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.

Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis

“…The hypermutator phenotype was detected in 20% of the isolates ( n = 11). Hypermutators have been found previously in A. xylosoxidans and other species isolated from CF infection, and it is assumed that the higher mutation rate has a positive effect on faster selection of adaptive phenotypes in this environment ( 14 , 25 , 49 , 54 , 55 ). It is also likely that this phenotype is fixed in CF1 as a result of its longer colonization in the patient, since it has been suggested that longer evolution history is associated with the hypermutator phenotype ( 56 ).…”

“…Infections of A. xylosoxidans have recently become more prevalent in patients with CF ( 5 , 6 , 9 ), but there are few studies that characterize the genetic adaptation of Achromobacter spp. in CF infections ( 24 , 48 , 49 ). To complement these studies, we used a combination of functional and genomic approaches to reflect on the biology of A. xylosoxidans adaptation in the CF model.…”

Mobilome Analysis of Achromobacter spp. Isolates from Chronic and Occasional Lung Infection in Cystic Fibrosis Patients

“…Libraries were prepared using the KAPA PCR-free kit (Roche Sequencing Solutions, Pleasanton, CA, USA) and sequenced on a NextSeq500 Illumina platform (Illumina, Hayward, CA, USA) generating 150bp paired end reads with a mean read yield of 10978104 and a mean coverage of 190X. Read quality controls, de novo assembly, and genome annotation were performed similarly to our previous work [ 35 ]. Details on the sequencing and de novo assembly are available in Table S2 .…”

Transmission and antibiotic resistance ofAchromobacterin cystic fibrosis

“…Four isolates were previously analysed by Veschetti et al . (2020) (12) where patients A and B correspond to patients P0802 and P8603, respectively, in this study. The use of clinical isolates was approved by the local ethics committee at the Capital Region of Denmark (Region Hovedstaden; approval registration number H-4-2015-FSP), and the use of clinical registry data was approved by the Danish Agency for Patient Safety (approval registration number 31-1521-428).…”