Genomic sequence of C1, the first streptococcal phage

The virtue of training: extending phage host spectra against vancomycin-resistant Enterococcus faecium strains using the Appelmans method

Phage therapy has (re)emerged as a serious possibility for combating multidrug-resistant bacterial infections, including those caused by vancomycin-resistant Enterococcus faecium strains. These opportunistic pathogens belong to a specific clonal complex 17, against which relatively few phages have been screened. We isolated a collection of 21 virulent phages growing on these vancomycin-resistant isolates. Each of these phages harbored a typical narrow plaquing host range, lysing at most 5 strains and covering together 10 strains of our panel of 14 clinical isolates. To enlarge the host spectrum of our phages, the Appelmans protocol was used. We mixed four out of our most complementary phages in a cocktail that we iteratively grew on eight naive strains from our panel, of which six were initially refractory to at least three of the combined phages. Fifteen successive passages permitted to significantly improve the lytic activity of the cocktail, from which phages with extended host ranges within the E. faecium species could be isolated. A single evolved phage able to kill up to 10 of the 14 initial E. faecium strains was obtained, and it barely infected nearby species. All evolved phages had acquired point mutations or a recombination event in the tail fiber genetic region, suggesting these genes might have driven phage evolution by contributing to their extended host spectra.

Characterization of two lytic bacteriophages, infecting Streptococcus bovis/equinus complex (SBSEC) from Korean ruminant

Streptococcus bovis/equinus complex (SBSEC) is one of the most important lactic acid-producing rumen bacteria causing subacute ruminal acidosis. Despite the significance of the ruminal bacteria, lytic bacteriophages (phages) capable of infecting SBSEC in the rumen have been rarely characterized. Hence, we describe the biological and genomic characteristics of two lytic phages (designated as vB_SbRt-pBovineB21 and vB_SbRt-pBovineS21) infecting various SBSEC species, including the newly reported S. ruminicola. The isolated SBSEC phages were morphologically similar to Podoviridae and could infect other genera of lactic acid-producing bacteria, including Lactococcus and Lactobacillus. Additionally, they showed high thermal- and pH-stability, and those characteristics induce strong adaptation to the ruminal environment, such as the low pH found in subacute ruminal acidosis. Genome-based phylogeny revealed that both phages were related to Streptococcus phage C1 in the Fischettivirus. However, they had a lower nucleotide similarity and distinct genomic arrangements than phage C1. The phage bacteriolytic activity was evaluated using S. ruminicola, and the phages efficiently inhibited planktonic bacterial growth. Moreover, both phages could prevent bacterial biofilms of various SBSEC strains and other lactic acid-producing bacteria in vitro. Thus, the newly isolated two SBSEC phages were classified as new Fischettivirus members and could be considered as potential biocontrol agents against ruminal SBSEC bacteria and their biofilms.

Endolysins against Streptococci as an antibiotic alternative

Multi-drug resistance has called for a race to uncover alternatives to existing antibiotics. Phage therapy is one of the explored alternatives, including the use of endolysins, which are phage-encoded peptidoglycan hydrolases responsible for bacterial lysis. Endolysins have been extensively researched in different fields, including medicine, food, and agricultural applications. While the target specificity of various endolysins varies greatly between species, this current review focuses specifically on streptococcal endolysins. Streptococcus spp. causes numerous infections, from the common strep throat to much more serious life-threatening infections such as pneumonia and meningitis. It is reported as a major crisis in various industries, causing systemic infections associated with high mortality and morbidity, as well as economic losses, especially in the agricultural industry. This review highlights the types of catalytic and cell wall-binding domains found in streptococcal endolysins and gives a comprehensive account of the lytic ability of both native and engineered streptococcal endolysins studied thus far, as well as its potential application across different industries. Finally, it gives an overview of the advantages and limitations of these enzyme-based antibiotics, which has caused the term enzybiotics to be conferred to it.

