Colistin resistance. COINCIDE

Prokaryotic microbes - Assembly, annotation, pangenome analysis and GWAS This practical is part of the Microbial Genomics practical course of Utrecht University adapted for the JPIAMR COINCIDE project. We will make use of E. coli genomes sequencing using Nanopore sequencing. The genomes have different resistance patterns and in this course we will identify which gene(s) are responsible for the resistance. In the lessons you will learn how to assemble genomes, how to check for problems in assemblies, how to annotate genomes, how to work with annotations, how to determine the pan genome and the core genome and you will associate gene presence/absence with phenotypes using contingency testing (“GWAS”). Additionally you will learn how to make phylogenetic trees, determine MLST type and detected resistance genes and mutations of the strains.