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Natural occurrence of a slow lytic pseudomonas phage in a Pediatric case of multidrug-resistant P. aeruginosa severe pneumonia.

Pseudomonas aeruginosa (P. aeruginosa) is widely distributed in the environment. As an opportunistic pathogen, it commonly causes infections in immunocompromised individuals, including respiratory tract infections and burn wound infections. P. aeruginosa possesses multiple antibiotic resistance mechanisms, including efflux pumps, resistance genes, and population dynamics. Phage therapy is a potential approach for addressing drug-resistant P. aeruginosa infections; however, clinical experience and standardized guidelines for its application in severe pneumonia remain limited. A 14-month-old infant was hospitalized for pneumonia. Four days later, he developed acute pneumonia and was sent to the ICU for 38 days of antibiotic therapy; nonetheless, P. aeruginosa remained detectable in the patient's respiratory secretions. During the clinical course, phage zjk6 was detected from a longitudinal P. aeruginosa isolate in the absence of phage therapy. This finding documents the coexistence of a naturally detected phage and MDR P. aeruginosa during prolonged pneumonia, but does not establish that the phage mediated bacterial clearance or clinical recovery. We performed whole-genome sequencing on P. aeruginosa isolates from patients to ascertain if they were infected by the same infection and assessed their antibiotic resistance using drug sensitivity testing. We isolated phages using the drip technique and double-layer plate method, examined their appearance by transmission electron microscopy, and assessed their biological properties through one-step growth curve analysis and lysis spectrum detection. Genome sequencing and comparative genomic analyses were performed to characterize phage zjk6 and representative bacterial isolates and to evaluate phage-host genomic relatedness. P. aeruginosa was isolated repeatedly during 49 days of treatment. Comparative genomic analysis of representative longitudinal isolates revealed multiple strain backgrounds, including distinct ST508 and ST266 lineages and a closely related ST836 lineage. Phage zjk6 was isolated from the fifth clinical isolate, which served as the propagation/reference host. This phage possesses an elongated tail and a limited lysis spectrum, which is capable of gradually lysing the fifth isolated P. aeruginosa strain. Genomic analysis showed that zjk6 formed plaques and displayed slow lytic behavior under the tested conditions, while also carrying lysogeny-associated regulatory modules, indicating temperate potential rather than a strictly lytic lifestyle. A naturally detected slow lytic Pseudomonas phage may coexist with MDR P. aeruginosa during prolonged infection. These findings support further study of phage-bacterium interactions in clinical infections, while the therapeutic significance of zjk6 requires additional validation.

Antibiotic resistance↗

Environmental factors that influence the transition from lysogenic to lytic existence in the phiHSIC/Listonella pelagia marine phage-host system.

The marine phage varphiHSIC has been previously reported to enter into a pseudolysogenic-like interaction with its host Listonella pelagia. This phage-host system displays behaviors that are characteristic of both pseudolysogeny and lysogeny including a high rate of spontaneous induction and chromosomal integration of the prophage. To determine what parameters may influence the transition from lysogenic to lytic existence in the varphiHSIC/L. pelagia phage-host system, cultures of this organism were incubated under different environmental conditions, while host cell growth and bacteriophage production were monitored. The environmental parameters tested included salinity, temperature, a rapid temperature shift, and degree of culture aeration. The highest titers of phage were produced by HSIC-1a cells grown in high-salinity nutrient artificial seawater media (67 ppt with a natural salinity equivalent of 57 ppt) or those cultured in highly aerated nutrient artificial seawater media (cultures shaken at 300 rpm). Conversely, the lowest titers of phage were produced under low salinity or rate of aeration. In general, conditions that stimulated growth resulted in greater lytic phage production, whereas slow growth favored lysogeny. These results indicate that elevated salinity and aeration influenced the switch from lysogenic to lytic existence for the phage varphiHSIC. These results may have implications for environmental controls of the lysogenic switch in natural populations of marine bacteria.

