Genetic and microbial analysis of invasiveness for Escherichia coli strains associated with inflammatory bowel disease

Background & AimsThe adherent-invasive Escherichia coli (AIEC) pathotype is implicated in inflammatory bowel disease (IBD) pathogenesis. AIEC strains are currently defined by phenotypic measurement of their pathogenicity, including invasion of epithelial cells. This broad definition, combined with the genetic diversity of AIEC across IBD patients, has complicated the identification of virulence determinants. We sought to quantify the invasion phenotype of clinical isolates from IBD patients and identify the genetic basis for their invasion into epithelial cells. MethodsA pangenome with core and accessory genes (genotype) was assembled using whole genome sequencing of 168 E. coli samples isolated from 13 IBD patients. A modified assay for invasion of epithelial cells (phenotype) was established with consideration of antibiotic resistance phenotypes. Isolate genotype was correlated to invasiveness phenotype to identify genetic factors that co-segregate with invasion. ResultsPangenome-wide comparisons of E. coli clinical isolates identified accessory genes that can co-segregate with invasion phenotype. These correlations found the acquisition of antibiotic resistance genes in clinical isolates compromised the traditional gentamicin protection assays used to quantify invasion. Therefore, an alternate assay, based on amikacin resistance, identified genes co-segregating with invasion. These genes encode an arylsulfatase, a glycoside hydrolase, and genetic islands carrying propanediol utilization and sulfoquinovose metabolism pathways. ConclusionsThis study highlights the importance of incorporating antibiotic resistance screening for invasion assays used in AIEC identification. Accurately screened invasion phenotypes identified accessory genome elements among E. coli IBD isolates that correlate with their ability to invade epithelial cells. These results help explain why single genetic markers for the AIEC phylotype are challenging to identify. SynopsisWe established a pangenome of Escherichia coli isolates from inflammatory bowel disease patients using whole genome sequencing. The genotypes were correlated with a newly developed measurement of invasion phenotype to identify co-segregating genes.