Abstract
In Staphylococcus aureus, the disease impact of chromosomally integrated prophages on virulence is well described. However, the existence of extra-chromosomal prophages, both plasmidial and episomal, remains obscure. Despite the recent explosion in bacterial and bacteriophage genomic sequencing, studies have failed to specifically focus on extra-chromosomal elements. We selectively enriched and sequenced extra-chromosomal DNA from S. aureus isolates using Roche-454 technology and uncovered evidence for the widespread distribution of multiple extra-chromosomal prophages (ExPΦs) throughout both antibiotic-sensitive and -resistant strains. We completely sequenced one such element comprised of a 43.8 kbp, circular ExPΦ (designated ФBU01) from a vancomycin-intermediate S. aureus (VISA) strain. Assembly and annotation of ФBU01 revealed a number of putative virulence determinants encoded within a bacteriophage immune evasion cluster (IEC). Our identification of several potential ExPΦs and mobile genetic elements (MGEs) also revealed numerous putative virulence factors and antibiotic resistance genes. We describe here a previously unidentified level of genetic diversity of stealth extra-chromosomal elements in S. aureus, including phages with a larger presence outside the chromosome that likely play a prominent role in pathogenesis and strain diversity driven by horizontal gene transfer (HGT).
Highlights
Integrated prophages are known to play key roles in the pathogenicity and virulence of S. aureus
BLASTN homology searches of these contigs revealed that ExPWs were prevalent; seven of nine vancomycinintermediate S. aureus (VISA), three of seven methicillin-resistant S. aureus (MRSA), and three of five methicillin-sensitive S. aureus (MSSA) extra-chromosomal DNA samples possessed phage genes (Figure 2 and Figure S1 in File S1)
Phage DNA was not identified in the two vancomycin-resistant S. aureus (VRSA) strains (VRS2 and VRS3a) and the one vancomycin-intermediate S. epidermidis (VISE) strain (NRS53)
Summary
Integrated prophages are known to play key roles in the pathogenicity and virulence of S. aureus. In addition to chromosomally integrated forms, prophages have been reported to exist as lysogenic linear and circular ‘plasmidial’ elements extra-chromosomally in Escherichia, Bacillus, Halomonas, Chlamydia, and Borrelia species [4,5,6,7,8,9]. The presence of plasmidial prophages in B. burgdorferi and C. pneumoniae is attributed to evolutionary pressure on their smaller genomes to remove all non-essential DNA [10,11]. B. anthracis strains isolated worldwide have nearly identical chromosomal prophage sequences, yet up to 20% of isolates encode a diverse array of additional inducible phages [9,12,13,14,15,16,17]. The potential importance of these extra-chromosomal prophages is described in a recent study of B. anthracis phages (likely plasmidial) with significant roles in the adaptive behavior of the pathogen [18]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
