Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands.
Open Biol. 2017 Sep;7(9). doi: 10.1098/rsob.170074.
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease ( = 101) and from carriage ( = 103), and on non-typeable pneumococci from asymptomatic individuals ( = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for , targeting , , , , Spn9802, and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of and were 100% specific for , whereas assays targeting , , Spn9802, and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.
绝大多数定植于人体上呼吸道的链球菌是共生菌，仅偶尔与疾病相关。其中，最具致病性的是米氏链球菌群成员。链球菌之间的表型和遗传相似性可能导致物种鉴定困难。我们使用从 501 株链球菌全基因组序列发表的核糖体 S2-基因序列开发了一种鉴定链球菌种的方法。我们在从严重链球菌病病例（=101）和携带（=103）培养的非肺炎球菌分离株以及无症状个体的非分型肺炎球菌（=17）以及荷兰脑膜炎的 1157 株肺炎球菌分离株的全基因组序列上验证了该方法。在此之后，我们在分子检测中测试了 221 株链球菌分离株，这些检测最初被假定为针对 Spn6313、Spn1670、Spn1919、Spn2121、Spn2524、Spn9802 和荚膜型特异性基因的特异性检测。S2-序列的聚类分析显示，根据发表的链球菌核心基因组系统发育树，按照种分组。S2 分型令人信服地区分了肺炎球菌和非肺炎球菌种（敏感性 99.2%，特异性 100%）。针对和区域的分子检测对 100%特异性，而针对、、Spn9802 和选定的血清型特异性检测（但不包括荚膜序列分型）显示缺乏特异性。虽然携带分离株没有独特的混杂信号，但假阳性结果在与携带相关的种中占比较高。
