School of Women and Children's Health, University of New South Wales, Sydney, NSW, Australia; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.
Lancet Microbe. 2022 Jul;3(7):e503-e511. doi: 10.1016/S2666-5247(22)00066-0. Epub 2022 May 9.
Pneumococcal disease is a leading cause of bacterial pneumonia and invasive bacterial disease among children globally. The reason some strains of pneumococci are more likely to cause disease, and how interventions such as vaccines and antibiotics affect pneumococcal strains is poorly understood. We aimed to identify genetic regions under selective pressure and those associated with disease through the analysis of pneumococcal whole-genome sequences.
Whole-genome sequencing was performed on pneumococcal isolates collected between January, 2005, and May, 2018, in Kathmandu, Nepal, which included programmatic ten-valent pneumococcal conjugate vaccine (PCV10) introduction in 2015. Isolates were from three distinct cohorts: nasopharyngeal swabs of healthy community-based children, nasopharyngeal swabs of children admitted to hospital with pneumonia, and sterile-site cultures from children admitted to hospital. Across these cohorts we examined serotype distribution, antibiotic resistance, strain distribution, and regions of recombination to determine genes that were undergoing diversifying selection. Genome-wide association studies comparing pneumonia and sterile-site isolates with healthy carriage were used to determine novel variants associated with disease.
After programmatic introduction of PCV10, there was a decline in vaccine covered serotypes; however, strains that had expressed these serotypes continued to exist in the post-PCV population. We identified GPSC9 to be a strain of concern due to its high prevalence in disease, multidrug resistance, and ability to switch to an unencapsulated phenotype via insertion of virulence factor pspC into the cps locus. Antibiotic resistance loci to co-trimoxazole were found to be prevalent (pre-PCV10 78% vs post-PCV10 81%; p=0·27) and increasingly prevalent to penicillin (pre-PCV10 15% vs post-PCV10 32%; p<0·0001). Regions with multiple recombinations were identified spanning the surface protein virulence factors pspA and pspC and antibiotic targets pbpX, folA, folC, folE, and folP. Furthermore, we identified variants in lacE2 to be strongly associated with isolates from children with pneumonia and PRIP to be strongly associated with isolates from sterile sites.
Our work highlights the effect of pneumococcal conjugate vaccines, antibiotics, and host-pathogen interaction in pneumococcal variation, and the pathogen's capability of adapting to these factors at both population-wide and strain-specific levels. Ongoing surveillance of disease-associated strains and further investigation of lacE2 and PRIP as serotype-independent targets for therapeutic interventions is required.
Gavi, The Vaccine Alliance; WHO; Bill & Melinda Gates Foundation; Wellcome Sanger Institute; and US Centers for Disease Control and Prevention.
肺炎球菌疾病是导致儿童细菌性肺炎和侵袭性细菌性疾病的主要原因。一些肺炎球菌菌株更容易导致疾病的原因，以及疫苗和抗生素等干预措施如何影响肺炎球菌菌株，这些都知之甚少。我们旨在通过分析肺炎球菌全基因组序列，确定受选择压力影响的遗传区域和与疾病相关的遗传区域。
对 2005 年 1 月至 2018 年 5 月在尼泊尔加德满都采集的肺炎球菌分离株进行全基因组测序，其中包括 2015 年计划实施的十价肺炎球菌结合疫苗（PCV10）。分离株来自三个不同的队列：来自健康社区儿童的鼻咽拭子、因肺炎住院的儿童的鼻咽拭子和住院儿童的无菌部位培养物。在这些队列中，我们检查了血清型分布、抗生素耐药性、菌株分布和重组区域，以确定正在经历多样化选择的基因。使用肺炎和无菌部位分离物与健康携带物的全基因组关联研究来确定与疾病相关的新变体。
在计划实施 PCV10 后，疫苗覆盖的血清型有所下降；然而，表达这些血清型的菌株继续存在于 PCV 后人群中。我们发现 GPSC9 是一个令人关注的菌株，因为它在疾病中的高流行率、多种药物耐药性以及通过将毒力因子 pspC 插入 cps 基因座将其转变为无荚膜表型的能力。发现对复方磺胺甲噁唑的抗生素耐药基因座很普遍（PCV10 前 78%，PCV10 后 81%；p=0·27），对青霉素的耐药性越来越普遍（PCV10 前 15%，PCV10 后 32%；p<0·0001）。鉴定出多个重组区域，跨越表面蛋白毒力因子 pspA 和 pspC 以及抗生素靶标 pbpX、folA、folC、folE 和 folP。此外，我们发现 lacE2 中的变体与肺炎患儿的分离物强烈相关，PRIP 与无菌部位分离物强烈相关。
我们的工作强调了肺炎球菌结合疫苗、抗生素和宿主-病原体相互作用对肺炎球菌变异的影响，以及病原体在人群水平和菌株水平适应这些因素的能力。需要对与疾病相关的菌株进行持续监测，并进一步研究 lacE2 和 PRIP 作为与血清型无关的治疗干预靶点。
全球疫苗免疫联盟（Gavi）、世界卫生组织（WHO）、比尔及梅琳达·盖茨基金会、桑格研究所（Wellcome Sanger Institute）和美国疾病控制与预防中心（US Centers for Disease Control and Prevention）。
