Generating a sucralose-resistant Escherichia coli strain and variant calling pipeline for whole genome sequence analysis of point mutations

Abstract

The gut microbiome is central to many physiological functions, therefore perturbations to microflora composition may pose a significant health concern. Sucralose is a non-caloric artificial sweetener that has been known to have bacteriostatic effects on the gut microbiota populations, and specifically been shown to reduce Escherichia coli colony forming units. Discovering the bacteriostatic mechanism of sucralose may allow for the prediction of specific bacteria affected as well as any potential physiological implications. Furthermore, E. coli grown in sucralose was found to eventually obtain quinolone antibiotic resistance, suggesting that the mechanism for sucralose and quinolone resistance potentially converges. Therefore, this study aims to determine the mutations conferring sucralose resistance in E. coli. Given the relationship to quinolone resistance and the stability of the resistance, the mutations were hypothesized to reside within genomic DNA around gene clusters involved in DNA replication and aminoglycoside transferases. A stable sucralose-resistant strain was successfully generated from E. coli MG1655, and a variant calling pipeline for whole genome sequence analysis of point mutations was developed. The pipeline was tested on the wildtype and 11 non-essential mutations were identified. Therefore, here we present a system that could potentially be applied to the sucralose-resistant strain generated here to determine in-frame mutants that may be contributing to the resistance.