Subcellular organization of viral particles during maturation of nucleus-forming jumbo phage

Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we show that viral particles of Pseudomonas nucleus-forming jumbo phage PhiPA3 assemble into a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to capsids, and these particles accumulate over time in a spherical pattern, with tails oriented inward and the heads outward to form bouquets at specific subcellular locations. Bouquets localize at the same fixed distance from the phage nucleus even when it is mispositioned, suggesting an active mechanism for positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phages, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle.

The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes

Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes.

IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.

Integrative Longitudinal Analysis of Metabolic Phenotype and Microbiota Changes During the Development of Obesity

Obesity has increased at an alarming rate over the past two decades in the United States. In addition to increased body mass, obesity is often accompanied by comorbidities such as Type II Diabetes Mellitus and metabolic dysfunction-associated fatty liver disease, with serious impacts on public health. Our understanding of the role the intestinal microbiota in obesity has rapidly advanced in recent years, especially with respect to the bacterial constituents. However, we know little of when changes in these microbial populations occur as obesity develops. Further, we know little about how other domains of the microbiota, namely bacteriophage populations, are affected during the progression of obesity. Our goal in this study was to monitor changes in the intestinal microbiome and metabolic phenotype following western diet feeding. We accomplished this by collecting metabolic data and fecal samples for shotgun metagenomic sequencing in a mouse model of diet-induced obesity. We found that after two weeks of consuming a western diet (WD), the animals weighed significantly more and were less metabolically stable than their chow fed counterparts. The western diet induced rapid changes in the intestinal microbiome with the most pronounced dissimilarity at 12 weeks. Our study highlights the dynamic nature of microbiota composition following WD feeding and puts these events in the context of the metabolic status of the mammalian host.

Cell wall polysaccharides of Gram positive ovococcoid bacteria and their role as bacteriophage receptors

Gram-positive bacterial cell walls are characterised by the presence of a thick peptidoglycan layer which provides protection from extracellular stresses, maintains cell integrity and determines cell morphology, while it also serves as a foundation to anchor a number of crucial polymeric structures. For ovococcal species, including streptococci, enterococci and lactococci, such structures are represented by rhamnose-containing cell wall polysaccharides, which at least in some instances appear to serve as a functional replacement for wall teichoic acids. The biochemical composition of several streptococcal, lactococcal and enterococcal rhamnose-containing cell wall polysaccharides have been elucidated, while associated functional genomic analyses have facilitated the proposition of models for individual biosynthetic pathways. Here, we review the genomic loci which encode the enzymatic machinery to produce rhamnose-containing, cell wall-associated polysaccharide (Rha cwps) structures of the afore-mentioned ovococcal bacteria with particular emphasis on gene content, biochemical structure and common biosynthetic steps. Furthermore, we discuss the role played by these saccharidic polymers as receptors for bacteriophages and the important role phages play in driving Rha cwps diversification and evolution.

High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus

Endolysin enzymes from bacteriophage cause bacterial lysis by degrading the peptidoglycan cell wall. The streptococcal C1 phage endolysin PlyC, is the most potent endolysin described to date and can rapidly lyse group A, C, and E streptococci. PlyC is known to bind the Group A streptococcal cell wall, but the specific molecular target or the binding site within PlyC remain uncharacterized. Here we report for the first time, that the polyrhamnose backbone of the Group A streptococcal cell wall is the binding target of PlyC. We have also characterized the putative rhamnose binding groove of PlyC and found four key residues that were critical to either the folding or the cell wall binding action of PlyC. Based on our results, we suggest that the interaction between PlyC and the cell wall may not be a high-affinity interaction as previously proposed, but rather a high avidity one, allowing for PlyC's remarkable lytic activity. Resistance to our current antibiotics is reaching crisis levels and there is an urgent need to develop the antibacterial agents with new modes of action. A detailed understanding of this potent endolysin may facilitate future developments of PlyC as a tool against the rise of antibiotic resistance.

