In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children’s immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008–2009): n=232, post-PCV10 (2012–2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l−1); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.

中文翻译：

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巴西 PCV10 前和 PCV10 后侵入性肺炎链球菌分离株的基因组监测

2010年，巴西将10价肺炎球菌结合疫苗（PCV10）纳入国家儿童免疫规划。本研究描述了PCV10 引入前后侵袭性肺炎链球菌分离株的遗传特征。466 个子集 [pre-PCV10 (2008–2009)：n =232，post-PCV10 (2012–2013)：n =234；<5 岁：n =310，≥5 岁：n =156] 通过国家实验室监测收集的肺炎球菌分离株进行全基因组测序 (WGS) 以确定血清型、菌毛基因座、抗菌素耐药性和遗传谱系。引入 PCV10 后，在 <5 岁年龄组中，非疫苗血清型 (NVT) 血清型 3 和血清型 19A 最常见，而血清型 12F、8 和 9 N 在≥5 岁组中最常见。该研究确定了 65 个全球肺炎球菌序列簇 (GPSC)：49 个 (88%) 是先前描述的 GPSC，16 个 (12%) 是巴西簇。总共有 36 个 GPSC (55%) 是 NVT 谱系，18 个 (28%) 疫苗血清型 (VT) 和 11 个 (17%) 是 VT 和 NVT 谱系。在两个采样周期中，最常见的谱系是 GPSC6（CC156，血清型 14/9V）。在<5岁组中，青霉素减少（P=0.0123）和复方新诺明（P <0.0001）耐药和四环素增加（P = 0.019）。预计 40% 的分离株对青霉素不敏感；确定了 127 种 PBP 组合（51 种预测的 MIC≥0.125 mg l -1）；复方新诺明（fol A 和/或fol P 改变）、大环内酯（mef和/或ermB）和四环素（tet M、tet O 或tet S /M) 预计分别有 63%、13% 和 21.6% 的肺炎球菌具有耐药性。PCV10 后与多药耐药相关的主要谱系包括 NVT、GPSC1（CC320，血清型 19A）和 GPSC47（ST386，血清型 6C）。该研究为未来的比较提供了一个基线，并确定了巴西 PCV10 后时期的重要 NVT 谱系。