Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.
Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.
PLoS One. 2021 Oct 28;16(10):e0259141. doi: 10.1371/journal.pone.0259141. eCollection 2021.
Adherent-invasive Escherichia coli (AIEC) is a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn's disease, and colorectal cancer. AIEC are genetically diverse, and in the absence of a universal molecular signature, are defined by in vitro functional attributes. The relative ability of difference AIEC strains to colonize, persist, and induce inflammation in an IBD-susceptible host is unresolved. To evaluate strain-level variation among tissue-associated E. coli in the intestines, we develop a long-read sequencing approach to identify AIEC by strain that excludes host DNA. We use this approach to distinguish genetically similar strains and assess their fitness in colonizing the intestine. Here we have assembled complete genomes using long-read nanopore sequencing for a model AIEC strain, NC101, and seven strains isolated from the intestinal mucosa of Crohn's disease and non-Crohn's tissues. We show these strains can colonize the intestine of IBD susceptible mice and induce inflammatory cytokines from cultured macrophages. We demonstrate that these strains can be quantified and distinguished in the presence of 99.5% mammalian DNA and from within a fecal population. Analysis of global genomic structure and specific sequence variation within the ribosomal RNA operon provides a framework for efficiently tracking strain-level variation of closely-related E. coli and likely other commensal/pathogenic bacteria impacting intestinal inflammation in experimental settings and IBD patients.
黏附侵袭型大肠杆菌（AIEC）是与炎症性肠病（IBD），尤其是克罗恩病和结直肠癌相关的一个血清型。AIEC 具有遗传多样性，在缺乏通用分子特征的情况下，通过体外功能特性来定义。不同 AIEC 菌株在易患 IBD 的宿主中定植、持续存在和引发炎症的相对能力尚未得到解决。为了评估肠道组织相关大肠杆菌中的菌株水平变异，我们开发了一种长读测序方法，通过菌株来识别 AIEC，排除宿主 DNA。我们使用这种方法来区分遗传上相似的菌株，并评估它们在定植肠道方面的适应性。在这里，我们使用长读纳米孔测序为模型 AIEC 菌株 NC101 以及从克罗恩病和非克罗恩病组织的肠道黏膜中分离的七株菌组装了完整的基因组。我们表明这些菌株可以定植易患 IBD 的小鼠的肠道并从培养的巨噬细胞中诱导炎症细胞因子。我们证明在存在 99.5%哺乳动物 DNA 的情况下，这些菌株可以被定量并区分，并且可以从粪便群体中区分。对核糖体 RNA 操纵子的全局基因组结构和特定序列变异的分析为在实验环境和 IBD 患者中追踪密切相关的大肠杆菌和可能影响肠道炎症的其他共生/病原体细菌的菌株水平变异提供了一个框架。
