Pneumococcal prophages are diverse, but not without structure or history

Abstract

Bacteriophages (phages) infect many bacterial species, but little is known about the diversity of phages among the pneumococcus, a leading global pathogen. The objectives of this study were to determine the prevalence, diversity and molecular epidemiology of prophages (phage DNA integrated within the bacterial genome) among pneumococci isolated over the past 90 years. Nearly 500 pneumococcal genomes were investigated and RNA sequencing was used to explore prophage gene expression. We revealed that every pneumococcal genome contained prophage DNA. 286 full-length/putatively full-length pneumococcal prophages were identified, of which 163 have not previously been reported. Full-length prophages clustered into four major groups and every group dated from the 1930–40 s onward. There was limited evidence for genes shared between prophage clusters. Prophages typically integrated in one of five different sites within the pneumococcal genome. 72% of prophages possessed the virulence genes pblA and/or pblB. Individual prophages and the host pneumococcal genetic lineage were strongly associated and some prophages persisted for many decades. RNA sequencing provided clear evidence of prophage gene expression. Overall, pneumococcal prophages were highly prevalent, demonstrated a structured population, possessed genes associated with virulence, and were expressed under experimental conditions. Pneumococcal prophages are likely to play a more important role in pneumococcal biology and evolution than previously recognised.

Prophages and satellite prophages are widespread amongStreptococcusspecies and may play a role in pneumococcal pathogenesis

“…We had previously determined the prevalence, diversity and molecular epidemiology of full-length prophages in a global and historical pneumococcal genome dataset 26 . Many shorter prophage sequences were also identified in that study, which were simply classified as partial prophage sequences and not characterised further at the time.…”

“…We previously reported that pneumococcal full-length prophages were consistently integrated in specific locations within the genome 26 . Likewise, pneumococcal satellite prophages were consistently integrated in seven precise locations (a-f) within the host genome, each of which was directly associated with the integrase gene they harboured (Figure 3d; Figure 4a).…”

“…Previous work has shown that prophage-related sequences are highly prevalent within S . pneumoniae 26,28 , S . pyogenes 25,30 and S .…”

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

“…Resolution rules for ICE/phage double calls were based on inspection of the 26 instances found among TIGER/Islander, temperate phage, and ICE datasets. Phage1/ICE double calls were found to be either an unresolved ICE/phage tandem or an IGE of one type integrated within another (54), yielding a new category of IGE call (ICE+Phage). Phage2/ICE double calls were converted to the ICE call.…”

Genome sequencing reveals thatStreptococcus pneumoniaepossesses a large and diverse repertoire of antimicrobial toxins

“…The exceptions were the blp clusters: their highly diverse and complicated genetic compositions among pneumococci genomes meant that a similar classification between partial and complete clusters could not be applied (ref. 12). Instead, their presence (irrespective of being partial or complete) is depicted by the green colour.…”