Bacteriolysis↗

Definition of bacteriophage groups according to their lytic action on mesophilic lactic streptococci.

The lytic activity of 132 phages isolated during slow acid production in cheese factories situated in all the dairying regions of France during the past 16 years has been determined on 291 strains of mesophilic lactic streptococci. The results have been treated according to a method of analysis of data so as to establish a classification. Six groups of phages have thus been formed. Sixty-six percent of the phages studied, which are very similar and for the most part nonspecific to one species, have been gathered together in one group. On the other hand, a classification of the bacterial strains has been made on their sensitivity to the phages. Six groups, each corresponding to one of these groups of phages, have thus been defined. One of them accounts for 40% of the strains studied, of which certain ones are sensitive to a large number of phages.

Journal Article↗

Genome structure of mycobacteriophage D29: implications for phage evolution.

Mycobacteriophage D29 is a lytic phage that infects both fast and slow-growing mycobacterial species. The complete genome sequence of D29 reveals that it is a close relative of the temperate mycobacteriophage L5, whose sequence has been described previously. The overall organization of the D29 genome is similar to that of L5, although a 3.6 kb deletion removing the repressor gene accounts for the inability of D29 to form lysogens. Comparison of the two genomes shows that they are punctuated by a large number of insertions, deletions, and substitutions of genes, consistent with the genetic mosaicism of lambdoid phages.

Amino Acid Sequence↗

Mycobacteriophage D29 integrase-mediated recombination: specificity of mycobacteriophage integration.

Mycobacteriophage D29 is a lytic phage that infects both fast- and slow-growing species of the mycobacteria. D29 forms clear plaques on lawns of Mycobacterium smegmatis and Mycobacterium bovis bacille Calmette-Guérin (BCG) in which a very high proportion of infected cells are killed. However, genomic analysis of D29 demonstrates that it is a close relative of the temperate mycobacteriophage L5, and is presumably a non-temperate derivative of a temperate parent. The D29 genome encodes a putative integrase protein with a primary amino acid sequence similar to that of the L5 integrase; the corresponding int genes fall in colinear positions within the D29 and L5 genomes, immediately flanking and transcribed away from their associated attP sites. We show here that the D29 integrase is functional and catalyzes integrative recombination between the D29 attP site and the M. smegmatis attB site in vitro in an mIHF-dependent manner. D29 integrase also mediates recombination between the L5 attP site and attB DNA and, reciprocally, L5 integrase catalyzes recombination with D29 attP DNA. However, in both in-vitro and in-vivo assays, the D29-encoded integrase recombines the D29 attP more efficiently than the L5 attP, and vice versa, suggesting that each integration system has evolved a degree of specificity of attP recognition. We also present the sequences of the putative attP site and integrase protein of the cryptic prophage-like element phiRv2, and compare them to those of mycobacteriophages L5 and D29.

Amino Acid Sequence↗

Phenotypic alterations in the colonial morphology of Brucella abortus due to a bacteriophage carrier state.

Jones, Lois M. (University of Wisconsin, Madison), C. R. McDuff, and J. B. Wilson. Phenotypic alterations in the colonial morphology of Brucella abortus due to a bacteriophage carrier state. J. Bacteriol. 83:860-866. 1962.-In the course of examining a number of Brucella cultures with a brucellaphage, it was observed that B. abortus cultures of intermediate colonial morphology, which had a blue-gray colonial appearance, were not lysed within 24 hr; in 48 hr they had developed sticky white growth in the area of the phage drop. When this growth was streaked on agar plates, both white and blue-gray colonies developed. White colonies which were sticky always carried phage and upon restreaking always gave rise to both white and blue-gray colonies. White colonies which were not sticky were rough and phage resistant. Blue-gray colonies produced only blue-gray colonies, did not carry phage, and were similar to the parent in their response to phage. When sticky white colonies were incubated for 6 hr or more in phage antiserum, all phage was eliminated and only blue-gray colonies developed. It was believed that the sticky white colonies were carrier clones in which lysis was delayed until after cell division, thus resulting in the establishment of a colony containing some phage-free progeny. With the accumulation of phage, the colony became sticky. This effect may be caused by the action of bacteriophage enzymes on the cell walls. Brucellaphage had an extremely slow rate of adsorption on a culture of intermediate colonial morphology. A phage mutant which was more strongly lytic for cultures of intermediate colonial morphology was selected from the original phage. The adsorption rate of this phage was more rapid and the latent period shorter. A serological difference between phages could not be demonstrated.

