Abstract
Abstract Background Chronic respiratory infection due to extensively drug-resistant Pseudomonas aeruginosa (XDR-Pa) is a significant cause of mortality in cystic fibrosis (CF) patients. The CF respiratory anatomy, chronic antibiotic use, and PA colonization creates a milieu for high evolutionary pressure and genetic diversity. We sought to explore the progression of antibiotic resistance and genome evolution of XDR-Pa in a longitudinal series of isolates collected from an18-year-old CF patient who underwent lung transplantation. Methods Consecutive respiratory isolates were collected from December 2016 to March 2018. Standard disk diffusion methods were used to evaluate antimicrobial susceptibility. Whole-genome sequencing (WGS) data were obtained on an Illumina NextSeq and assembled. Variants were identified using the GATK HaplotypeCaller and their functional impact was determined using snpEff. Maximum likelihood phylogenetic trees were constructed using MEGA and BEAST. Panther was used to test for enrichment of Gene Ontology functional categories among mutated genes. Results Phylogenetic analysis of complete genome sequences showed that 18 isolates formed a monophyletic group. Analysis using BEAST showed that genomes shared a common ancestor that was present prior to transplant. Over 300 single nucleotide variants and small insertion-deletion mutations were found, in comparison with a reconstruction of the ancestral sequence (Figure 1). Shared patterns of antibiotic susceptibility profiles were largely concordant with phylogenetic clustering and trended toward a decrease in susceptibility over time. Two different frameshift mutations in the DNA mismatch repair gene mutL were found in 15 genomes and these exhibited an increased rate of transition to transversion mutations, consistent with a hypermutator phenotype. Conclusion WGS of XDR-Pa identified variations in antibiotic resistance and virulence genes. Changes in mutL likely accelerated the accumulation of mutations. Multiple related sub-groups of strains appear to have been circulating prior to transplant and continued to diverge during the treatment period. Correlating antibiotic pressure, susceptibility profiles, and WGS in XDR-Pa from a single patient reveals the clinical impact of genomic evolution in CF. Disclosures All authors: No reported disclosures.