肺炎链球菌血清型分布与优势株基因组特征分析

Analysis of serotype distribution and genomic characteristics of dominant strains of streptococcus pneumoniae

目的了解肺炎链球菌血清型分布及优势株基因组特征,为防控肺炎链球菌引起的感染性疾病提供技术支持。方法收集2021—2023年哨点医院临床肺炎病例分离出的肺炎链球菌,经复核鉴定后开展药物敏感性试验、多重PCR血清分型、PFGE分子分型及全基因组测序,获得多位点序列分型(MLST)和核心基因组多位点序列分型(cgMLST)、耐药基因和毒力基因,应用FastTree对全基因组单核苷酸多态性(wgSNP)序列构建进化树。结果76株肺炎链球菌对莫西沙星、利奈唑胺、万古霉素、左氧氟沙星、替考拉宁、氯霉素、头孢吡肟敏感,但对红霉素、四环素、克林霉素耐药,耐药率分别为98.68%、93.42%、90.79%;耐药谱有17种,其中头孢噻肟—红霉素—四环素—青霉素—复方新诺明—克林霉素为优势耐药谱型、占34.21%;多重PCR血清分型为12种血清型,居前3位的血清型分别为19F型(48.68%)、6B型(14.47%)、14型(5.26%),19F型为优势血清型;64株肺炎链球菌的PFGE带型总体呈多样性,其中35株19F型呈现15种PFGE带型,spn004为优势PFGE带型,且具有同源性;27株肺炎链球菌全基因组特征分析,MLST型为5种,cgMLST型为12种,其中MLST优势型为ST271、占81.50%,cgMLST优势型为cgST3308型、占33.34%;27株肺炎链球菌共检测出14种耐药基因和35种毒力基因。全基因组SNP系统进化分析显示,分为3个进化分支,C1支为优势分支,遗传距离最近,与C2和C3分支间的遗传距离较远。结论2021—2023年监测哨点医院肺炎链球菌优势血清型为19F型,优势分支菌株间有遗传亲缘关系,耐药形势严峻。

Objective To understand the serotype distribution and genomic characteristics of dominant strains of streptococcus pneumoniae,and provide technical support for prevention and control of infectious diseases caused by Sp.Methods The Sp strains isolated from clinical pneumonia cases were collected in sentinel hospitals from 2021 to 2023.The drug sensitivity test,multiple PCR serotyping,PFGE molecular typing and whole genome sequencing were carried out after re-identification.The multi-site sequence typing(MLST),core genome multi-site sequence typing(cgMLST),drug resistance genes and virulence genes were obtained.The phylogenetic tree was constructed by FastTree as the genome-wide single nucleotide polymorphism(wgSNP)sequence.Results Totally 76 Sp strains were sensitive to moxifloxacin,linezolid,vancomycin,levofloxacin,teicoranin,chloramphenicol and cefepime,but resistant to erythromycin,tetracycline and clindamycin,with resistance rates of 98.68%,93.42%and 90.79%.There were 17 drug resistant spectrum,of which,cefotaxime-erythromycin-tetracycline-penicillin-sulfamethoxazole-clindamycin was the dominant drug resistant spectrum type,accounting for 34.21%.There were 12 serotypes after multiplex PCR,and the top 3 serotypes were 19F(48.68%),6B(14.47%),14(5.26%),and the 19F was the dominant serotype.The type of PFGE band of 64 Sp strains showed overall diversity.There were 35 strains of 19F type showed 15 PFGE band types,and the spn004 was the dominant PFGE band type with homology.The analysis of genome-wide of 27 strains of Sp showed that there were 5 MLST and 12 cgMLST.The dominant type was ST271,accounting for 81.50%in MLST types,and was cgST3308,accounting for 33.34%in cgMLST types.There were 14 drug resistance genes and 35 virulence genes detected in 27 strains of Sp.The genome-wide SNP phylogenetic analysis showed that there were three evolutionary branches,C1 branch was the dominant branch,with the closest genetic distance and the relatively long from C2 and C3.Conclusions From 2021 to 2023,the dominant serotype of Sp was 19F in sentinel hospitals,with genetic relationship among the dominant branch strains.The situation of drug resistanceis serious.