First Complete Genome Sequence of Two Staphylococcus epidermidis Bacteriophages

Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY 10021, USA.
Journal of Bacteriology (Impact Factor: 2.81). 04/2007; 189(5):2086-100. DOI: 10.1128/JB.01637-06
Source: PubMed


Staphylococcus epidermidis is an important opportunistic pathogen causing nosocomial infections and is often associated with infections in patients with implanted prosthetic devices. A number of virulence determinants have been identified in S. epidermidis, which are typically acquired through horizontal gene transfer. Due to the high recombination potential, bacteriophages play an important role in these transfer events. Knowledge of phage genome sequences provides insights into phage-host biology and evolution. We present the complete genome sequence and a molecular characterization of two S. epidermidis phages, phiPH15 (PH15) and phiCNPH82 (CNPH82). Both phages belonged to the Siphoviridae family and produced stable lysogens. The PH15 and CNPH82 genomes displayed high sequence homology; however, our analyses also revealed important functional differences. The PH15 genome contained two introns, and in vivo splicing of phage mRNAs was demonstrated for both introns. Secondary structures for both introns were also predicted and showed high similarity to those of Streptococcus thermophilus phage 2972 introns. An additional finding was differential superinfection inhibition between the two phages that corresponded with differences in nucleotide sequence and overall gene content within the lysogeny module. We conducted phylogenetic analyses on all known Siphoviridae, which showed PH15 and CNPH82 clustering with Staphylococcus aureus, creating a novel clade within the S. aureus group and providing a higher overall resolution of the siphophage branch of the phage proteomic tree than previous studies. Until now, no S. epidermidis phage genome sequences have been reported in the literature, and thus this study represents the first complete genomic and molecular description of two S. epidermidis phages.

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    • "In dsDNA phages, the combined action of the holin-lysin genes function in the release of new phage particles from an infected cell (Daniel et al., 2007). ORF 69 was found to encode a putative endolysin sharing 89% identity with that of 949, which possesses an amidase_2 domain pfam01510. "
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    ABSTRACT: Lactococci isolated from non-dairy sources have been found to possess enhanced metabolic activity when compared to dairy strains. These capabilities may be harnessed through the use of these strains as starter or adjunct cultures to produce more diverse flavor profiles in cheese and other dairy products. To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ΦL47, was isolated from a sewage sample using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. Visualization of phage virions by transmission electron microscopy established that this phage belongs to the family Siphoviridae and possesses a long tail fiber, previously unseen in dairy lactococcal phages. Determination of the lytic spectrum revealed a broader than expected host range, with ΦL47 capable of infecting 4 industrial dairy strains, including ML8, HP and 310, and 3 additional non-dairy isolates. Whole genome sequencing of ΦL47 revealed a dsDNA genome of 128, 546 bp, making it the largest sequenced lactococcal phage to date. In total, 190 open reading frames (ORFs) were identified, and comparative analysis revealed that the predicted products of 117 of these ORFs shared greater than 50% amino acid identity with those of L. lactis phage Φ949, a phage isolated from cheese whey. Despite their different ecological niches, the genomic content and organization of ΦL47 and Φ949 are quite similar, with both containing 4 gene clusters oriented in different transcriptional directions. Other features that distinguish ΦL47 from Φ949 and other lactococcal phages, in addition to the presence of the tail fiber and the genome length, include a low GC content (32.5%) and a high number of predicted tRNA genes (8). Comparative genome analysis supports the conclusion that ΦL47 is a new member of the 949 lactococcal phage group which currently includes the dairy Φ949.
    Frontiers in Microbiology 01/2014; 4:417. DOI:10.3389/fmicb.2013.00417 · 3.99 Impact Factor
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    • "We compared the genomes of the three S. epidermidis phages and the prophage to the genomes of two previously published S. epidermidis phages, PH15 and CNPH82 (Supplemental Fig. S10; Daniel et al. 2007). The genomes of the three phages exhibit similarity in terms of overall length and gene synteny (see Supplemental Material for a detailed discussion). "
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    ABSTRACT: The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. 96 % of the sequencing reads were assembled into scaffolds of >500 bp length that could be assigned to organisms at the strain level. Six essentially complete (~99 %) and two near-complete genomes were assembled for bacteria that comprised as little as 1 % of the community, as well as nine partial genomes of bacteria representing as little as 0.05 %. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phage that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals and phage. At the species level we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community. These results highlight the benefit of reconstructing complete genomes from metagenomic data and demonstrate methods for achieving this goal.
    Genome Research 08/2012; 23(1). DOI:10.1101/gr.142315.112 · 14.63 Impact Factor
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    • "The G + C content of phi-IPLA5 and phi-IPLA7 was 34.7%, which is slightly higher than that of S. epidermidis strains (32%) [17]. A BLASTN search revealed that nucleotide sequence of phi-IPLA5 and phi-IPLA7 shared a high degree of similarity with the other two S. epidermidis phages phiPH15 and phiCNPH82 (64% and 65%, for phi-IPLA5, and 81% and 67% for phi-IPLA7, respectively) [14]. Bioinformatic analysis revealed a similar organization of the two phages in five functional modules (packaging, structure/morphogenesis, host lysis, lysogeny and replication/regulation) that perfectly fits the general structure of most double-stranded DNA bacteriophages [18]. "
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    ABSTRACT: Background Staphylococcus epidermidis is a commensal bacterium but can colonize the hospital environment due to its ability to form biofilms favouring adhesion to host tissues, medical devices and increasing resistance to antibiotics. In this context, the use of phages to destroy biofilms is an interesting alternative. Results The complete genomes of two Staphylococcus epidermidis bacteriophages, vB_SepiS-phiIPLA5 and vB_SepiS-phiIPLA7, have been analyzed. Their genomes are 43,581 bp and 42,123 bp, and contain 67 and 59 orfs. Bioinformatic analyses enabled the assignment of putative functions to 36 and 29 gene products, respectively, including DNA packaging and morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, regulation, modification and replication. A point mutation in vB_SepiS-phiIPLA5 lysogeny control-associated genes explained its strictly lytic behaviour. Comparative analysis of phi-IPLA5 and phi-IPLA7 genome structure resembled those of S. epidermidis ϕPH15 and ϕCNPH82 phages. A mosaic structure of S. epidermidis prophage genomes was revealed by PCR analysis of three marker genes (integrase, major head protein and holin). Using these genes, high prevalence (73%) of phage DNA in a representative S. epidermidis strain collection consisting of 60 isolates from women with mastitis and healthy women was determined. Putative pectin lyase-like domains detected in virion-associated proteins of both phages could be involved in exopolysaccharide (EPS) depolymerization, as evidenced by both the presence of a clear halo surrounding the phage lysis zone and the phage-mediated biofilm degradation. Conclusions Staphylococcus epidermidis bacteriophages, vB_SepiS-phiIPLA5 and vB_SepiS-phiIPLA7, have a mosaic structure similar to other widespread S. epidermidis prophages. Virions of these phages are provided of pectin lyase-like domains, which may be regarded as promising anti-biofilm tools.
    BMC Genomics 06/2012; 13(1):228. DOI:10.1186/1471-2164-13-228 · 3.99 Impact Factor
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