The Bacteriophages of Streptococcus pyogenes

The bacteriophages of Streptococcus pyogenes (group A streptococcus) play a key role in population shaping, genetic transfer, and virulence of this bacterial pathogen. Lytic phages like A25 can alter population distributions through elimination of susceptible serotypes but also serve as key mediators for genetic transfer of virulence genes and antibiotic resistance via generalized transduction. The sequencing of multiple S. pyogenes genomes has uncovered a large and diverse population of endogenous prophages that are vectors for toxins and other virulence factors and occupy multiple attachment sites in the bacterial genomes. Some of these sites for integration appear to have the potential to alter the bacterial phenotype through gene disruption. Remarkably, the phage-like chromosomal islands (SpyCI), which share many characteristics with endogenous prophages, have evolved to mediate a growth-dependent mutator phenotype while acting as global transcriptional regulators. The diverse population of prophages appears to share a large pool of genetic modules that promotes novel combinations that may help disseminate virulence factors to different subpopulations of S. pyogenes. The study of the bacteriophages of this pathogen, both lytic and lysogenic, will continue to be an important endeavor for our understanding of how S. pyogenes continues to be a significant cause of human disease.

Enterococcus faecalis Countermeasures Defeat a Virulent Picovirinae Bacteriophage

Enterococcus faecalis is an opportunistic pathogen that has emerged as a major cause of nosocomial infections worldwide. Many clinical strains are indeed resistant to last resort antibiotics and there is consequently a reawakening of interest in exploiting virulent phages to combat them. However, little is still known about phage receptors and phage resistance mechanisms in enterococci. We made use of a prophageless derivative of the well-known clinical strain E. faecalis V583 to isolate a virulent phage belonging to the Picovirinae subfamily and to the P68 genus that we named Idefix. Interestingly, most isolates of E. faecalis tested—including V583—were resistant to this phage and we investigated more deeply into phage resistance mechanisms. We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abiα. It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis of infected E. faecalis. The abiα gene is widespread among prophages of enterococci and other Gram-positive bacteria. Furthermore, we identified two genes involved in the synthesis of the side chains of the surface rhamnopolysaccharide that are important for Idefix adsorption. Interestingly, mutants in these genes arose at a frequency of ~10⁻⁴ resistant mutants per generation, conferring a supplemental bacterial line of defense against Idefix.

Genomic Sequencing of High-Efficiency Transducing Streptococcal Bacteriophage A25: Consequences of Escape from Lysogeny

Lytic bacteriophage A25, which infects Streptococcus pyogenes and several related species, has been used to better understand phage-microbe interactions due to its ability to mediate high-efficiency transduction. Most of these studies, however, are decades old and were conducted prior to the advent of next-generation sequencing and bioinformatics. The aim of our study was to gain a better understanding of the mechanism of high-efficiency transduction through analysis of the A25 genome. We show here that phage A25 is related to a family of genome prophages and became a lytic phage following escape from lysogeny. A lambdoid-like residual lysogeny module consisting of an operator site with two promoters and a cro-like antirepressor gene was identified, but the genes for the cI-like repressor and integrase are missing. Additionally, the genetic organization of the A25 genome was found to be modular in nature and similar to that of many prophages of S. pyogenes as well as from other streptococcal species. A study of A25 homology to all annotated prophages within S. pyogenes revealed near identity within the remnant lysogeny module of the A25 phage genome to the corresponding regions in resident prophages of genome strains MGAS10270 (M2), MGAS315 (M3), MGAS10570 (M4), and STAB902 (M4). Host range studies of MGAS10270, MGAS315, and MGAS10750 demonstrated that these strains were resistant to A25 infection. The resistance mechanism of superinfection immunity was confirmed experimentally through complementation of the operator region and cI-like repressor from prophage MGAS10270.2 into susceptible strains SF370, CEM1Δ4 (SF370ΔSpyCIM1), and ATCC 12204, which rendered all three strains resistant to A25 infection. In silico prediction of packaging through homology analysis of the terminase large subunit from bacteriophages within the known packaging mechanism of Gram-positive bacteria as well as the evidence of terminally redundant and/or circularly permuted sequences suggested that A25 grouped with phages employing the less stringent pac-type packaging mechanisms, which likely explains the characteristic A25 high-efficiency transduction capabilities. Only a few examples of lytic phages appearing following loss of part or all of the lysogeny module have been reported previously, and the genetic mosaicism of A25 suggests that this event may not have been a recent one. However, the discovery that this lytic bacteriophage shares some of the genetic pool of S. pyogenes prophages emphasizes the importance of genetic and biological characterization of bacteriophages when selecting phages for therapeutics or disinfectants, as phage-phage and phage-microbe interactions can be complex, requiring more than just assessment of host range and carriage of toxoid or virulence genes.IMPORTANCE Bacteriophages (bacterial viruses) play an important role in the shaping of bacterial populations as well as the dissemination of bacterial genetic material to new strains, resulting in the spread of virulence factors and antibiotic resistance genes. This study identified the genetic origins of Streptococcus pyogenes phage A25 and uncovered the molecular mechanism employed to promote horizontal transfer of DNA by transduction to new strains of this bacterium as well as identified the basis for its host range.

