Hypermutation as an Evolutionary Mechanism for Achromobacter xylosoxidans in Cystic Fibrosis Lung Infection

Abstract

Achromobacter xylosoxidans can cause chronic infections in the lungs of patients with cystic fibrosis (CF) by adapting to the specific environment. The study of longitudinal isolates allows to investigate its within-host evolution to unravel the adaptive mechanisms contributing to successful colonization. In this study, four clinical isolates longitudinally collected from two chronically infected patients underwent whole genome sequencing, de novo assembly and sequence analysis. Phenotypic assays were also performed. The isolates coming from one of the patients (patient A) presented a greater number of genetic variants, diverse integrative and conjugative elements, and different protease secretion. In the first of these isolates (strain A1), we also found a large deletion in the mutS gene, involved in DNA mismatch repair (MMR). In contrast, isolates from patient B showed a lower number of variants, only one integrative and mobilizable element, no phenotypic changes, and no mutations in the MMR system. These results suggest that in the two patients the establishment of a chronic infection was mediated by different adaptive mechanisms. While the strains isolated from patient B showed a longitudinal microevolution, strain A1 can be clearly classified as a hypermutator, confirming the occurrence and importance of this adaptive mechanism in A. xylosoxidans infection.

Keywords: bacterial evolution; clonal diversification; comparative genomics; lung infection; opportunistic pathogen.

Figure 1

Growth rate (A), biofilm formation (B) and protease activity (C) of A. xylosoxidans isolates. Growth rate was calculated from 24 h growth curves in LB medium (A). Adhesion was measured by crystal violet staining of surface-attached bacteria divided by A₆₀₀ of non-attached bacteria (B). Protease activity was measured in culture supernatant by azocasein assay. Protease activity is expressed as enzymatic units per ml (C). Each value represents the mean ± SEM of three experiments. Statistical analysis was performed by t test, ** p < 0.01.