Whole-genome sequencing has enabled detailed studies on bacterial evolution during infection, but there is limited knowledge on intraclonal variation. In this study, we sought to provide a snapshot of the intraclonal diversity of Escherichia coli as both commensal in the faecal environment and pathogen during urinary tract infection, respectively. This was performed by whole-genome sequencing and analyses of single nucleotide polymorphisms (SNPs) and gene-content variation in ten isolates belonging to the same clone and isolated from rectal swabs or urine samples. We identified only one clone in eight of the nine urines sampled (89 %). In both the commensal and pathogenic state, the within-host diversity was limited with intraclonal SNP diversity of 0–2 non-synonymous SNPs for each clone. The genetic diversity showed variation in gene content in a range of 2–15 genes in total for all clones, including genes positioned on plasmids, and in the K- and O-antigen cluster. The observed SNP- and gene variation shows that sampling of one colony would be enough for surveillance, outbreak investigations and clonal evolution. However, for studies of adaptation during or between colonization and infection, this variation is relevant to consider.

全基因组测序已使人们能够对感染过程中细菌的进化进行详细研究，但对克隆内变异的了解还很有限。在这项研究中，我们试图提供大肠杆菌克隆内多样性的快照。既在粪便环境中常见，又在尿路感染中致病。这是通过全基因组测序和单核苷酸多态性（SNP）和10个属于同一克隆并从直肠拭子或尿液样本中分离出的分离株的基因含量变异分析来进行的。我们在采样的九种尿液中只有八种（89％）只鉴定出一个克隆。在共生和致病状态下，每个克隆的宿主内多样性都受到克隆内SNP多样性的限制，即0–2个非同义SNP。遗传多样性表明，所有克隆的基因含量在总共2-15个基因范围内变化，包括位于质粒上的基因以及K和O抗原簇中的基因。观察到的SNP和基因变异表明，采样一个菌落就足以进行监测，爆发调查和克隆进化。但是，对于在定植和感染期间或之间进行适应性研究，需要考虑这种变异。