Clostridium perfringens Virulent Bacteriophage CPS2 and Its Thermostable Endolysin LysCPS2

Clostridium perfringens is one of the most common causes of food-borne illness. The increasing prevalence of multidrug-resistant bacteria requires the development of alternatives to typical antimicrobial treatments. Here, we isolated and characterized a C. perfringens-specific virulent bacteriophage CPS2 from chicken feces. The CPS2 phage contains a 17,961 bp double-stranded DNA genome with 25 putative ORFs, and belongs to the Picovirinae, subfamily of Podoviridae. Bioinformatic analysis of the CPS2 genome revealed a putative endolysin, LysCPS2, which is homologous to the endolysin of Clostridium phage phiZP2 and phiCP7R. The enzyme showed strong lytic activity against C. perfringens with optimum conditions at pH 7.5–10, 25–65 °C, and over a broad range of NaCl concentrations. Interestingly, LysCPS2 was found to be highly thermostable, with up to 30% of its lytic activity remaining after 10 min of incubation at 95 °C. The cell wall binding domain in the C-terminal region of LysCPS2 showed a binding spectrum specific to C. perfringens strains. This is the first report to characterize highly thermostable endolysin isolated from virulent C. perfringens bacteriophage. The enzyme can be used as an alternative biocontrol and detection agent against C. perfringens.

Insights into new bacteriophages of Lactococcus garvieae belonging to the family Podoviridae

Lactococcus garvieae is an emerging pathogen responsible for lactococcosis, a serious disease in trout aquaculture. The identification of new bacteriophages against L. garvieae strains may be an effective way to fight this disease and to study the pathogen's biology. Three L. garvieae phages, termed WP-1, WWP-2 and SP-2, were isolated from different environments, and their morphological features, genome restriction profiles and structural protein patterns were studied. Random cloning of HindIII-cut fragments was performed, and the fragments were partially sequenced for each phage. Although slight differences were observed by transmission electron microscopy, all of the phages had hexagonal heads and short non-contractile tails and were classified as members of the family Podoviridae. Restriction digestion analysis of the nucleic acids of the different phages revealed that the HindIII and AseI digests produced similar DNA fragment patterns. Additionally, SDS-PAGE analysis indicated that the isolated phages have similar structural proteins. The sequence BLAST results did not show any significant similarity with other previously identified phages. To the best of our knowledge, this study provides the first molecular characterization of L. garvieae phages.

Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation

Background

The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart.

Results

The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in VNTR numbers that occurred over the course of one year.

Conclusions

The comparative genomic analysis of the SAG clarifies the phylogenetics of these bacteria and supports the distinct species classification. Numerous potential virulence determinants were identified and provide a foundation for further studies into SAG pathogenesis. Furthermore, the data may be used to enable the development of rapid diagnostic assays and therapeutics for these pathogens.

