英国威康桑格研究所Sophie Belman等研究人员合作揭示肺炎链球菌的地理迁移和适应动态。2024年7月3日，国际知名学术期刊《自然》在线发表了这一成果。

研究人员通过分析从南非收集的地理定位基因组序列（n=6,910，收集时间为2000年至2014年），开发了模型来重建肺炎链球菌的传播路径，并结合了详细的人类流动数据和基因组数据。研究还估算了2009年南非首次实施肺炎球菌结合疫苗后，包含在疫苗中的菌株（疫苗型，VT）和不包含在疫苗中的菌株（非疫苗型，NVT）在群体水平上的适应性变化，评估了对青霉素耐药和不耐药菌株之间的适应性差异。

结果显示，肺炎链球菌在南非需要经过50年的传播才能在全国范围内均匀混合，这种缓慢的传播主要由人类流动的集中性所驱动。在疫苗实施后的几年里，NVT菌株相对于VT菌株的相对适应性增加（相对风险为1.68；95%置信区间为1.59-1.77），并且越来越多的NVT菌株对青霉素产生耐药性。研究结果表明，最初由疫苗引发的抗菌素耐药性减少可能是暂时的。

据介绍，肺炎链球菌是全球肺炎和脑膜炎的主要致病菌。在任何一个地区，多种血清型菌株都会同时流行。然而，传播范围和机制，以及疫苗驱动的适应性和抗菌素耐药性变化仍未被充分量化。

附：英文原文

Title: Geographical migration and fitness dynamics of Streptococcus pneumoniae

Author: Belman, Sophie, Lefrancq, Nomie, Nzenze, Susan, Downs, Sarah, du Plessis, Mignon, Lo, Stephanie W., McGee, Lesley, Madhi, Shabir A., von Gottberg, Anne, Bentley, Stephen D., Salje, Henrik

Issue&Volume: 2024-07-03

Abstract: Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location1,2. The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n=6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59–1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient.

DOI: 10.1038/s41586-024-07626-3

Source: https://www.nature.com/articles/s41586-024-07626-3