Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Escherichia coli is a commensal of birds and mammals, including humans. It can act as an opportunistic pathogen and is also found in water and sediments. Since most population studies have focused on clinical isolates, we studied the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000, mostly non-clinical, isolates originating from humans, poultry, wild animals and water sampled from the Australian continent. These strains represent the species diversity and show large variations in gene repertoires within sequence types. Recent gene transfer is driven by mobile elements and determined by habitat sharing and by phylogroup membership, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. The phylogroups with smallest genomes had the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements, suggesting that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these small genomes were in freshwater isolates suggesting that some lineages are specifically adapted to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

大肠杆菌（Escherichia coli）是鸟类与哺乳动物（包括人类）的共生菌，可作为机会致病菌，同时也可在水体及沉积物中被检出。鉴于此前多数群体研究均聚焦于临床分离株，本研究针对来自澳大利亚大陆的1294株分离株展开系统发育、遗传多样化及生境关联分析——这些菌株代表了5000余株（多数为非临床来源）分离株的系统发育多样性，该批分离株的来源涵盖人类、家禽、野生动物及采集自澳大利亚大陆的水体样本。这批菌株覆盖了该物种的多样性，且在同一序列型（sequence type）内的基因组分存在显著差异。近期的基因转移事件由可移动遗传元件（mobile genetic element）介导，其发生受生境共享与系统群（phylogroup）归属调控，这表明基因流强化了特定遗传背景与专属生境之间的关联。基因组最小的系统群，其基因组分的多样化速率最高，且可移动遗传元件数量更少但类型更多样，提示基因组尺寸较小与更高（而非更低）的遗传信息更新速率相关。这类小基因组菌株多分离自淡水样本，表明部分谱系已特化适应淡水生境。综上，本研究数据有助于解释：即便该物种存在广泛的水平基因转移，流行病学克隆仍倾向于从特定系统发育类群中产生。