Endolysins as antimicrobials

Peptidoglycan (PG) is the major structural component of the bacterial cell wall. Bacteria have autolytic PG hydrolases that allow the cell to grow and divide. A well-studied group of PG hydrolase enzymes are the bacteriophage endolysins. Endolysins are PG-degrading proteins that allow the phage to escape from the bacterial cell during the phage lytic cycle. The endolysins, when purified and exposed to PG externally, can cause "lysis from without." Numerous publications have described how this phenomenon can be used therapeutically as an effective antimicrobial against certain pathogens. Endolysins have a characteristic modular structure, often with multiple lytic and/or cell wall-binding domains (CBDs). They degrade the PG with glycosidase, amidase, endopeptidase, or lytic transglycosylase activities and have been shown to be synergistic with fellow PG hydrolases or a range of other antimicrobials. Due to the coevolution of phage and host, it is thought they are much less likely to invoke resistance. Endolysin engineering has opened a range of new applications for these proteins from food safety to environmental decontamination to more effective antimicrobials that are believed refractory to resistance development. To put phage endolysin work in a broader context, this chapter includes relevant studies of other well-characterized PG hydrolase antimicrobials.

Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry

The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus were calculated using cryo-electron microscopy. The capsid protein has an HK97 fold arranged into a T = 4 icosahedral lattice. The C1 tail is terminated with a ϕ29-like knob, surrounded by a skirt of twelve long appendages with novel morphology. Several C1 structural proteins have been identified, including a candidate for an appendage. The crystal structure of the knob has an N-terminal domain with a fold observed previously in tube forming proteins of Siphoviridae and Myoviridae phages. The structure of C1 suggests the mechanisms by which the virus digests the cell wall and ejects its genome. Although there is little sequence similarity to other phages, conservation of the structural proteins demonstrates a common origin of the head and tail, but more recent evolution of the appendages.

Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae

Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium responsible for human food-borne disease as well as non-food-borne human, animal and poultry diseases. Because bacteriophages or their gene products could be applied to control bacterial diseases in a species-specific manner, they are potential important alternatives to antibiotics. Consequently, poultry intestinal material, soil, sewage and poultry processing drainage water were screened for virulent bacteriophages that lysed C. perfringens. Two bacteriophages, designated ΦCPV4 and ΦZP2, were isolated in the Moscow Region of the Russian Federation while another closely related virus, named ΦCP7R, was isolated in the southeastern USA. The viruses were identified as members of the order Caudovirales in the family Podoviridae with short, non-contractile tails of the C1 morphotype. The genomes of the three bacteriophages were 17.972, 18.078 and 18.397 kbp respectively; encoding twenty-six to twenty-eight ORF's with inverted terminal repeats and an average GC content of 34.6%. Structural proteins identified by mass spectrometry in the purified ΦCP7R virion included a pre-neck/appendage with putative lyase activity, major head, tail, connector/upper collar, lower collar and a structural protein with putative lysozyme-peptidase activity. All three podoviral bacteriophage genomes encoded a predicted N-acetylmuramoyl-L-alanine amidase and a putative stage V sporulation protein. Each putative amidase contained a predicted bacterial SH3 domain at the C-terminal end of the protein, presumably involved with binding the C. perfringens cell wall. The predicted DNA polymerase type B protein sequences were closely related to other members of the Podoviridae including Bacillus phage Φ29. Whole-genome comparisons supported this relationship, but also indicated that the Russian and USA viruses may be unique members of the sub-family Picovirinae.

Bacteriophage endolysins: a novel anti-infective to control Gram-positive pathogens

Endolysins (or lysins) are highly evolved enzymes produced by bacteriophage (phage for short) to digest the bacterial cell wall for phage progeny release. In Gram-positive bacteria, small quantities of purified recombinant lysin added externally results in immediate lysis causing log-fold death of the target bacterium. Lysins have been used successfully in a variety of animal models to control pathogenic antibiotic-resistant bacteria found on mucosal surfaces and infected tissues. Their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance, and their ability to kill colonizing pathogens on mucosal surfaces, a capacity previously unavailable, make them ideal anti-infectives in an age of mounting resistance. Here we review the current literature showing the effectiveness of these enzymes in controlling a variety of infections.

