Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae.
Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae.
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DOI：
10.1371/journal.pone.0189163
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Lefebvre B
中科院分区：
文献类型：
--
作者：
Mauffrey F;Fournier É;Demczuk W;Martin I;Mulvey M;Martineau C;Lévesque S;Bekal S;Domingo MC;Doualla-Bell F;Longtin J;Lefebvre B
肺炎链球菌是引起肺炎、脑膜炎和其他肺炎球菌感染的主要原因之一。循环S.肺炎血清型鉴定是公共卫生实验室的一项基本服务，用于监测引入肺炎球菌结合疫苗（PCV）后推定的血清型替代和免疫接种计划的有效性。Quellung方法仍然是S分型的金标准。肺炎。虽然这种方法非常有效，但由于其主观性质，它也是昂贵的，耗时的并且不完全可靠。本研究的目的是测试和评价3种不同分子方法与Quellung方法相比的效率。选择了多重PCR、sequetyping和全基因组测序（WGS），并使用一组不同的S。肺炎。118株，涵盖83个血清型进行多重PCR和分离分型，而88株，涵盖53个血清型进行WGS。顺序多重PCR允许在血清组或亚组水平上鉴定显着比例（49%）的血清型，但在血清型水平上仅鉴定了27%。使用WGS，55%-60%的分离株在血清型水平上被鉴定，这取决于所使用的分析策略。最后，分离分型表现出最低的性能，有17%的血清型被错误识别。使用Jin cpsB数据库代替GenBank数据库略微改善了结果，但没有显著影响sequetyping的效率。虽然这些分子方法目前都不能取代Quellung方法，但WGS仍然是最有前途的分子肺炎球菌血清分型方法。
Streptococcus pneumoniae is one of the major causes of pneumonia, meningitis and other pneumococcal infections in young children and elders. Determination of circulating S. pneumoniae serotypes is an essential service by public health laboratories for the monitoring of putative serotype replacement following the introduction of pneumococcal conjugate vaccines (PCVs) and of the efficacy of the immunization program. The Quellung method remains the gold standard for typing S. pneumoniae. Although this method is very effective, it is also costly, time consuming and not totally reliable due to its subjective nature. The objectives of this study were to test and evaluate the efficiency of 3 different molecular methods compared to the Quellung method. Sequential multiplex PCR, sequetyping and whole genome sequencing (WGS) were chosen and tested using a set of diverse S. pneumoniae. One-hundred and eighteen isolates covering 83 serotypes were subjected to multiplex PCR and sequetyping while 88 isolates covering 53 serotypes were subjected to WGS. Sequential multiplex PCR allowed the identification of a significant proportion (49%) of serotypes at the serogroup or subset level but only 27% were identified at the serotype level. Using WGS, 55% to 60% of isolates were identified at the serotype level depending on the analysis strategy used. Finally, sequetyping demonstrated the lowest performance, with 17% of misidentified serotypes. The use of Jin cpsB database instead of the GenBank database slightly improved results but did not significantly impact the efficiency of sequetyping. Although none of these molecular methods may currently replace the Quellung method, WGS remains the most promising molecular pneumococcal serotyping method.
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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：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
3.7
作者：
Elberse K;Witteveen S;van der Heide H;van de Pol I;Schot C;van der Ende A;Berbers G;Schouls L
通讯作者：
Schouls L
影响因子：
12.7
作者：
Feikin, DR;Schuchat, A;Jorgensen, JH
通讯作者：
Jorgensen, JH
影响因子：
3.7
作者：
Everett, Dean B.;Cornick, Jennifer;Bentley, Stephen D.
通讯作者：
Bentley, Stephen D.