Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

Adherent-invasive Escherichia coli (AIEC) is a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn's disease, and colorectal cancer. AIEC have no known molecular or genomic markers, but instead are defined by in vitro functional attributes. Futhermore, it is unknown if strains classified as AIEC truly colonize intestinal tissues better than non-AIEC strains. To evaluate strain-level variation among tissue-associated E. coli, we develop a long-read sequencing approach capable of discriminating closely-related strains and with the ability to exclude host DNA. We use this approach to evaluate genomic variation among strains that have demonstrated ability to colonize intestinal tissues. 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 intestinal tissue in a Crohn's disease mouse model and induce varying levels of 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 mice and IBD patients.