Antibacterial and biofilm removal activity of a podoviridae Staphylococcus aureus bacteriophage SAP-2 and a derived recombinant cell-wall-degrading enzyme

Antibacterial and biofilm removal activity of a new podoviridae Staphylococcus aureus bacteriophage (SAP-2), which belongs to the phi29-like phage genus of the Podoviridae family, and a cell-wall-degrading enzyme (SAL-2), which is derived from bacteriophage SAP-2, have been characterized. The cell-wall-degrading enzyme SAL-2 was expressed in Escherichia coli in a soluble form using a low-temperature culture. The cell-wall-degrading enzyme SAL-2 had specific lytic activity against S. aureus, including methicillin-resistant strains, and showed a minimum inhibitory concentration of about 1 microg/ml. In addition, this enzyme showed a broader spectrum of activity within the Staphylococcus genus compared with bacteriophage SAP-2 in its ability to remove the S. aureus biofilms. Thus, the cell-wall-degrading enzyme SAL-2 can be used to prevent and treat biofilm-associated S. aureus infections either on its own or in combination with other cell-wall-degrading enzymes with anti-S. aureus activity.

Complete genome sequence of a newly isolated lytic bacteriophage, EFAP-1 of Enterococcus faecalis, and antibacterial activity of its endolysin EFAL-1

AIMS

In this work, we aimed to identify an effective treatment of infections caused by Enterococcus spp. strains resistant to conventional antibiotics.

METHODS AND RESULTS

We report the isolation and characterization of a new lytic bacteriophage, designated bacteriophage EFAP-1, that is capable of lysing Enterococcus faecalis bacteria that exhibit resistance to multiple antibiotics. EFAP-1 has low sequence similarity to all known bacteriophages. Transmission electron microscopy confirmed that EFAP-1 belongs to the Siphoviridae family. A putative lytic protein of EFAP-1, endolysin EFAL-1, is encoded in ORF 2 and was expressed in Escherichia coli. Recombinant EFAL-1 had broad-spectrum lytic activity against several Gram-positive pathogens, including Ent. faecalis and Enterococcus faecium.

CONCLUSIONS

The complete genome sequence of the newly isolated enterococcal lytic phage was analysed, and it was demonstrated that its recombinant endolysin had broad lytic activity against various Gram-positive pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacteriophage EFAP-1 and its lytic protein, EFAL-1, can be utilized as potent antimicrobial agents against Enterococcus spp. strains resistant to conventional antibiotics in hospital infections and also as environmental disinfectants to control disease-causing Enterococcus spp. in dairy farms.

In silico identification of genes in bacteriophage DNA

One of the most satisfying aspects of a genome sequencing project is the identification of the genes contained within it.These are of two types: those which encode tRNAs and those which produce proteins. After a general introduction on the properties of protein-encoding genes and the utility of the Basic Local Alignment Search Tool (BLASTX) to identify genes through homologs, a variety of tools are discussed by their creators. These include for genome annotation: GeneMark, Artemis, and BASys; and, for genome comparisons: Artemis Comparison Tool (ACT), Mauve, CoreGenes, and GeneOrder.

Bacteriophage lysins as effective antibacterials

Lysins are highly evolved enzymes produced by bacteriophage (phage for short) to digest the bacterial cell wall for phage progeny release. In Gram-positive bacteria, small quantities of purified recombinant lysin added externally results in immediate lysis causing log-fold death of the target bacterium. Lysins have been used successfully in a variety of animal models to control pathogenic antibiotic resistant bacteria found on mucosal surfaces and infected tissues. The advantages over antibiotics are their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance to lysins, and their ability to kill colonizing pathogens on mucosal surfaces, a capacity previously unavailable. Thus, lysins may be a much needed anti-infective in an age of mounting antibiotic resistance.

Streptococcus equi bacteriophage SeP9 binds to group C carbohydrate but is not infective for the closely related S. zooepidemicus

Streptococcus equi (S. equi subsp. equi) is widely believed to have evolved from an ancestral strain of S. zooepidemicus (S. equi subsp. zooepidemicus) based on high sequence homology. A striking difference is the absence of phage sequences from S. zooepidemicus. In this study we show that the receptor for SeP9, a temperate bacteriophage of S. equi, is the Lancefield group C carbohydrate. However, although SeP9 binds to group C carbohydrate from S. zooepidemicus, it appears not to replicate and produce plaques.

