Wright Meredith S, McCorrison Jamison, Gomez Andres M, Beck Erin, Harkins Derek, Shankar Jyoti, Mounaud Stephanie, Segubre-Mercado Edelwisa, Mojica Aileen May R, Bacay Brian, Nzenze Susan A, Kimaro Sheila Z M, Adrian Peter, Klugman Keith P, Lucero Marilla G, Nelson Karen E, Madhi Shabir, Sutton Granger G, Nierman William C, Losada Liliana
J. Craig Venter InstituteRockville, MD, United States.
Research Institute of Tropical MedicineMuntinlupa City, Philippines.
Front Microbiol. 2017 Sep 6;8:1661. doi: 10.3389/fmicb.2017.01661. eCollection 2017.
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the sp. carriage using a qPCR assay, whole metagenomic sequencing, and serotyping of , as well as 16S rRNA amplicon based community profiling. The carriage in both populations increased with infant age and + samples ranged from 24 to 85% of the samples at each sampling time point. We next developed informatic tools for determining community composition and pneumococcal serotype from metagenomic sequences derived from a subset of longitudinal -positive enrichment cultures from The Philippines ( = 26 infants, 50% vaccinated) and South African ( = 7 infants, 100% vaccinated). NP samples from infants were passaged in enrichment media, and metagenomic DNA was purified and sequenced. capsular serotyping of these 51 metagenomic assemblies assigned known serotypes in 28 samples, and the co-occurrence of serotypes in 5 samples. Eighteen samples were not typeable using known serotypes but did encode for capsule biosynthetic cluster genes similar to non-encapsulated reference sequences. In addition, we performed metagenomic assembly and 16S rRNA amplicon profiling to understand co-colonization dynamics of sp. and other NP genera, revealing the presence of multiple species as well as potential respiratory pathogens in healthy infants. A range of virulence and drug resistant elements were identified as circulating in the NP microbiomes of these infants. This study revealed the frequent co-occurrence of multiple strains along with sp. and other potential pathogens such as in the NP microbiome of these infants. In addition, the serotype analysis proved powerful in determining the serotypes in carriage, and may lead to developing better targeted vaccines to prevent invasive pneumococcal disease (IPD) in these countries. These findings suggest that NP colonization by during the first years of life is a dynamic process involving multiple serotypes and species.
自肺炎球菌结合疫苗（PCV）实施以来，肺炎球菌肺炎显著减少，然而，在许多发展中国家，婴儿肺炎死亡率仍然很高。我们对来自菲律宾和南非的婴儿出生后第一年的鼻咽（NP）微生物群进行了一项研究。该研究包括使用定量聚合酶链反应（qPCR）测定法、全宏基因组测序和肺炎链球菌血清分型，以及基于16S rRNA扩增子的群落分析来确定肺炎链球菌的携带情况。两个群体中的肺炎链球菌携带率均随婴儿年龄增加，每个采样时间点的阳性样本占样本总数的24%至85%。接下来，我们开发了信息学工具，用于从菲律宾（n = 26名婴儿，50%接种疫苗）和南非（n = 7名婴儿，100%接种疫苗）纵向肺炎链球菌阳性富集培养物子集的宏基因组序列中确定群落组成和肺炎链球菌血清型。来自婴儿的NP样本在富集培养基中传代培养，然后纯化宏基因组DNA并进行测序。对这51个宏基因组组装体进行的肺炎链球菌荚膜血清分型在28个样本中确定了已知血清型，并在5个样本中确定了血清型的共现情况。18个样本无法使用已知血清型分型，但确实编码了与非包膜参考序列相似的荚膜生物合成簇基因。此外，我们进行了宏基因组组装和16S rRNA扩增子分析，以了解肺炎链球菌与其他NP属的共定殖动态，揭示了健康婴儿中多种肺炎链球菌物种以及潜在呼吸道病原体的存在。在这些婴儿的NP微生物群中发现了一系列毒力和耐药元件在传播。这项研究揭示了在这些婴儿的NP微生物群中，多种肺炎链球菌菌株与肺炎链球菌以及其他潜在病原体（如金黄色葡萄球菌）频繁共现。此外，肺炎链球菌血清型分析在确定携带的肺炎链球菌血清型方面被证明很有效，可能会促使开发出更好的靶向疫苗，以预防这些国家的侵袭性肺炎球菌疾病（IPD）。这些发现表明，在生命的最初几年中，肺炎链球菌在NP中的定殖是一个涉及多种血清型和物种的动态过程。
