Infection Medicine, Department of clinical sciences, Lund University, Lund, Sweden.
Centre for Translational Genomics, Division of Clinical Genetics, Lund University, Lund, Sweden.
J Med Microbiol. 2021 Mar;70(3). doi: 10.1099/jmm.0.001330. Epub 2021 Feb 22.
subspecies (SDSE) is becoming increasingly recognized as an important human pathogen. Recurrent bacteremia with SDSE has been described previously. The aims of the study were to establish the genetic relatedness of SDSE isolates with -type stG643 that had caused recurrent bacteraemia in three patients and to search for signs of horizontal gene transfer of the gene in a collection of SDSE stG643 genomes. Recurring SDSE bacteremia is caused by the same clone in one patient. Whole genome sequencing of 22 clinical SDSE stG643 isolates was performed, including three paired blood culture isolates and sixteen isolates from various sites. All assemblies were aligned to a reference assembly and SNPs were extracted. A total of 53 SDSE genomes were downloaded from GenBank. Two phylogenetic trees, including all 75 SDSE isolates, were created. One tree was based on the gene only and one tree was based on all variable positions in the genomes. The genomes from the three pairs of SDSE isolates showed high sequence similarity (1-17 SNPs difference between the pairs), whereas the median SNP difference between the 22 isolates in our collection was 1694 (range 1-11257). The paired isolates were retrieved with 7-53 months between episodes. The 22 SDSE isolates from our collection formed a cluster in the phylogenetic tree based on the gene, while they were more scattered in the tree based on all variable positions. Our results show that the paired isolates were of the same clonal origin, which in turn supports carriage between bacteraemia episodes. The phylogenetic analysis indicates that horizontal gene transfer of the gene between some of the SDSE isolates has occurred.
亚种（SDSE）正日益被认为是一种重要的人类病原体。先前已有报道称 SDSE 反复引起菌血症。本研究的目的是确定导致三名患者反复发生菌血症的 -型 stG643 SDSE 分离株的遗传相关性，并在 SDSE stG643 基因组集中寻找基因水平转移的迹象。一位患者的反复 SDSE 菌血症是由同一克隆引起的。对 22 例临床 SDSE stG643 分离株进行全基因组测序，包括三对血培养分离株和 16 例来自不同部位的分离株。所有组装均与参考组装对齐，并提取 SNPs。从 GenBank 下载了总共 53 个 SDSE 基因组。创建了两棵包含所有 75 个 SDSE 分离株的系统发育树。一棵树仅基于基因，另一棵树基于基因组中所有可变位置。三对 SDSE 分离株的基因组显示出高度的序列相似性（两对之间的差异为 1-17 个 SNPs），而我们收集的 22 个分离株之间的中位数 SNP 差异为 1694（范围为 1-11257）。两次感染之间的时间间隔为 7-53 个月。我们收集的 22 个 SDSE 分离株在基于基因的系统发育树中形成一个聚类，而在基于所有可变位置的树中则更加分散。我们的结果表明，配对分离株来自同一克隆起源，这反过来又支持菌血症发作之间的传播。系统发育分析表明，基因在一些 SDSE 分离株之间发生了水平基因转移。
