Application of phylogenetic, statistical and computational approaches to unravel genotype-phenotype associations in pathogenic bacteria

The introduction of genome-wide association studies (GWAS) in microbial genetics has recently become possible as a result of falling DNA sequencing costs. GWAS can help us discover the genes that make bacterial strains resistant to antibiotics, able to cause infection and colonise and transmit within and beyond their host population. Despite the potential of GWAS to characterise the genetic determinants of bacterial phenotypes, its wider adoption has been hindered by limited expertise and lack of methods suitable to bacterial genomes. 

I will develop robust GWAS designs suitable for bacterial genomes and provide practical guidelines for future studies. I will evaluate the performance of different GWAS designs using four large bacterial collections with available whole-genome sequences (WGS) and antimicrobial resistance phenotypes. I will also develop and release a software tool implementing the GWAS methods.