First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Abstract

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, PH15 (PH15) and CNPH82 (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.Staphylococcus epidermidis, a member of the novobiocin-susceptible coagulase-negative staphylococci, is an important opportunistic pathogen and a major cause of nosocomial infections (42, 55). S. epidermidis predominantly colonizes the mucous membranes, groin, and axillar areas, as well as the cutaneous system of human body, with bacterial counts of up to 10 to 10 3 CFU/cm 2 (26). S. epidermidis is usually considered a harmless commensal microorganism; however, infections can occur in immunocompromised individuals and in patients with indwelling or implanted medical devices such as prosthetic heart valves and joint prostheses, where the staphylococci penetrate cutaneous and mucosal barriers (79). With the increasing use of such devices in medical practice, several million people are affected by complications arising from S. epidermidis infections (49). The widespread use of various antimicrobial agents, including penicillins, macrolides, aminoglycosides, and semisynthetic penicillins such as methicillin, has now led to the emergence of multiple-drug-resistant S. epidermidis strains (21, 72).Two S. epidermidis genomes have been sequenced: those of the non-biofilm-forming, non-infection-associated strain ATCC 12228 and the infecti...

Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages

“…1). The tails end in multiple-disc baseplate structures reminiscent of those observed for the PH15 and CNPH82 phages previously isolated from the coagulase-negative S. epidermidis species (14). Hence, the three phages belong to the family Siphoviridae within the order Caudovirales (1).…”

“…Accordingly, several classification systems were proposed for staphylococcal phages based on morphology and serology (10,49) or on comparative genomics (14,37) or using specific marker genes representative of functional modules (e.g., integrase genes) (26,34). A recent classification proposed by Kwan et al (37) groups 27 S. aureus phages into three classes depending on their genome sizes (class I, Podoviridae; class II, Siphoviridae; and class III, Myoviridae).…”

“…Using comparative genomics, class II was further divided into three clades. A new clade was added later in class II by Daniel et al after including additional Siphoviridae phage sequences, including S. epidermidis phages (14).…”

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

“…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).…”

Deciphering Genomic Virulence Traits of a Staphylococcus epidermidis Strain Causing Native-Valve Endocarditis

“…A first cluster of 42 kb comprised of 64 genes was identified by BLASTP as a complete S. epidermidis bacteriophage previously described as vB_SepiS-phiIPLA7 (14). As in other bacterial species, bacteriophages are known in S. epidermidis to play a role in lateral gene transfer (15). A second cluster of 34 kb was identified as arginine catabolic mobile element II (ACME II) (16).…”