Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998–1999 (pre-PCV), before the introduction of PCV13 2010–2011 (PCV7) and after the introduction of PCV13 2012–2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.

中文翻译：

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阿根廷儿童侵袭性疾病肺炎链球菌种群遗传结构、血清型分布及抗生素耐药性

肺炎链球菌引起的侵袭性疾病 (IPD) 是全球幼儿发病率和死亡率的主要原因之一。在阿根廷，PCV13 于 2012 年被引入全国儿童免疫计划，PCV7 从 2000 年开始上市，但仅限于私人市场。自 1993 年以来，由 150 家医院组成的国家 IPD 监测计划作为 SIREVA II-OPS 网络的一部分，在阿根廷对 6 岁以下儿童进行了全国性肺炎球菌监测。共有 1713 株肺炎球菌分离株，其特征为对 10 种抗生素具有血清型 (Quellung) 和抗菌素耐药性（琼脂稀释度），属于三个研究时期：PCV7 前时代 1998-1999 (pre-PCV)，PCV13 引入之前 2010-2011 (PCV7) 和引入 PCV13 2012–2013 (PCV13) 后，可纳入。在整个集合中鉴定出 54 种血清型，血清型 14、5 和 1 占分离株的 50%。对青霉素的耐药率为 34.9%、头孢噻肟 10.6%、美罗培南 4.9%、复方新诺明 45%、红霉素 21.5%、四环素 15.4% 和氯霉素 0.4%。所有分离株均对左氧氟沙星、利福平和万古霉素敏感。在 1713 个分离株中，1061 个（61.9%）对至少一种抗生素不敏感，235 个（13.7%）对多药耐药。作为全球肺炎球菌测序项目 (GPS) 的一部分，随机选择了 413 个分离株的一个子集并对其进行全基因组测序。基因组数据被用于研究种群结构 红霉素 21.5 %、四环素 15.4 % 和氯霉素 0.4 %。所有分离株均对左氧氟沙星、利福平和万古霉素敏感。在 1713 个分离株中，1061 个（61.9%）对至少一种抗生素不敏感，235 个（13.7%）对多药耐药。作为全球肺炎球菌测序项目 (GPS) 的一部分，随机选择了 413 个分离株的一个子集并对其进行全基因组测序。基因组数据被用于研究种群结构 红霉素 21.5 %、四环素 15.4 % 和氯霉素 0.4 %。所有分离株均对左氧氟沙星、利福平和万古霉素敏感。在 1713 个分离株中，1061 个（61.9%）对至少一种抗生素不敏感，235 个（13.7%）对多药耐药。作为全球肺炎球菌测序项目 (GPS) 的一部分，随机选择了 413 个分离株的一个子集并对其进行全基因组测序。基因组数据被用于研究种群结构 肺炎链球菌 使用全球肺炎球菌序列簇 (GPSCs)、序列类型 (STs) 和克隆复合物 (CCs)、流行的血清型及其相关的肺炎球菌谱系和抗菌素耐药性的基因组推断来定义肺炎球菌谱系。该集合显示出非常多样化的菌株。在 413 个分离株中，鉴定出 73 个已知 STs 和 36 个新 STs，属于 38 个 CC 和 25 个单例，分为 52 个 GPSC。在比较 PCV 前和 PCV13 时期时，观察到疫苗类型之间的重要变化；血清型 14、6B 和 19F 显着减少，而 7F 和 3 显着增加。在非 PCV13 类型中，血清组 24 从 PCV 前的 0% 增加到 PCV13 时期的 3.2%。我们的分析表明，预计 66.1 % (273/413) 的分离株对至少一种抗生素和 11 种抗生素不敏感。9 % (49/413) 具有多重耐药性。在比较由 Quellung 和基于 WGS 的血清分型确定的血清型和抗菌素耐药性的 98.4% 时，我们发现一致性为 100%。需要继续监测肺炎球菌种群，以揭示阿根廷肺炎球菌分离株在 PCV13 后的动态。本文包含由 Microreact 托管的数据。