Adsorption↗

Inhibition of spontaneous induction of lambdoid prophages in Escherichia coli cultures: simple procedures with possible biotechnological applications.

BACKGROUND: Infections of bacterial cultures by bacteriophages are serious problems in biotechnological laboratories. Apart from such infections, prophage induction in the host cells may also be dangerous. Escherichia coli is a commonly used host in biotechnological production, and many laboratory strains of this bacterium harbour lambdoid prophages. These prophages may be induced under certain conditions leading to phage lytic development. This is fatal for further cultivations as relatively low, though still significant, numbers of phages may be overlooked. Thus, subsequent cultures of non-lysogenic strains may be infected and destroyed by such phage. RESULTS: Here we report that slow growth of bacteria decreases deleterious effects of spontaneous lambdoid prophage induction. Moreover, replacement of glucose with glycerol in a medium stimulates lysogenic development of the phage after infection of E. coli cells. A plasmid was constructed overexpressing the phage 434 cI gene, coding for the repressor of phage promoters which are necessary for lytic development. Overproduction of the cI repressor abolished spontaneous induction of the lambda(imm434) prophage. CONCLUSIONS: Simple procedures that alleviate problems with spontaneous induction of lambdoid prophage and subsequent infection of E. coli strains by these phages are described. Low bacterial growth rate, replacement of glucose with glycerol in a medium and overproduction of the cI repressor minimise the risk of prophage induction during cultivation of lysogenic bacteria and subsequent infection of other bacterial strains.

Bacteriophage lambda↗

DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics.

Genetic studies of Mycobacterium tuberculosis and other mycobacterial pathogens have suffered from the lack of a sophisticated genetic system. To address this issue we have developed a viral system through a detailed characterization of mycobacteriophage L5, a temperate phage that infects both fast- and slow-growing mycobacteria. We describe here the complete DNA sequence of the L5 genome and initial characterization of L5 virion structure and gene expression. In addition to providing a genetic 'tool-box' for the mycobacteria we find that L5 offers a new paradigm for dsDNA phages, being phenotypically temperate but employing genetic strategies for phage growth usually associated with lytic bacteriophages.

Amino Acid Sequence↗

A revised strategy for cloning antibody gene fragments in bacteria.

The ability to clone and overexpress genes encoding mouse Fab (antigen-binding fragment) proteins in bacteria led to the development of a methodology which has the potential to replace traditional hybridoma technology [Huse et al., Science 246 (1989) 1275-1281]; however, several observations have suggested that clones with desirable chemical properties may be missed in immunoscreens of large combinatorial libraries due to low levels of functional Ab protein. To increase the efficiency of cloning and characterization of Ab gene fragments, we have reconsidered several features of the original cloning vehicles. These studies show that at the present time a unique expression system cannot adequately accommodate the requirements of plaque-lift immunoassays for clonal selection and biochemical assays for further characterization in vitro. A monocistronic arrangement of heavy- and light-chain-encoding genes using two lacP promoters produces sufficient amounts of functional Ab protein for clonal selection from phage lambda libraries and minimizes interference with the lytic cycle of recombinant vectors. In liquid culture, a strong coliphage promoter and a relatively abundant RNA polymerase can be used to produce quantities of Ab protein sufficient for further characterization in vitro. A rapid purification protocol obviates the need for fusing heavy-chain protein to a decapeptide sequence, an affinity-tail sequence which slows the folding and assembly of the Ig heterodimer. These results have been used to formulate a new strategy for cloning and characterization of Ab gene fragments in bacteria.

