肺炎链球菌(肺炎球菌)是一种革兰氏阳性球菌,可引起非侵袭性和侵袭性传染病。肺炎球菌疾病是可预防的疫苗。符合国际病例定义的侵袭性肺炎球菌疾病(IPD)在国家和国际上都有报告,并在许多国家接受监测计划。包括捷克共和国。IPD监测的一个重要部分是监测致病性血清型及其随时间变化的频率以及与正在进行的疫苗接种计划的关系。在世界和捷克共和国,全基因组测序(WGS)越来越多地用于肺炎球菌,这允许从测序数据中进行血清分型,精确分析它们的遗传关系,以及对基因组中存在的基因的研究。全基因组测序能够生成可靠且具有国际可比性的数据,这些数据可以轻松共享。使用生物信息学工具分析测序数据,这些工具需要自然科学领域的知识,重点是遗传学和生物信息学专业知识。本出版物提供了一些肺炎球菌分析的选择,即,血清分型,多位点序列分型(MLST),核糖体MLST(rMLST),核心基因组MLST(cgMLST),全基因组MLST(wgMLST),单核苷酸多态性(SNP)分析,分配到全球肺炎球菌序列簇(GPSC),毒力基因和抗生素抗性基因的鉴定。介绍了WGS在欧洲的战略和应用以及WGS在实践中的实施。肺炎球菌的WGS分析可以改善IPD监测,多亏了分子血清分型,更详细的打字,生成国际可比数据,和改进对疫苗接种计划有效性的评估。
Streptococcus pneumoniae (pneumococcus) is a Gram-positive coccus causing both non-invasive and invasive infectious diseases. Pneumococcal diseases are vaccine preventable. Invasive pneumococcal diseases (IPD) meeting the international case definition are reported nationally and internationally and are subject to surveillance programmes in many countries, including the Czech Republic. An important part of IPD surveillance is the monitoring of causative serotypes and their frequency over time and in relation to ongoing vaccination programmes. In the world and in the Czech Republic, whole genome sequencing (WGS) is increasingly used for pneumococci, which allows for serotyping from sequencing data, precise analysis of their genetic relationships, and the study of genes present in their genome. Whole-genome sequencing enables the generation of reliable and internationally comparable data that can be easily shared. Sequencing data are analysed using bioinformatics tools that require knowledge in the field of natural sciences with an emphasis on genetics and expertise in bioinformatics. This publication presents some options for pneumococcal analysis, i.e., serotyping, multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), whole genome MLST (wgMLST), single nucleotide polymorphism (SNP) analysis, assignment to Global Pneumococcal Sequence Cluster (GPSC), and identification of virulence genes and antibiotic resistance genes. The WGS strategies and applications for Europe and WGS implementation in practice are presented. WGS analysis of pneumococci allows for improved IPD surveillance, thanks to molecular serotyping, more detailed typing, generation of internationally comparable data, and improved evaluation of the effectiveness of vaccination programmes.