G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia.
Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
Microb Genom. 2022 Sep;8(9). doi: 10.1099/mgen.0.000851.
Invasive pneumococcal disease remains one of the leading causes of morbidity and mortality worldwide. In Russia, 13- valent pneumococcal conjugate vaccine (PCV13) was introduced into the childhood immunization programme nationwide in 2014. As part of the Global Pneumococcal Sequencing Project (GPS), we used genome data to characterize 179 pneumococcal isolates collected from Russia in 2011-2018 to investigate the circulating pneumococcal strains using a standardized genomic definition of pneumococcal lineages (global pneumococcal sequence clusters, GPSCs), prevalent serotypes and antimicrobial resistance profiles.We observed high serotype and lineage diversity among the 179 isolates recovered from cerebrospinal fluid (=77), nasopharyngeal swabs (=99) and other non-sterile site swabs (=3). Overall, 60 GPSCs were identified, including 48 clonal complexes (CCs) and 14 singletons, and expressed 42 serotypes (including non-typable). Among PCV13 serotypes, 19F, 6B and 23F were the top three serotypes while 11A, 15B/C and 8 were the top three among non-PCV13 serotypes in the collection. Two lineages (GPSC6 and GPSC47) expressed both PCV13 and non-PCV13 serotypes that caused invasive disease, and were penicillin- and multidrug-resistant (MDR), highlighting their potential to adapt and continue to cause infections under vaccine and antibiotic selective pressure. PCV13 serotypes comprised 92 % (11/12) of the CSF isolates from the children aged below 5 years; however, the prevalence of PCV13 serotype isolates dropped to 53 % (31/58) among the nasopharyngeal isolates. Our analysis showed that 59 % (105/179) of the isolates were predicted to be non-susceptible to at least one class of antibiotics and 26 % (46/179) were MDR. Four MDR lineages (GPSC1, GPSC6, GPSC10 and GPSC47) accounted for 65 % (30/46) of the MDR isolates and expressed PCV13 serotypes (93 %, 28/30).This study provides evidence of high genetic and serotype diversity contributed by a mix of globally spreading and regionally circulating lineages in Russia. The observations suggest that the PCV13 vaccine could be important in reducing both invasive disease and antimicrobial resistance. We also identify potential lineages (GPSC6 and GPSC47) that may evade the vaccine.
侵袭性肺炎球菌病仍然是全球发病率和死亡率的主要原因之一。在俄罗斯，13 价肺炎球菌结合疫苗（PCV13）于 2014 年在全国儿童免疫计划中引入。作为全球肺炎球菌测序项目（GPS）的一部分，我们使用基因组数据来描述 2011 年至 2018 年从俄罗斯收集的 179 株肺炎球菌分离株，使用肺炎球菌谱系的标准化基因组定义（全球肺炎球菌序列群，GPSCs）、流行血清型和抗微生物药物耐药性特征来研究循环肺炎球菌菌株。我们观察到从脑脊液中回收的 179 株分离株的血清型和谱系多样性很高（=77），鼻咽拭子（=99）和其他非无菌部位拭子（=3）。总体而言，确定了 60 个 GPSCs，包括 48 个克隆复合物（CCs）和 14 个单体，表达了 42 种血清型（包括不可分型）。在 PCV13 血清型中，19F、6B 和 23F 是前三种血清型，而 11A、15B/C 和 8 是该组中前三种非 PCV13 血清型。两个谱系（GPSC6 和 GPSC47）表达了引起侵袭性疾病的 PCV13 和非 PCV13 血清型，并且对青霉素和多种抗微生物药物耐药（MDR），突出了它们在疫苗和抗生素选择压力下适应和继续引起感染的潜力。PCV13 血清型占 5 岁以下儿童脑脊液分离株的 92%（11/12）；然而，鼻咽分离株中 PCV13 血清型分离株的流行率下降至 53%（31/58）。我们的分析表明，59%（105/179）的分离株至少对一类抗生素具有预测的耐药性，26%（46/179）为 MDR。四个 MDR 谱系（GPSC1、GPSC6、GPSC10 和 GPSC47）占 46/179 株 MDR 分离株的 65%，并表达了 PCV13 血清型（93%，28/30）。本研究提供了证据，证明俄罗斯存在由全球传播和区域流行谱系混合引起的高遗传和血清型多样性。这些观察结果表明，PCV13 疫苗可能对抗肺炎球菌疾病和抗微生物药物耐药性都很重要。我们还确定了可能逃避疫苗的潜在谱系（GPSC6 和 GPSC47）。