Amino Acid Sequence↗

Morphological and molecular characterization of several actinophages isolated from soil which lyse Streptomyces cattleya or S. venezuelae.

Several lytic and lysogenic actinophages were isolated from soil samples infected with Streptomyces cattleya and S. venezuelae. The morphologies and some biological properties of the phages, and the physico-chemical characteristics of their DNAs, were compared. Electron micrographs indicated that all the phage heads were of an icosahedral form, but head size and length of the tail varied. Two of the phages had a broad host range; the other isolates could lyse only a limited number of species. The molecular sizes of the phage DNAs were between 32.2 and 98.5 kb as estimated by electron microscopy and restriction enzyme analysis. The same study also indicated that one of the DNA species contained cohesive ends. The G + C content of the DNAs ranged between 45.1 and 74.2 mol % as estimated from melting studies. Sedimentation velocity experiments implied that several of the phage DNAs were probably heavily glycosylated or methylated. These modifications might explain the partial or slow digestion of some of the DNAs by several of the 23 restriction enzymes tested. Protoplasts of the appropriate Streptomyces strains could be efficiently transfected with phage DNA in the presence of 25% (w/v) polyethylene glycol (mol. wt 6000).

Bacteriophages↗

Mechanism of cell wall penetration by viruses. II. Demonstration of cyclic permeability change accompanying virus infection of Escherichia coli B cells.

The virus-induced leakage of host-cell constituents represents a true increase in cellular permeability rather than an unpeeling of cell surface components, since an intracellular enzyme participates in the leakage. All of the T-system bacteriophages exhibit this leakage. The leakage does not occur with salt concentrations which permit only reversible virus-cell attachment but no penetration. These facts support the idea that the reaction underlying cell leakage is a part of the invasive mechanism. With increasing multiplicity of T2 infection of young, fresh Escherichia coli B cells, progressively larger molecules leak out of the cell. Acid-soluble P(32) appears in large amounts with single infection. Appreciable amounts of galactosidase enzyme and RNA do not leak until multiplicities of 5 to 30 are attained. Cellular DNA is not liberated unless sufficiently high multiplicities are used to cause the extensive cell destruction and clearing of the suspension characteristic of lysis-from-without. This progression is interpreted as an increase with T2 multiplicity in the maximum hole size produced in the cell membrane. Calculation shows that this increase in hole size must result from a spreading change in the character of the cell wall, rather than the coincidental juxtaposition of 2 or more viruses at adjacent attachment sites. T1 virus liberates less macromolecular constituents than T2 from E. coli B. The following experimental results constitute evidence that in the course of normal virus infection, a resealing reaction is rapidly instituted in the cell wall which reverses the effect of the original permeability increase, and renders the cell refractory to a second lytic reaction by a homologous virus: (a) Cell leakage induced by T2 virus in the course of normal infection markedly slows down or stops within a few minutes, even when only a small fraction of the material potentially available for leakage has been released, (b) Superinfection after 8 minutes at 37 degrees C., of a cell previously infected with a homologous virus causes little or no appearance of a second leakage of cell constituents. This experiment also leads to the conclusion that the sealing reaction, like that which causes the leakage, also involves a disturbance which spreads over all or most of the cell wall. (c) If a multiple virus infection is allowed to occur at 0 degrees C. and then the cells are placed in a 37 degrees C. bath after completion of attachment, a much greater cell leakage results than if the entire course had occurred at 37 degrees C., as would be expected if a resealing reaction comes into play at 37 degrees C. within a time less than that required by the completion of attachment. The virus particles attaching secondarily at 37 degrees C. are prevented from exercising their permeability-increasing effect by the sealing reaction of the virus which had penetrated first. Although a second homologous cell infection with T1 or T2 phages after a 37 degrees C. incubation fails to yield a second leakage, a second heterologous infection always causes exacerbation of new leakage, which, especially if T1 has preceded T2, may be much greater than the sum of those produced individually by each virus in separate cell suspensions. This phenomenon may be the action responsible for the "depressor" effect which occurs when 2 unrelated viruses attack the same cell. The properties of the sealing phenomenon are such as to make it appear a logical candidate for the mechanism underlying the exclusion of a superinfecting phage from participating in reproductive processes in a cell previously infected with a homologous virus, since the DNA of the second virus would be unable to penetrate the new barrier. Experiments to test this hypothesis revealed that the DNA from such superinfecting virus is completely extractable from cells by washing in dilute buffer, whereas about 40 to 50 per cent of the attached DNA of virus which has invaded virgin cells remains bound to the cells. Most of the viral DNA which appears in the original supernatant when P(32)-labelled T2 invades E. coli B in a multiplicity less than one, does not represent inert material but rather virus DNA which has been split, or split and hydrolyzed as a result of its interaction with the cells, as judged by the altered susceptibility to hydrolytic enzyme or to TCA precipitation. This suggests that 25 per cent or more of the virus DNA may be expendable, at least after the penetration stage of the infection cycle. Mg(++) which strongly depresses the amount of cell leakage attending T2 infection, does not prevent T2 penetration nor does it block the appearance of the exclusion reaction. Hence, if the initial leakage does mirror the lytic process by which a hole for the DNA injection is provided, the Mg(++) does not function by preventing this hole formation. Its effect would have to lie in prevention of the spreading lysis-potentiating reaction or in augmenting the sealing mechanism. A large number of independent lines of evidence indicate that the phenomenon of lysis-from-without exhibited by the T-even coliphages is the result of failure of the sealing mechanism to keep pace with the lytic reaction. This can result from an excess of infecting phages or inhibition of the cellular energy-liberating reaction required by the sealing mechanism. The complete parallelism between the development of refractoriness to lysis-from-without and development of refractoriness to the production of a new leakage from a homologous superinfection is especially convincing in this connection. It is proposed that the early phase of bacteriophage invasion involves the following steps: reversible electrostatic attachment; splitting of the viral DNA from its protein coat; initiation of a lytic reaction in the cell wall at the site of virus attachment; injection of the DNA through the hole so produced; a spreading disturbance over the cell surface which makes it momentarily more susceptible to the lytic reaction; sealing of the hole and a concommittant spread over the cell wall of a reaction making the cell refractory to initiation of a second lytic reaction. Na(+), K(+), and Mg(++) all behave differently in their effect on the leakage produced in the course of T2 invasion of E. coli.

