on Escherichia coli. The phages were divided into two groups on the basis of UV-inducibility, the ability to form plaques on Rep-E. coli mutants and particle morphology: lambdoid (23 phages) and related to P2 (46 phages). Hybrid phages isolated from the crosses of lambdoid phages with phage lambda harboured the region imm lambda and the gene of adsorption specificity from other parent. Ten groups of heteroimmune phages were found in the collection of new temperate phages are homoimmune with known phages: lambda, phi 80, phi 81, 434. Another 7 phages involved in 6 groups of immunity which were heteroimmune to known phages. Diversity of lambdoid phage genes determining the structure of repressor is discussed.

Coliphages↗
PubMed1986

[Two loci in the genome of the transposable phage B39 of Pseudomonas aeruginosa affecting the process of integration. I. Study of the properties of phages with the Pde- phenotype and mapping of the rms site].

Mutants and recombinants of transposable Pseudomonas aeruginosa bacteriophage B39 with a specific phenotype Pde- (pleiotropic developmental effect) were studied. Pde- phages produce clear minute plaques on lawns of P. aeruginosa PAO1 and fail to grow in cells of PAO1 harbouring Rms 163 (Inc P5) plasmid. Pde+ character is under control of the two loci in phage genome which were designated pdeX and pdeY. In hybrid phages the pdeX and pdeY loci originating from different transposable phages (pdeX from B39 and pdeY from PH132) do not accomplish their function and, as a result, the hybrid phages have the Pde- phenotype. The frequency of integration (f.o.i.) of Pde- phages into bacterial chromosome is lower than f.o.i. for Pde+ phages, as well as the frequency of stable lysogenization of infected bacteria; lytic development of the Pde- phages is also limited. The great difference among the transposable phages in their reaction to the presence of Rms163 plasmid is caused by some differences in the specific rms site in the phage genome. The site is located inside the interval 1.1-3.9 kb of the physical genome map, being closely linked to cI gene of phage B39. The growth of Pde- phages in cells with Rms163 can be restored, due to additional mutations in phage genes affecting lysogenization.

Bacteriophages↗
PubMed1998

The polyvalent staphylococcal phage phi 812: its host-range mutants and related phages.

Ninety-five percent of 782 culture collection strains, as well as hospital strains of Staphylococcus aureus subsp. aureus of different provenance and 43% of 89 culture collection strains of different coagulase-negative species of the genus Staphylococcus, were found to be sensitive to the polyvalent phage phi 812 or to at least one of its host-range mutants or to the polyvalent phages SK311, phi 131, and U16. Thus sensitivity to the polyvalent staphylococcal phages seems to be one of the common features of S. aureus subsp. aureus strains. The adsorption kinetics and one-step growth characteristics of the phages phi 812 and SK311 were estimated. Restriction genomic maps of the phages phi 812 (146.5 kb) and SK311 (141.1 kb) were constructed by use of the restriction endonucleases AvaII, PstI, KpnI, SacI, SmaI, and XhoI. The host-range mutations of the phage phi 812 were localized on this map. Comparison of restriction patterns of the phages phi 812 and SK311 with those of the polyvalent phages U16 and phi 131 suggests that all these phages are closely related. Their genomes differ from each other mostly by some deletions, insertions (1-3 kb), or inversions. Evidence was given that the phage phi 812 together with SK311, phi 131, and U16 belongs in the phage species Twort, the description of which is substantially supplemented with the data on the phage phi 812 reported in this paper.

Adsorption↗
PubMed2006

The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1.

A new Escherichia coli phage, named Rtp, was isolated and shown to be closely related to phage T1. Electron microscopy revealed that phage Rtp has a morphologically unique tail tip consisting of four leaf-like structures arranged in a rosette, whereas phage T1 has thinner, flexible leaves that thicken toward the ends. In contrast to T1, Rtp did not require FhuA and TonB for infection. The 46.2-kb genome of phage Rtp encodes 75 open reading frames, 47 of which are homologous to phage T1 genes. Like phage T1, phage Rtp encodes a large number of small genes at the genome termini that exhibit no sequence similarity to known genes. Six predicted genes larger than 300 nucleotides in the highly homologous region of Rtp are not found in T1. Two predicted HNH endonucleases are encoded at positions different from those in phage T1. The sequence similarity of rtp37, -38, -39, -41, -42, and -43 to equally arranged genes of lambdoid phages suggests a common tail assembly initiation complex. Protein Rtp43 is homologous to the lambda J protein, which determines lambda host specificity. Since the two proteins differ most in the C-proximal area, where the binding site to the LamB receptor resides in the J protein, we propose that Rtp43 contributes to Rtp host specificity. Lipoproteins similar to the predicted lipoprotein Rtp45 are found in a number of phages (encoded by cor genes) in which they prevent superinfection by inactivating the receptors. We propose that, similar to the proposed function of the phage T5 lipoprotein, Rtp45 prevents inactivation of Rtp by adsorption to its receptor during cells lysis. Rtp52 is a putative transcriptional regulator, for which 10 conserved inverted repeats were identified upstream of genes in the Rtp genome. In contrast, the much larger E. coli genome has only one such repeat sequence.

Amino Acid Sequence↗
PubMed1982

[Interaction of Pseudomonas aeruginosa plasmids and mu-like phages: the suppression of the early stages of cell infection by phage D3112 in the presence of plasmid RPL11].

