Genomic characterization of Achromobacter spp. isolates from chronic and occasional lung infection in cystic fibrosis patients

Achromobacter spp. are increasingly being detected in cystic fibrosis (CF) patients, where they can establish occasional or chronic infections by adapting to the lower airways environment. To better understand the mechanisms contributing to a successful colonization by Achromobacter spp., we sequenced the whole genome of 54 isolates from 26 patients with occasional and chronic infection followed at the CF Center of Verona (Italy). In this study, we performed a phylogenetic analysis and comparisons of virulence and resistance genes, genetic variants and mutations and hypermutability mechanisms, both among different Achromobacter species and between chronic and occasional isolates. Moreover, we investigated the presence of phages, insertion sequences (ISs) and integrative and conjugative elements (ICEs).