Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185  S . pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.

中文翻译：

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疫苗引入前后西非肺炎球菌脑膜炎的系统地理学和耐药组

尽管在西非造成了巨大的疾病负担，但人们对导致该地区 5 岁以下儿童脑膜炎的肺炎链球菌的基因组流行病学知之甚少。我们分析了来自 185 S的全基因组测序数据 。肺炎链球菌 作为 2010 年至 2016 年世界卫生组织 (WHO) 侵入性细菌性疾病监测的一部分，从疑似小儿脑膜炎病例中回收的分离株。重建系统发育，计算辅助基因组相似性，并从基因组数据中推断出抗微生物药物耐药性模式，并与椎间盘扩散的表型抗性。我们分别研究了中西部次区域引入肺炎球菌结合疫苗 (PCV) 前后血清型分布的变化。非疫苗、PCV7（4、6B、9V、14、18C、19F 和 23F）和其他 PCV13 血清型（1、3、5、6A、19A 和 7F）的总体分布在 PCV 引入前后没有显着变化在中部地区（Fisher 检验P值 0.27），尽管在 PCV 引入后期间非疫苗血清型的比例增加到 40%（n =6），而相比 21.9%（n =14）。在西部次区域，PCV13 血清型在引入 PCV7 后冈比亚的分离株中占主导地位，占 81 % ( n = 17)，而邻国塞内加尔的 PCV 前时期为 51 % ( n=27)。系统发育说明了与西非小儿脑膜炎相关的菌株的多样性，并强调了系统地理聚类的存在，来自同一亚区域的分离株聚类并共享相似的辅助基因组内容。在所有子区域均检测到已知对青霉素、氯霉素、复方新诺明和四环素产生耐药性的抗生素耐药基因型。然而，没有明显的趋势将耐药基因型的存在与疫苗引入期或菌株是疫苗血清型还是非疫苗血清型联系起来。抗性基因型在系统发育树的选定亚进化枝中似乎是保守的，表明克隆遗传。我们的数据强调需要继续监测非疫苗血清型以及氯霉素和青霉素耐药性的出现，因为这些抗生素可能仍在资源匮乏地区用于经验性治疗。本文包含由 Microreact 托管的数据。