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

The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 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 (clonal complex 180). A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics, and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain’s evolution. GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage ϕOXC141. Prior to the introduction of PCV13, this clade’s composition shifted towards a ϕOXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also ϕOXC141-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 ϕOXC141 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 experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competence-stimulating peptide pheromone. This resulted in a reduction in the induction of competence for transformation. This interference with the quorum sensing needed to induce competence reduces 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. The online version contains supplementary material available at 10.1186/s13073-022-01147-2.

呼吸道病原体肺炎链球菌（肺炎球菌）是一种基因多样的细菌，与101种以上免疫学上不同的多糖荚膜（血清型）相关。多糖结合疫苗（PCVs）已成功消除了多种靶向血清型，但黏液型血清型3尽管被纳入PCV13中却依然存在。这种荚膜类型主要与一种全球传播的单一菌株GPSC12（克隆复合体180）相关。 一项基因组流行病学研究结合了先前血清型3肺炎球菌的监测数据集，以分析在引入PCV期间GPSC12内的种群结构、动态以及多样化速率的差异。转录组分析、全基因组测序、诱变和电子显微镜被用于表征假设影响该菌株进化的基因座的表型影响。 通过基因组分析，GPSC12被分为不同的分支。分支I是最常见的，很少发生转化，但通常感染有前噬菌体ϕOXC141。在引入PCV13之前，在一个系统抽样的英国样本集中，该分支的组成朝着ϕOXC141阴性的亚群转变。在PCV13使用后的时代，重组更迅速的非分支I分离株（也是ϕOXC141阴性）的流行率有所上升。分支I分离株的低体外转化效率不能完全由血清型3荚膜导致的约100倍降低来解释。因此，发现前噬菌体ϕOXC141会修饰csRNA3，这是一种抑制转化诱导的非编码RNA。这种改变在约30%的所有肺炎球菌中被发现，在异常克隆的血清型1 GPSC2菌株中尤为常见。使用一种基因易于操作的肺炎球菌进行的RNA - seq和定量逆转录酶PCR实验表明，改变后的csRNA3在抑制感受态刺激肽信息素的产生方面更有效。这导致转化感受态诱导的降低。 这种对诱导感受态所需的群体感应的干扰降低了前噬菌体通过同源重组被删除的风险。因此，自私的前噬菌体驱动的调节性RNA的改变限制了细胞间通讯和水平基因转移，使疫苗接种后种群动态的解释变得复杂。 网络版包含补充材料，可在10.1186/s13073 - 022 - 01147 - 2获取。