Curated list of prokaryote viruses with fully sequenced genomes

Genome sequencing is of enormous importance for classification of prokaryote viruses and for understanding the evolution of these viruses. This survey covers 284 sequenced viruses for which a full description has been published and for which the morphology is known. This corresponds to 219 (4%) of tailed and 75 (36%) of tailless viruses of prokaryotes. The number of sequenced tailless viruses almost doubles if viruses of unknown morphology are counted. The sequences are from representatives of 15 virus families and three groups without family status, including eight taxa of archaeal viruses. Tailed phages, especially those with large genomes and hosts other than enterobacteria or lactococci, mycobacteria and pseudomonads, are vastly under investigated.

Phage Therapy - Everything Old is New Again

The study of bacterial viruses (bacteriophages or phages) proved pivotal in the nascence of the disciplines of molecular biology and microbial genetics, providing important information on the central processes of the bacterial cell (DNA replication, transcription and translation) and on how DNA can be transferred from one cell to another. As a result of the pioneering genetics studies and modern genomics, it is now known that phages have contributed to the evolution of the microbial cell and to its pathogenic potential. Because of their ability to transmit genes, phages have been exploited to develop cloning vector systems. They also provide a plethora of enzymes for the modern molecular biologist. Until the introduction of antibiotics, phages were used to treat bacterial infections (with variable success). Western science is now having to re-evaluate the application of phage therapy - a therapeutic modality that never went out of vogue in Eastern Europe - because of the emergence of an alarming number of antibiotic-resistant bacteria. The present article introduces the reader to phage biology, and the benefits and pitfalls of phage therapy in humans and animals.

PlyC: a multimeric bacteriophage lysin

Lysins are murein hydrolases produced by bacteriophage that act on the bacterial host cell wall to release progeny phage. When added extrinsically in their purified form, these enzymes produce total lysis of susceptible Gram-positive bacteria within seconds, suggesting a unique antimicrobial strategy. All known Gram-positive lysins are produced as a single polypeptide containing a catalytic activity domain, which cleaves one of the four major peptidoglycan bonds, and a cell-wall-binding domain, which may bind a species-specific carbohydrate epitope in the cell wall. Here, we have cloned and expressed a unique lysin from the streptococcal bacteriophage C(1), termed PlyC. Molecular characterization of the plyC operon reveals that PlyC is, surprisingly, composed of two separate gene products, PlyCA and PlyCB. Based on biochemical and biophysical studies, the catalytically active PlyC holoenzyme is composed of eight PlyCB subunits for each PlyCA. Inhibitor studies predicted the presence of an active-site cysteine, and bioinformatic analysis revealed a cysteine, histidine-dependent amidohydrolase/peptidase domain within PlyCA. Point mutagenesis confirmed that PlyCA is responsible for the observed catalytic activity, and Cys-333 and His-420 are the active-site residues. PlyCB was found to self-assemble into an octamer, and this complex alone was able to direct streptococcal cell-wall-specific binding. Similar to no other proteins in sequence databases, PlyC defines a previously uncharacterized structural family of cell-wall hydrolases.

Bacteriophage lytic enzymes: novel anti-infectives

Bacteriophage lytic enzymes, or lysins, are highly evolved molecules produced by bacterial viruses (bacteriophage) to digest the bacterial cell wall for bacteriophage progeny release. Small quantities of purified recombinant lysin added to gram-positive bacteria causes immediate lysis resulting in log-fold death of the target bacterium. Lysins have now been used successfully in animal models to control pathogenic antibiotic resistant bacteria found on mucosal surfaces and in blood. The advantages over antibiotics are their specificity for the pathogen without disturbing the normal flora, the low chance of bacterial resistance to lysins and their ability to kill colonizing pathogens on mucosal surfaces, capabilities that were previously unavailable. Thus, lysins could be an effective anti-infective in an age of mounting antibiotic resistance.

Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

Background

Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. In this paper we analyzed oligonucleotide usage (OU) biases in a comprehensive collection of 155 completely sequenced bacterial chromosomes, 316 plasmids and 104 phages.

