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首页> 外文期刊>Journal of Clinical Microbiology >Evaluation of Pneumococcal Serotyping of Nasopharyngeal-Carriage Isolates by Latex Agglutination, Whole-Genome Sequencing (PneumoCaT), and DNA Microarray in a High-Pneumococcal-Carriage-Prevalence Population in Malawi
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Evaluation of Pneumococcal Serotyping of Nasopharyngeal-Carriage Isolates by Latex Agglutination, Whole-Genome Sequencing (PneumoCaT), and DNA Microarray in a High-Pneumococcal-Carriage-Prevalence Population in Malawi

机译：乳胶凝集，全基因组测序（PNEumocat）和DNA微阵列在马拉维的高肺炎球菌 - 载流性血液中的肺炎骨膜血管型血管型

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Accurate assessment of the serotype distribution associated with pneumococcal colonization and disease is essential for evaluating and formulating pneumococcal vaccines and for informing vaccine policy. For this reason, we evaluated the concordance between pneumococcal serotyping results by latex agglutination, whole-genome sequencing (WGS) with PneumoCaT, and DNA microarray for samples from community carriage surveillance in Blantyre, Malawi. Nasopharyngeal swabs were collected according to WHO recommendations between 2015 and 2017 by using stratified random sampling among study populations. ABSTRACT Accurate assessment of the serotype distribution associated with pneumococcal colonization and disease is essential for evaluating and formulating pneumococcal vaccines and for informing vaccine policy. For this reason, we evaluated the concordance between pneumococcal serotyping results by latex agglutination, whole-genome sequencing (WGS) with PneumoCaT, and DNA microarray for samples from community carriage surveillance in Blantyre, Malawi. Nasopharyngeal swabs were collected according to WHO recommendations between 2015 and 2017 by using stratified random sampling among study populations. Participants included healthy children 3 to 6?years old (vaccinated with the 13-valent pneumococcal conjugate vaccine [PCV13] as part of the Expanded Program on Immunization [EPI]), healthy children 5 to 10?years old (age-ineligible for PCV13), and HIV-infected adults (18 to 40 years old) on antiretroviral therapy (ART). For phenotypic serotyping, we used a 13-valent latex kit (Statens Serum Institut [SSI], Denmark). For genomic serotyping, we applied the PneumoCaT pipeline to whole-genome sequence libraries. For molecular serotyping by microarray, we used the BUGS Bioscience Senti-SP microarray. A total of 1,347 samples were analyzed. Concordance was 90.7% (95% confidence interval [CI], 89.0 to 92.2%) between latex agglutination and PneumoCaT, 95.2% (95% CI, 93.9 to 96.3%) between latex agglutination and the microarray, and 96.6% (95% CI, 95.5 to 97.5%) between the microarray and PneumoCaT. By detecting additional vaccine serotype (VT) pneumococci carried at low relative abundances (median, 8%), the microarray increased VT detection by 31.5% over that by latex serotyping. To conclude, all three serotyping methods were highly concordant in identifying dominant serotypes. Latex serotyping is accurate in identifying vaccine serotypes and requires the least expertise and resources for field implementation and analysis. However, WGS, which adds population structure, and microarray, which adds multiple-serotype carriage, should be considered at regional reference laboratories for investigating the importance of vaccine serotypes at low relative abundances in transmission and disease.
机译：准确评估与肺炎球菌定植和疾病相关的血清型分布对于评估和配制肺炎球菌疫苗并通知疫苗政策是必不可少的。因此，我们评估了乳胶凝集，全基因组测序（WGS）与肺炎粥样族的血管基血管型血清型结果之间的一致性，以及来自Blantyre，Malawi的社区托运监测的样品的DNA微阵列。根据2015年和2017年在研究人口中使用分层随机抽样，根据世卫组织建议收集鼻咽拭子。摘要准确评估与肺炎球菌殖民化和疾病相关的血清型分布对于评估和配制肺炎球菌疫苗并告知疫苗政策至关重要。因此，我们评估了乳胶凝集，全基因组测序（WGS）与肺炎粥样族的血管基血管型血清型结果之间的一致性，以及来自Blantyre，Malawi的社区托运监测的样品的DNA微阵列。根据2015年和2017年在研究人口中使用分层随机抽样，根据世卫组织建议收集鼻咽拭子。与会者包括健康的儿童3至6岁？岁（用13价肺炎球菌缀合物疫苗[PCV13]作为免疫免疫[EPI]）的一部分，健康儿童5至10岁？岁（仅适用于PCV13的年龄）和艾滋病毒感染的成人（18至40岁）对抗逆转录病毒治疗（艺术）。对于表型血清型，我们使用了一个13价乳胶套件（Statens血清Institut [SSI]，丹麦）。对于基因组血清型，我们将肺炎管道施用于全基因组序列文库。对于微阵列的分子血清型，我们使用了Buiscience Senti-SP微阵列。共分析了1,347个样品。胶乳凝集和肺泡之间的95.7％（95％置信区间，89.0至92.2％），胶乳凝集和微阵列之间的95.2％（95％CI，93.9％至96.3％），96.6％（95％CI微阵列和肺泡之间的95.5至97.5％。通过检测在低相对丰度（中位数，8％）的携带的额外疫苗血清型（VT）肺炎球菌，通过乳胶血清型，微阵列将VT检测增加31.5％。为了得出结论，在鉴定显性血清型时，所有三种血清型化方法都是非常一致的。乳胶血清型在识别疫苗血清型方面是准确的，并且需要最少的专业知识和资源进行现场实施和分析。然而，在区域参考实验室应考虑增加增加多种血清型载体的群体结构和微阵列的WGS，用于研究疫苗血清型在透射率和疾病中低相对丰富的重要性。

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