Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing.
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing.
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DOI：
10.1099/mgen.0.000494
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发表时间：
2021-01
影响因子：
3.9
通讯作者：
Weinberger DM
中科院分区：
文献类型：
--
作者：
Knight JR;Dunne EM;Mulholland EK;Saha S;Satzke C;Tothpal A;Weinberger DM
肺炎链球菌的血清分型是病原体监测以及疫苗开发和评价的关键工具。全基因组DNA测序和分析正变得越来越普遍，是一种有效的方法，肺炎球菌血清型鉴定的纯菌株。然而，由于肺炎球菌荚膜位点的复杂性，目前的分析软件要求样品是纯的（或接近纯的），并且仅含有单一的肺炎球菌血清型。我们介绍了一种新的软件工具SeroCall，它可以识别和定量样品中存在的血清型，即使存在几种血清型。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，并可在https://github.com/knightjimr/serocall上以开源许可证免费获得。使用已知浓度的不同血清型样本以及盲样，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室研究，并且可以提供比替代方法更便宜和更有效的血清分型方法。
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.
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影响因子：
2.7
作者：
Kapatai G;Sheppard CL;Al-Shahib A;Litt DJ;Underwood AP;Harrison TG;Fry NK
通讯作者：
Fry NK
影响因子：
5
作者：
Weinberger, Daniel M.;Bruden, Dana T.;Feikin, Daniel R.
通讯作者：
Feikin, Daniel R.
DOI：
10.1016/j.cmi.2017.10.013
发表时间：
2018-04
期刊：
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
影响因子：
--
作者：
Besser J;Carleton HA;Gerner-Smidt P;Lindsey RL;Trees E
通讯作者：
Trees E
影响因子：
2.7
作者：
Carvalho, Maria da Gloria;Pimenta, Fabiana C.;Beall, BernardW.
通讯作者：
Beall, BernardW.
影响因子：
5.5
作者：
Satzke, Catherine;Turner, Paul;O'Brien, Katherine L.
通讯作者：
O'Brien, Katherine L.