The growth of Mu-like, D3112, B39 and B3 bacteriophages of Pseudomonas aeruginosa on bacterial strains containing R plasmids was studied. Plasmids RPL11, Rms148 and Rms163 were shown to interfere with phage growth: 1) D3112 and B39 phages do not produce plaques on a lawn of PAO1 (Rms148) giving e.o.p. less than 10(-9); 2) RPL11 plasmid restricts phage D3112 growth (e.o.p. less than 10(-9), the growth of phage B3 being also restricted by this plasmid, though in considerably less extent; 3) phage B39 makes small and very turbid plaques on a lawn of PAO1 (Rms163) with e.o.p. 0,13, while c mutants form clear plaques on this lawn and grow with e.o.p. 1,0. The interference of plasmid RPL11 with phage D3112 growth was examined in detail. The plasmid did not affect phage D3112 adsorption and no restriction of phage DNA in R+ cells was found. However, phage genes controlling establishment of lysogeny and the lytic cycle were not expressed after infection. It was observed though, that if a cell contains both prophage D3112 and plasmid RPL11, no interference with repressor synthesis or phage development takes place after induction of prophage. The results obtained allow to conclude that: 1) RPL11 plasmid interference with phage D3112 growth is caused by the plasmid effect on one of the early stages in the development preceding phage DNA integration; 2) the process of primary integration after infection and that of reintegration of DNA after prophage induction are likely to differ.

Adsorption↗
PubMed2000

Combining phage display and screening of cDNA expression libraries: a new approach for identifying the target antigen of an scFv preselected by phage display.

A potential method for identifying new tumor-specific antibody structures as well as tumor-associated antigens is by selecting scFv phage libraries on tumor cells. This phage display technique involves multiple rounds of phage binding to target cells, washing to remove non-specific phage and elution to retrieve specific binding phage. Although the binding properties of an isolated tumor-specific scFv can be evaluated by ELISA, FACS and immunohistochemistry, it still remains a challenge to define the corresponding antigen. Here, we provide evidence that the target antigen of a given scFv displayed on phages can be detected in an immobilized lambda phage cDNA expression library containing thousands of irrelevant clones. The library contained CD30-negative breast-cancer specific cDNA as well as human CD30 receptor cDNA. The interaction of anti-CD30 scFv phages and their target antigen after blotting onto nitrocellulose filters was documented under defined conditions. Screening of different ratios between CD30 receptor and breast cancer specific clones (1:1 and 1:200) revealed that the CD30 antigen could be detected by anti-CD30 scFv phages using at least 5x10(12) plaque forming units of filamentous phages per blot. These investigations demonstrate that it is possible to detect the target antigen of a preselected scFv displayed on filamentous phages in lambda phage cDNA expression libraries.

Antibodies, Monoclonal↗
PubMed1976

Phage and defective phage of strains of Myxococcus.

1. Phage-like particles were found in the supernatants of cultures of strains of Myxococcus xanthus, M. virescens and M. fulvus. The largest number of such particles was associated with M. virescens V2. Most of the particles were similar in morphology to the virulent Myxococcus phage, MX-1. 2. Several new phages were isolated from soil and animal droppings. A new phage was isolated from cultures of M. virescens V2. All resembled phage MX-1 in morphology and were related to phage MX-1 serologically. One of these phage, om, was characterized by fractionation of its proteins by SDS-polyacrylamide gel electrophoresis and by analysis of restriction fragments of its DNA. The very close relatedness with MX-1 was confirmed by these techniques. Phage om, was found to exist in a state of pseudolysogeny with strains of M. virescens and M. fulvus. 3. Two types of bacteriocin-like activity were found associated with Myxococcus strains. In one case, the activity was extracted from chloroformkilled or from sonicated cells. In the second case it was associated with extracellular material. Strains of Salmonella and Cytophaga were found to be good indicators for this latter activity. These strains were found to be killed by phage MX-1. 4. The significance of these data for origin of the phages of myxococci are discussed and it is proposed that MX-1 and the newly isolated phages may be virulent mutants of a family of lysogenic phages.

Bacteriocins↗
PubMed1997

Characterization of Natronobacterium magadii phage phi Ch1, a unique archaeal phage containing DNA and RNA.

A novel archaeal bacteriophage, phi Ch1, was isolated from a haloalkalophilic archaeon Natronobacterium magadii upon spontaneous lysis. The phage-cured strain N. magadii(L13) was used to demonstrate infectivity of phage phi Ch1. The turbid-plaque morphology and the fact that N. magadii cells isolated from plaques were able to produce phage indicated that phi Ch1 is a temperate phage. The phage morphology resembles other members of Myoviridae-infecting Halobacterium species. In solution below 2M NaCl, the phage lost its morphological stability and infectivity. One- and two-dimensional SDS-PAGE of phage particles revealed at least four major and five minor proteins with molecular masses ranging from 15 to 80 kDa and acidic isoelectric points. Southern blot analysis of chromosomal DNA of a lysogenic N. magadii strain showed that phi Ch1 exists as a chromosomally integrated prophage. The phage particles contain both double-stranded, linear DNA (approx. 55 kbp) as well as several RNA species (80-700 nucleotides). Hybridization of labelled RNA fragments to total DNA from N. magadii and phi Ch1 showed that the virion-associated RNA is host encoded. Part of the phage DNA population is modified and restriction analysis revealed evidence for adenine methylation. Phage phi Ch1 is the first virus described for the genus natronobacterium, and the first phage containing DNA and RNA in mature phage particles.

Archaea↗