Stanley Sydney, Silva-Costa Catarina, Gomes-Silva Joana, Melo-Cristino Jose, Malley Richard, Ramirez Mario
Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA; Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
EBioMedicine. 2025 Jun 3;117:105781. doi: 10.1016/j.ebiom.2025.105781.
Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn) causing disease among children and adults worldwide. The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal to conduct our population genomics and molecular epidemiology comparative study.
We performed whole-genome sequencing (WGS) of 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999 and 2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics.
Relative to strains from all other lineages, CC180 Clades I, II, III, IV, and VI strains trend towards a decreased association with invasive disease cases compared to non-invasive pneumonia cases (binomial logistic regression, odds ratio or OR = 0.59, 95% confidence interval or CI = [0.34, 0.98], P = 0.046) and adult patients compared to paediatric patients (binomial logistic regression, OR = 0.34, 95% CI = [0.098, 0.92], P = 0.054). The serotype 3 CCs shifted post-PCV13 such that Clades I-VI comprise the majority of post-PCV13 lineages (binomial logistic regression, OR = 7.33, 95% CI = 4.36, 12.80, P < 0.0001), with Clade I representing 54% (220/404) of all post-PCV13 strains. As observed elsewhere, Clade I strains from Portugal are largely antibiotic-sensitive and carry the ΦOXC141 prophage. However, strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins.
Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The additional accessory genome content may mitigate these fitness costs. Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape.
National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.
克隆复合体180（CC180）是目前全球范围内引起儿童和成人疾病的3型肺炎链球菌（Spn）的主要克隆株。尽管13价肺炎球菌结合疫苗（PCV13）中包含多糖，但对3型血清型的疗效并不显著。据推测，PCV13可能有效控制CC180的I分支，但III和IV分支具有抗性，从而引发种群转移，使3型血清型得以持续存在。在美国、英格兰和威尔士已观察到这种情况，但在西班牙未观察到。我们利用来自葡萄牙的数据集进一步验证这一假设，进行了群体基因组学和分子流行病学比较研究。
我们对1999年至2020年间从葡萄牙肺炎球菌感染患者中分离出的501株3型菌株进行了全基因组测序（WGS）。对草图基因组进行了系统发育分析、泛基因组分析和全基因组关联研究（GWAS）。我们还完成了抗生素敏感性测试，并汇总了2600多个3型多位点序列类型180（MLST180）的WGS，以进行全球比较基因组学研究。
相对于所有其他谱系的菌株，CC180的I、II、III、IV和VI分支菌株与侵袭性疾病病例的关联趋势低于非侵袭性肺炎病例（二项式逻辑回归，优势比或OR = 0.59，95%置信区间或CI = [0.34, 0.98]，P = 0.046），与成年患者的关联低于儿科患者（二项式逻辑回归，OR = 0.34，95% CI = [0.098, 0.92]，P = 0.054）。3型CCs在PCV13接种后发生了变化，使得I-VI分支构成了PCV13接种后的主要谱系（二项式逻辑回归，OR = 7.33，95% CI = 4.36, 12.80，P < <0.0001），其中I分支占所有PCV13接种后菌株的54%（220/404）。如在其他地方所观察到的，来自葡萄牙的I分支菌株在很大程度上对抗生素敏感，并携带ΦOXC141原噬菌体。然而，在PCV13接种后I分支仍然占主导地位的葡萄牙和西班牙的菌株具有更大的泛基因组，并与两个编码假设蛋白的基因的存在有关。
尽管存在原噬菌体负担和抗生素敏感性，但I分支在PCV13接种后的葡萄牙占主导地位。额外的辅助基因组内容可能减轻了这些适应性成本。I分支流行率和泛基因组异质性的区域差异表明，分支动态不是理解3型疫苗逃逸的通用方法。
美国国立儿童健康与人类发展研究所、辉瑞公司和默克雪兰诺公司。
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