Results

Two global features were analyzed: pattern skew (PS) and variance of OU deviations normalized by mononucleotide content of the sequence (OUV). OUV reflects the strength of OU biases and taxonomic signals. PS denotes asymmetry of OU in direct and reverse DNA strands. A trend towards minimal PS was observed for almost all complete sequences of bacterial chromosomes and plasmids, however, PS was substantially higher in separate genomic loci and several types of plasmids and phages characterized by long stretches of non-coding DNA and/or asymmetric gene distribution on the two DNA strands. Five of the 155 bacterial chromosomes have anomalously high PS, of which the chromosomes of Xylella fastidiosa 9a5c and Prochlorococcus marinus MIT9313 exhibit extreme PS values suggesting an intermediate unstable state of these two genomes.

Conclusions

Strand symmetry as indicated by minimal PS is a universally conserved feature of complete bacterial genomes that results from the matching mutual compensation of local OU biases on both replichors while OUV is more a taxon specific feature. Local events such as inversions or the incorporation of genome islands are balanced by global changes in genome organization to minimize PS that may represent one of the leading evolutionary forces driving bacterial genome diversification.

The bifunctional peptidoglycan lysin of Streptococcus agalactiae bacteriophage B30

A group B streptococcal (GBS) bacteriophage lysin gene was cloned and expressed inEscherichia coli. The purified recombinant enzyme, calculated to have a molecular mass of 49 677 Da, lysed GBS cells. The susceptibility of GBS cells to lysis by the enzyme depended upon the growth stage at which they were harvested, with early exponential phase cells most sensitive. Calcium ions enhanced the activity of the enzyme. The enzyme also lysed otherβ-haemolytic streptococci, including groups A, C, E and G streptococci, but not common oral streptococci, includingStreptococcus mutans. The generation of both reducing activity and N-terminal alanine residues during lysis indicated that the lysin is a bifunctional enzyme, possessing both glycosidase and endopeptidase activities. This is consistent with the presence of two conserved sequence domains, an Acm (acetylmuramidase) domain associated with lysozyme activity, and a CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain associated with endopeptidase activity. Site-directed mutagenesis of conserved cysteine and histidine residues in the CHAP domain and conserved aspartate and glutamate residues in the Acm domain confirmed their importance for lysozyme and endopeptidase activity respectively.

Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an atypical pneumococcus

We report the complete genomic sequence of EJ-1, an inducible prophage isolated from an atypical Streptococcus pneumoniae strain that belongs to the Myoviridae morphology family. The phage and bacterial recombinational sites (attachment sites) have been also determined. The genome of the EJ-1 prophage (42935 bp) is organized in 73 open reading frames (ORFs) and in at least five major clusters. Bioinformatic and N-terminal amino acid sequence analyses enabled the assignment of possible functions to 52 ORFs. The predicted proteins coded for the EJ-1 genome revealed similarities in the lysogeny, DNA replication, regulation, packaging, and head morphogenesis protein clusters with those from several siphoviruses infecting lactic acid bacteria. However, the proteins encoded by genes orf53 to orf64, corresponding to putative tail proteins of the virion, were very similar to those of the defective Bacillus subtilis myovirus PBSX with the notable exception of the gene product of orf56 (the tape measure tail protein) that was similar to proteins from phages infecting Gram-negative bacteria. The first description of the genome of a myovirus infecting a low G + C content Gram-positive bacterium, a member of a group embracing important human pathogens and industrial relevant species, will contribute to expand our current knowledge on phage biology and evolution.

Isolation and characterization of the bacteriophage WO from Wolbachia, an arthropod endosymbiont

Wolbachia is a group of obligate symbiotic bacteria found in many insects and other arthropods. The presence of Wolbachia alters reproduction in the host, but the mechanisms are unknown. Molecular biological studies of Wolbachia have delayed significantly, and one of the reasons is the lack of transformation techniques of this bacterium. In the present study, bacteriophage particles were isolated from Wolbachia for the first time. The purified phage had an isometric head that was approximately 40 nm in diameter and contained linear double-stranded DNA of approximately 20 kbp. Partial sequence information (total of 20,484 bp) revealed that there were 24 open reading frames including a structural gene module, and genes for replication and lysogenic conversion. This bacteriophage is the only known mobile genetic element potentially used for transformation of Wolbachia.