Prevalence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis

Defective OprD porins contribute to carbapenem resistance and may be important in Pseudomonas aeruginosa adaptation to cystic fibrosis airways. It is unclear whether oprD mutations are fixed in populations of shared strains that are transmitted between patients or whether novel variants arise during infection. We investigated oprD sequences and antimicrobial resistance of two common Australian shared strains, constructed P. aeruginosa mutants with the most common oprD allelic variants and compared characteristics between patients with or without evidence of infection with strains harbouring these variants. Our data show that three independently acquired nonsense mutations arising from a 1-base pair substitution are fixed in strain sub-lineages. These nonsense mutations are likely to contribute to reduced carbapenem susceptibility in the sub-lineages without compromising in vitro fitness. Not only was lung function worse among patients infected with strains harbouring the nonsense mutations than those without, but they also had an increased hazard rate of lung transplantation/death. Our findings further highlight that understanding adaptive changes may help to distinguish patients with greater adverse outcomes despite infection with the same strain. ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial Not a clinical trial ### Funding Statement Work funded by IMPACT Philanthropy Application Program (grant IPAP2016/01112), UQ-QIMRB (Australian Infectious Disease Grant initiative), The National Health and Medical Research Council (NHMRC) Project (grant 455919), The Children’s Health Foundation Queensland (grant 50007) and The Health Innovation, Investment and Research Office of Queensland Health. TJK. acknowledges NHMRC Early Career (GNT10884488) and ERS-EU RESPIRE2 Marie Sklodowska-Curie Postdoctoral Research (#4571-2013) Fellowship support. ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Genome sequence data available at the European Nucleotide Archive under studies PRJEB14781, PRJEB14771, PRJEB21755, PRJEB35026 and PRJNA325248