Serotyping of Streptococcus pneumoniae is a critical tool in the surveillance of the pathogen and in the development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software requires samples to be pure (or nearly pure) and only contain a single pneumococcal serotype. We introduce a new software tool called SeroCall, which can identify and quantitate the serotypes present in samples, even when several serotypes are present. The sample preparation, library preparation and sequencing follow standard laboratory protocols. The software runs as fast as or faster than existing identification tools on typical computing servers and is freely available under an open source licence at https://github.com/knightjimr/serocall. Using samples with known concentrations of different serotypes as well as blinded samples, we were able to accurately quantify the abundance of different serotypes of pneumococcus in mixed cultures, with 100 % accuracy for detecting the major serotype and up to 86 % accuracy for detecting minor serotypes. We were also able to track changes in serotype frequency over time in an experimental setting. This approach could be applied in both epidemiological field studies of pneumococcal colonization and experimental laboratory studies, and could provide a cheaper and more efficient method for serotyping than alternative approaches.

中文翻译：

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使用全基因组测序确定肺炎球菌混合样本的血清型组成


肺炎链球菌的血清分型是病原体监测以及疫苗开发和评估的重要工具。全基因组 DNA 测序和分析变得越来越普遍，是鉴定纯分离株肺炎球菌血清型的有效方法。然而，由于肺炎球菌荚膜位点的复杂性，当前的分析软件要求样品是纯的（或接近纯的）并且仅包含单一肺炎球菌血清型。我们推出了一种名为 SeroCall 的新软件工具，即使存在多种血清型，它也可以识别和定量样本中存在的血清型。样品制备、文库制备和测序遵循标准实验室方案。该软件的运行速度与典型计算服务器上的现有识别工具一样快，甚至更快，并且可以在 https://github.com/knightjimr/serocall 上的开源许可证下免费获取。使用已知浓度的不同血清型样品以及盲样样品，我们能够准确定量混合培养物中不同血清型肺炎球菌的丰度，检测主要血清型的准确度为 100%，检测次要血清型的准确度高达 86% 。我们还能够在实验环境中跟踪血清型频率随时间的变化。这种方法可应用于肺炎球菌定植的流行病学现场研究和实验实验室研究，并且可以提供比其他方法更便宜、更有效的血清分型方法。