(458) Mycobacterium avium adapts during chronic cystic fibrosis infection through increased mutation rates leading to the acquisition of antibiotic resistance

Background: Nontuberculous mycobacteria (NTM) have recently emerged as detrimental pathogens in the cystic fibrosis (CF) community with substantial challenges surrounding diagnosis and treatment. However, the mechanisms by which NTM adapts during chronic CF infection (i.e. increasing virulence, persistence, antibiotic resistance) are largely unknown.

Methods: We conducted whole-genome sequencing (WGS) on 24 longitudinal samples collected from a single CF patient with chronic Mycobacterium avium complex infection over 5 years. We constructed phylogenetic trees using RAxML and BEAST to assess the relationships between isolates, and we used ClonalFrameML to estimate the recombination-to-mutation rate. Mutation rates were also estimated in vitro using fluctuation tests. We used liquid chromatography-mass spectrometry (LC-MS) to assess proteomic expression differences among isolates. We also assessed other phenotypic properties such as colony morphology, sliding motility, biofilm formation, and susceptibility to antibiotic and oxidative stress.

Results: Phylogenetic analysis revealed two distinct, coexisting populations of M. avium with a very recent common ancestor and fewer than 10 SNP differences in their core genomes. One lineage was characterized by high levels of resistance to macrolide and aminoglycoside antibiotics and had mutations in the DNA repair and recombination genes, recR and uvrA. In addition, both phylogenetic and preliminary fluctuation analyses suggest that the antibiotic-resistant lineage has increased rates of mutation compared to the susceptible population.

Conclusions: Increased mutation rates can aid in NTM adaptation during chronic CF infection and are associated with the acquisition of antibiotic resistance. These findings highlight the role of hypermutability in bacterial adaptation during chronic CF infection.

Acknowledgements: This work was supported by the National Institute of Allergy and Infectious Disease [5R21AI144561-02]; and the Cystic Fibrosis Foundation [PLANET19G0].

References: