title: Within-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis.
abstract: A Pseudomonas aeruginosa AUST-02 strain sub-type (M3L7) has been identified in Australia, infects the lungs of some people with cystic fibrosis and is associated with antibiotic resistance. Multiple clonal lineages may emerge during treatment with mutations in chromosomally encoded antibiotic resistance genes commonly observed. Here we describe the within-host diversity and antibiotic resistance of M3L7 during and after antibiotic treatment of an acute pulmonary exacerbation using whole genome sequencing and show both variation and shared mutations in important genes. Eleven isolates from an M3L7 population (n = 134) isolated over 3 months from an individual with cystic fibrosis underwent whole genome sequencing. A phylogeny based on core genome SNPs identified three distinct phylogenetic groups comprising two groups with higher rates of mutation (hypermutators) and one non-hypermutator group. Genomes were screened for acquired antibiotic resistance genes with the result suggesting that M3L7 resistance is principally driven by chromosomal mutations as no acquired mechanisms were detected. Small genetic variations, shared by all 11 isolates, were found in 49 genes associated with antibiotic resistance including frame-shift mutations (mexA, mexT), premature stop codons (oprD, mexB) and mutations in quinolone-resistance determining regions (gyrA, parE). However, whole genome sequencing also revealed mutations in 21 genes that were acquired following divergence of groups, which may also impact the activity of antibiotics and multi-drug efflux pumps. Comparison of mutations with minimum inhibitory concentrations of anti-pseudomonal antibiotics could not easily explain all resistance profiles observed. These data further demonstrate the complexity of chronic and antibiotic resistant P. aeruginosa infection where a multitude of co-existing genotypically diverse sub-lineages might co-exist during and after intravenous antibiotic treatment.
authors.affiliation: Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Sherrard
authors.affiliation: Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|School of Medicine, The University of Queensland, Brisbane, QLD, Australia.|Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.|Western Australia Adult Cystic Fibrosis Centre, Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia.
authors.forename: Anna S
authors.initials: AS
authors.lastname: Tai
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
authors.forename: Bryan A
authors.initials: BA
authors.lastname: Wee
authors.affiliation: Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|School of Medicine, The University of Queensland, Brisbane, QLD, Australia.
authors.forename: Kay A
authors.initials: KA
authors.lastname: Ramsay
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.|Centre for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom.|Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Kidd
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
authors.forename: Nouri L
authors.initials: NL
authors.lastname: Ben Zakour
authors.affiliation: UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.|Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia.
authors.forename: David M
authors.initials: DM
authors.lastname: Whiley
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Beatson
authors.affiliation: Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.|Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Bell
mesh_terms: D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology / Q000627:therapeutic use; D002874:Chromosome Mapping; D003550:Cystic Fibrosis / Q000150:complications / Q000175:diagnosis / Q000382:microbiology*; D004352:Drug Resistance, Microbial / Q000235:genetics*; D016368:Frameshift Mutation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D011552:Pseudomonas Infections / Q000150:complications / Q000175:diagnosis / Q000188:drug therapy / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D015363:Quinolones / Q000494:pharmacology / Q000627:therapeutic use; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D015363:Quinolones