Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance.

ABSTRACT: Quinolone resistance presents a growing global health threat. We employed word-based GWAS to explore genomic data, aiming to enhance our understanding of this phenomenon. Unlike traditional variant-based GWAS analyses, this approach simultaneously captures multiple genomic factors, including single and interacting resistance mutations and genes. Analyzing a dataset of 92 genomic E. coli samples from a wastewater treatment plant in Dresden, we identified 54 DNA unitigs significantly associated with quinolone resistance. Remarkably, our analysis not only validated known mutations in gyrA and parC genes and the results of our variant-based GWAS but also revealed new (mutated) genes such as mdfA, the AcrEF-TolC multidrug efflux system, ptrB, and hisI,

SUBMITTER: Malekian N 

PROVIDER: S-EPMC10751334 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature