Genotypic Diversity within a Single Pseudomonas aeruginosa Strain Commonly Shared by Australian Patients with Cystic Fibrosis

• Published in: PloS one Vol. 10; no. 12; p. e0144022
• Main Authors: Tai, Anna Sze, Bell, Scott Cameron, Kidd, Timothy James, Trembizki, Ella, Buckley, Cameron, Ramsay, Kay Annette, David, Michael, Wainwright, Claire Elizabeth, Grimwood, Keith, Whiley, David Mark
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 03.12.2015; Public Library of Science (PLoS)
• Subjects: Adult; Adults; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antibiotic resistance; Antibiotics; Australia; Biodiversity; Children & youth; Clinics; Complications and side effects; Confidence intervals; Cystic fibrosis; Cystic Fibrosis - microbiology; Distribution; Drug resistance; Epidemics; Female; Genes, Bacterial; Genetic Variation; Health aspects; Hospitals; Humans; Infections; Intravenous administration; Laboratories; Lung transplantation; Male; Medical research; Medicine; Microbial Sensitivity Tests; Mortality; Multidrug resistance; Mutation; Pathogens; Patients; Physiological aspects; Polymerase chain reaction; Pseudomonas aeruginosa; Pseudomonas aeruginosa - drug effects; Pseudomonas aeruginosa - genetics; Strains (organisms); Surveillance; Thorax; Transplantation; Treatment Outcome; Young Adult; Australia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0144022

In cystic fibrosis (CF), Pseudomonas aeruginosa undergoes intra-strain genotypic and phenotypic diversification while establishing and maintaining chronic lung infections. As the clinical significance of these changes is uncertain, we investigated intra-strain diversity in commonly shared strains from CF patients to determine if specific gene mutations were associated with increased antibiotic resistance and worse clinical outcomes. Two-hundred-and-one P. aeruginosa isolates (163 represented a dominant Australian shared strain, AUST-02) from two Queensland CF centres over two distinct time-periods (2001-2002 and 2007-2009) underwent mexZ and lasR sequencing. Broth microdilution antibiotic susceptibility testing in a subset of isolates was also performed. We identified a novel AUST-02 subtype (M3L7) in adults attending a single Queensland CF centre. This M3L7 subtype was multi-drug resistant and had significantly higher antibiotic minimum inhibitory concentrations than other AUST-02 subtypes. Prospective molecular surveillance using polymerase chain reaction assays determined the prevalence of the 'M3L7' subtype at this centre during 2007-2009 (170 patients) and 2011 (173 patients). Three-year clinical outcomes of patients harbouring different strains and subtypes were compared. MexZ and LasR sequences from AUST-02 isolates were more likely in 2007-2009 than 2001-2002 to exhibit mutations (mexZ: odds ratio (OR) = 3.8; 95% confidence interval (CI): 1.1-13.5 and LasR: OR = 2.5; 95%CI: 1.3-5.0). Surveillance at the adult centre in 2007-2009 identified M3L7 in 28/509 (5.5%) P. aeruginosa isolates from 13/170 (7.6%) patients. A repeat survey in 2011 identified M3L7 in 21/519 (4.0%) P. aeruginosa isolates from 11/173 (6.4%) patients. The M3L7 subtype was associated with greater intravenous antibiotic and hospitalisation requirements, and a higher 3-year risk of death/lung transplantation, than other AUST-02 subtypes (adjusted hazard ratio [HR] = 9.4; 95%CI: 2.2-39.2) and non-AUST-02 strains (adjusted HR = 4.8; 95%CI: 1.4-16.2). This suggests ongoing microevolution of the shared CF strain, AUST-02, was associated with an emerging multi-drug resistant subtype and possibly poorer clinical outcomes.