Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA

Abstract

The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 100 immunologically-distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally-disseminated strain, GPSC12 (CC180), which was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage {phi}OXC141. Prior to the introduction of PCV13, this clades composition shifted towards a {phi}OXC141-negative subpopulation in a systematically-sampled UK collection. In the post-PCV era, more rapidly-recombining non-Clade I isolates, also {phi}OXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the [~]100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage {phi}OXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in [~]30% of all pneumococci, and was particularly common in the unusually-clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR data demonstrated the altered csRNA3 was more effective at inhibiting production of the competence stimulating peptide pheromone. This interference with the quorum sensing needed to induce competence lowered the rate of spontaneous transformation, reducing the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.