Background Pneumococcal pneumonia is one of the major causes of mortality in children less than 5 years in Asia, especially in India. Available PCVs have less serotype coverage in India compared to western countries. Moreover, the baseline pneumococcal serotype and sequence type data is limited and available data doesn't represent the entire India. With this background we aimed to characterize invasive and carriage isolates of S. pneumoniae from a tertiary care hospital in South India. Materials and Methods A total of 221 S. pneumoniae isolates, invasive (n=138) and carriage (n=83) between the time period of 2012-2018 were included. Isolates was identified and confirmed using standard laboratory protocols. Serotyping was performed by Customized sequential multiplex PCR and MLST as described in www.pubmlst.org. Results The major serotypes were 19F, 6B, 14, 6A and 19A and the sequence types (ST) were ST63, 236 and 230. Predominant STs in invasive was ST 63 whereas in carriage were ST4894 and 1701. High level ST diversity in carriage was observed. Majority of the STs were SLVs or DLVs of previously reported STs or PMEN clones. Phylogenetic analyses of the STs revealed gradual expansion of three PMEN CCs CC320, 63 and 230. Conclusion The vaccine serotypes were the predominant ones found to be associated with IPD, PMEN clones, new STs and antimicrobial resistance. Accordingly, PCV13 is expected to provide invasive serotype coverage of 75% in Indian children less than 5 years. This study provides baseline serotype and sequence type data prior to the introduction of PCV in South India.

中文翻译：

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印度 5 岁以下儿童中侵袭性和携带性肺炎链球菌的克隆相似性和序列类型多样性。

背景 肺炎球菌肺炎是亚洲（尤其是印度）5 岁以下儿童死亡的主要原因之一。与西方国家相比，印度现有 PCV 的血清型覆盖率较低。此外，基线肺炎球菌血清型和序列类型数据有限，可用数据不能代表整个印度。在此背景下，我们旨在描述来自印度南部一家三级护理医院的肺炎链球菌的侵入性和携带分离株的特征。材料和方法 2012-2018 年期间总共纳入 221 株肺炎链球菌分离株，包括侵袭性肺炎链球菌 (n=138) 和携带性肺炎链球菌 (n=83)。使用标准实验室方案对分离株进行鉴定和确认。如 www.pubmlst.org 中所述，通过定制序贯多重 PCR 和 MLST 进行血清分型。结果 主要血清型为 19F、6B、14、6A 和 19A，序列类型（ST）为 ST63、236 和 230。侵入性中主要的 ST 是 ST 63，携带性中的主要 ST 是 ST4894 和 1701。携带性中的高水平 ST 多样性是观察到的。大多数 ST 是先前报道的 ST 或 PMEN 克隆的 SLV 或 DLV。ST 的系统发育分析揭示了三个 PMEN CC CC320、63 和 230 的逐渐扩展。 结论 疫苗血清型是与 IPD、PMEN 克隆、新 ST 和抗菌素耐药性相关的主要血清型。因此，PCV13 预计将为印度 5 岁以下儿童提供 75% 的侵入性血清型覆盖率。本研究提供了在印度南部引入 PCV 之前的基线血清型和序列类型数据。