目的 对深圳市3例人感染猪链球菌(Streptococcus suis,Ss)分离株进行病原学及基因组学分析,为预防与控制Ss感染疫情提供依据.方法 对3家医院共3名重症患者的3份血平板培养可疑菌株进行生化鉴定、基质辅助激光解析电离-飞行时间质谱和实时荧光PCR鉴定,获得3株猪链球菌血清2型(Streptococcus suis serotype 2,SS2)阳性菌株.取阳性纯培养物进行药敏试验、提取核酸用于全基因组测序及分析.全基因组序列分析包括物种鉴定、耐药基因比对、多位点序列分型、毒力基因比对和基于coregene的系统进化树分析.结果 3例患者的血平板分离株均鉴定为Ss,VITEK 2生化结果鉴定为SS2,基质辅助激光解析电离-飞行时间质谱鉴定结果为Ss.Ss通用基因gdh及血清型2型cps2基因实时荧光PCR结果均为阳性.药敏试验结果显示,3株菌均对红霉素、克林霉素耐药,对四环素药敏试验表现出差异.全基因组测序结果发现3株菌物种鉴定均为Ss,包括1株ST7型和2株ST1型.基于VFDB数据库毒力基因预测结果显示,3株菌均为mrp、sly和cps阳性,显示出高毒力株基因特征.基于coregene的系统进化树分析显示,3株菌处于不同进化分支,且ST1型的2株菌进化距离较近.结论 从3名重症患者中均检出SS2,3株菌均对红霉素和克林霉素耐药.在基因组学上均携带有高毒力株所具有的毒力基因,同时在多位点序列分型和系统进化树上表现出差异,表明在深圳地区存在不同基因型的高致病性SS2输入且已引起散发病例,需要引起高度关注.
Pathogenetic and genomic analysis of three cases of Streptococcus suis infection in Shenzhen
Objective To perform the pathogenic and genomics analyses on isolates of Streptococcus suis(Ss)from three human infections in Shenzhen,aiming to provide a basis for the prevention and control of Ss outbreaks.Methods The suspected bacterial strains from three blood plate cultures of three critically ill patients in three hospitals were subjected to biochemical identification,matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS),and real-time fluorescent PCR identification,resulting in the identification of three strains positive for Streptococcus suis serotype 2(SS2).Pure positive cultures were taken for an antimicrobial susceptibility test and extracted nucleic acids for whole-genome sequencing and analysis.The whole-genome sequencing and analysis included species identification,antibiotic resistance genes alignment,multilocus sequence typing(MLST),virulence genes alignment,and coregene-based phylogenetic tree analysis.Results The blood agar isolates from three patients were all identified as Ss,the VITEK 2 identified them as SS2,and MALDI-TOF-MS identified them as Ss.Real-time PCR results for the universal gene gdh and serotype 2 cps2 gene of Ss were both positive.The antimicrobial susceptibility test results showed that all three strains were resistant to erythromycin and clindamycin,with variable sensitivity to tetracycline.Whole-genome sequencing results showed that all three strains were identified as Ss,including one ST7 strain and two ST1 strains.The virulence gene prediction results based on the VFDB database showed that all three strains were positive for mrp,sly,and cps,indicating high virulence gene characteristics.The analysis of the phylogenetic tree based on coregene showed that the three strains were in different evolutionary branches,with two ST1 strains having a closer evolutionary distance.Conclusions The pathogens responsible for these three critically ill patients were SS2,and all three strains were resistant to erythromycin and clindamycin.Genetically,they all carried virulence genes that are found in highly virulent strains,while showed differences in MLST typing and phylogenetic tree analysis,indicating the presence of different genotypes of high pathogenicity SS2 in Shenzhen area and had caused sporadic cases,which requires high attention.
Streptococcus suisantimicrobial resistancegenomics analysisphylogenetic tree
NETL
NSTL
万方数据
