Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing

Since implementation of the 13-valent polyvalent conjugate vaccine (PCV13) in Canada during 2010, the proportion of PCV13 serotypes causing invasive pneumococcal disease (IPD) has declined from 55% (n = 1492) in 2010 to 31% (n = 764) in 2014. A concurrent increase of non-PCV13 serotypes has occurred and 22F has become the most prevalent serotype in Canada increasing from 7% (n = 183) to 11% (n = 283). Core single nucleotide variant phylogenetic analysis was performed on 137 Streptococcus pneumoniae serotype 22F isolates collected across Canada from 2005–2015. Six phylogenetic lineages (n = 117) were identified among a serotype 22F/ST433 clonal complex (CC), including a recently expanding erythromycin-resistant clone. Erythromycin-resistance was observed in 25 isolates possessing ermB, mef or a 23S rRNA A2061G point mutation; 2 penicillin-resistant isolates had recombinant pbp1a, pbp2a and/or pbp2x; 3 tetracycline-resistant isolates contained tetM; and 1 isolate was multidrug-resistant. Virulence factor analysis indicated a high level of homogeneity among the 22F/ST433 clonal complex strains. A group of 6 phylogenetic outlier strains had differing MLST, antimicrobial resistance and molecular profiles suggestive of capsule switching events. While capsule switch events among S. pneumoniae serotype 22F has been observed, increasing prevalence of S. pneumoniae serotype 22F can be attributed to an evolving homogenous clone expanding nationally through local transmission events.自2010年加拿大启用13价多价结合疫苗（13-valent polyvalent conjugate vaccine, PCV13）以来，导致侵袭性肺炎球菌疾病（invasive pneumococcal disease, IPD）的PCV13血清型占比已从2010年的55%（n=1492）降至2014年的31%（n=764）。与此同时，非PCV13血清型的占比出现同步上升，且22F血清型已成为加拿大最流行的肺炎球菌血清型，其占比从7%（n=183）升至11%（n=283）。本研究对2005至2015年加拿大全国范围内收集的137株肺炎链球菌22F血清型分离株开展了核心单核苷酸变异系统发育分析。在22F血清型/ST433克隆复合体（clonal complex, CC）中鉴定出6个系统发育谱系（n=117），其中包含一个近期正在扩散的红霉素耐药克隆。25株分离株携带ermB、mef基因或23S rRNA A2061G点突变，表现为红霉素耐药；2株青霉素耐药分离株携带重组的pbp1a、pbp2a和/或pbp2x基因；3株四环素耐药分离株携带tetM基因；另有1株为多重耐药株。毒力因子分析显示，22F/ST433克隆复合体菌株具有高度的同源性。另有6株系统发育异常株，其多位点序列分型（multilocus sequence typing, MLST）、抗菌药物耐药谱及分子特征均提示存在荚膜转换事件。尽管此前已在肺炎链球菌22F血清型中观察到荚膜转换事件，但加拿大22F血清型肺炎球菌流行率的上升，可归因于一个不断演化的同源克隆通过本地传播事件在全国范围内扩散。