B-Lymphocytes↗

A long lytic cycle in filamentous phage Cf1tv infecting Xanthomonas campestris pv. citri.

In this study the lytic cycle of a filamentous phage is reported. Under normal laboratory cultivation conditions a virulent form could spontaneously and easily arise from a temperate phage. The virulent one could superinfect cells containing Cf1t lysogen. Therefore, we have named it Cf1tv. In a colony formation assay using cells from an infected culture, two types of colonies were observed, small and large. It could be proven that the formation of small colonies is the result of killing during Cf1tv infection. The number of small colony forming units (cfu) increased with infection time and reached a maximum at 16 h after infection, then dropped to the initial cell concentration at 28 h after infection; 28 h were required to kill all infected cells. Large colonies contained uninfected or phage-resistant cells, but no lysogenic cells. Bacterial death was further confirmed by a microculture assay. At 2 h after infection, normal-dividing cells (cfu giving large colonies) contained about 40% of Cf1tv-infected cells, then the percentage decreased with infection time. Slow-dividing cells (infected cfu giving small colonies) initially contained 55% of cells; this percentage increased slightly at 4 h after infection, then decreased at 8 h after infection. Non-dividing cells initially contained 5% of infected cells, then their numbers rapidly increased with time after infection. The cell division was seriously affected and finally stopped. During one-step growth, the latent period was 30 min and there was no burst; phages were released at 30 min after infection and the rate of release increased gradually with time after infection. Phage DNA integration into host chromosome could not be observed.

Bacteriophages↗