Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections
Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections
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全基因组测序对于诊断实验室爆发评估的重要性：侵袭性化脓性链球菌感染病例系列分析
DOI：
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发表时间：
2017
影响因子：
4.5
通讯作者：
Gilbert GREUB
中科院分区：
文献类型：
--
作者：
F. Tagini;B. Aubert;N. Troillet;T. Pillonel;G. Praz;P. Crisinel;G. Prod'Hom;S. Asner;Gilbert GREUB
化脓性链球菌高毒力克隆的爆发是持续的公共卫生威胁。在瑞士西部，2015 年 12 月至 2016 年 3 月期间，观察到化脓性链球菌侵袭性感染的严重病例有所增加。我们的目的是 (i) 通过使用全基因组测序 (WGS) 来调查这些病例，以及 (ii) 确定每个分离株的具体病毒组和耐药组，以便采取适当的公共卫生措施。我们的研究包括从2015年12月13日至2016年3月12日期间从11名严重侵袭性感染患者中分离出的11株化脓性链球菌。实际上，emm 分型、MLST 和 WGS 用于研究分离株之间的相关性。评估了毒力和抗生素抗性基因的存在以及毒力转录调节因子和抗生素靶点编码基因的突变。三组和两组分离株分别具有相同的 emm 型和 ST 型。单核苷酸多态性 (SNP) 分析显示，同一 emm 型组的菌株之间存在 14 至 32 个 SNP，排除了克隆爆发的可能性。 covS 和 rocA 中发现的突变可以部分解释毒力的增加。由于在不到 10 天内就获得了这些令人放心的结果，因此无需采取特定的医院卫生措施和专门的公共卫生措施。 WGS 是一种强大的技术，可以区分密切相关的菌株，并在 10 天内排除爆发。此外，全基因组测序提供了所有这些菌株的病毒组和耐药组的大量数据。
Outbreaks of Streptococcus pyogenes hypervirulent clones are constant public health threats. In western Switzerland, an increase of severe cases of S. pyogenes invasive infections was observed between December 2015 and March 2016. Our aim was (i) to investigate these cases by the use of Whole Genome Sequencing (WGS) and (ii) to determine the specific virulome and resistome of each isolate in order to undertake adequate public health measures. Eleven Streptococcus pyogenes strains isolated from 11 patients with severe invasive infections between December 13, 2015 and March 12, 2016 were included in our study. Practically, emm-typing, MLST and WGS were used to investigate the relatedness between the isolates. The presence of virulence and antibiotic resistance genes as well as mutations in transcriptional regulators of virulence and in genes encoding for antibiotic targets were assessed. Three and two groups of isolates shared the same emm-type and ST type, respectively. Single Nucleotide Polymorphism (SNP) analysis revealed 14 to 32 SNPs between the strains of the same emm-type group, ruling out the possibility of a clonal outbreak. Mutations found in covS and rocA could partially explain an increased virulence. As these reassuring results were obtained in less than 10 days, no specific hospital hygiene and no dedicated public health measures had to be undertaken. WGS is a powerful technique to discriminate between closely related strains, excluding an outbreak in less than 10 days. Moreover, WGS provided extensive data on the virulome and resistome of all these strains.
脉冲场凝胶电泳。
DOI：
10.1007/7651_2014_191
发表时间：
2016
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
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作者：
Sharma-Kuinkel,BatuK;Rude,ThomasH;FowlerJr,VanceG
通讯作者：
FowlerJr,VanceG