Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including an enrichment in genes involved in a metabolic pathway (mhp cluster) and the presence of a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.

中文翻译：

---

菌株、系统群和环境限制塑造了 20 年人类肠道时间序列中大肠杆菌的动力学和多样性


大肠杆菌是一种抗生素耐药性越来越强的机会性病原体。关于其主要共生生态位（脊椎动物肠道）的生态和进化动力学的数据很少。使用 Illumina 和/或 Nanopore 技术，我们对 20 年期间从居住在法国巴黎的一名健康男性 （ED） 的 22 例粪便中采样的 210 个大肠杆菌分离株的全基因组进行了测序。除 C 外，所有系统群都有代表，以 B2 （34.3%） 为主，其次是 A 和 F （各 19%）系统群。根据单倍群和成对基因组单核苷酸多态性距离鉴定出 35 个克隆，并根据其丰度和停留时间分为 3 个表型：25 个亚显性/瞬时 （52 个分离株） 、5 个显性/瞬时 （48 个分离株） 和 5 个显性/驻留 （110 个分离株）。4 个超过 5 个显性系/驻留性系属于 B2 和密切相关的 F 系群，而亚显性/瞬时克隆主要属于 B1 、 A 和 D 系群。B2 克隆的长停留时间似乎被较低的定植能力所抵消。宿主内频率较高的克隆持续时间更长。通过将 ED 菌株基因组与来自 359 名法国个体的共生大肠杆菌基因组集合进行比较，我们确定了 ED 特异性基因组特性，包括参与代谢途径 （mhp 簇） 的基因富集和非常罕见的抗病毒防御岛的存在。肠道微生物群中的大肠杆菌定植是由菌株谱系的内在特性（特别是系统群 B2 的较长时间驻留）和环境限制（如饮食或噬菌体）决定的。