Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis

Abstract

Chronic airway infections caused by Pseudomonas aeruginosa contribute to the progression of pulmonary disease in individuals with cystic fibrosis (CF). In the setting of CF, within-patient adaptation of a P. aeruginosa strain generates phenotypic diversity that can complicate microbiological analysis of patient samples. We investigated within- and between- sample diversity of 34 phenotypes among 235 P. aeruginosa isolates cultured from sputum samples collected from a single CF patient over the span of one year, and assessed colony morphology as a screening tool for predicting phenotypes, including antimicrobial susceptibilities. We identified 15 distinct colony morphotypes that varied significantly in abundance both within and between sputum samples. Substantial within sample phenotypic heterogeneity was also noted in other phenotypes, with morphotypes being unreliable predictors of antimicrobial susceptibility and other phenotypes. Emergence of isolates with reduced susceptibility to β-lactams was observed during periods of clinical therapy with aztreonam. Our findings confirm that the P. aeruginosa population in chronic CF lung infections is highly dynamic, and that intra-sample phenotypic diversity is underestimated if only one or few colonies are analyzed per sample.

Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

“…For instance, a random sampling of 44 P. aeruginosa colonies from a single sputum sample of a clinically stable CF patient showed a wide range of phenotypes, from variations in protease and exotoxin productions to antibiotic susceptibility (Darch et al 2015). Consistent with this, we observed broad phenotypic and genotypic variation for B. cenocepacia isolates obtained from the same patient at the same time point (Zlosnik et al 2014;Clark et al 2015). We thus emphasize the value of bacterial isolate collections that not only sample longitudinally but also sample populations at single time points, irrespective of observed variation of colony morphology.…”

“…We now know there can be a large phenotypic and genotypic diversity within a single patient at any sampling point (Smith et al 2006;Clark et al 2015;Darch et al 2015). For instance, a random sampling of 44 P. aeruginosa colonies from a single sputum sample of a clinically stable CF patient showed a wide range of phenotypes, from variations in protease and exotoxin productions to antibiotic susceptibility (Darch et al 2015).…”

Impact of High Diversity of Achromobacter Populations within Cystic Fibrosis Sputum Samples on Antimicrobial Susceptibility Testing

“…Our study thus showed that Achromobacter spp. are CF pathogens, for which the intrasample and the intramorphotype antimicrobial susceptibility diversity leads to an underestimation of antibiotic resistance and impairs current strategies of antimicrobial susceptibility testing on each colonial morphotype (10,30). Consequently, some authors have suggested that performing direct sputum susceptibility testing may be more accurate and may overcome the impact of resistance phenotype diversity (30,31).…”

“…This diversity is considered in French microbiological procedures for CF samples, which recommend the performance of antimicrobial susceptibility testing on each P. aeruginosa colonial morphotype detected by visual inspection of agar medium plates (9). However, morphotypes were previously shown to be unreliable predictors of antimicrobial susceptibility (10), suggesting that, depending on the choice of colonies to be submitted for in vitro antimicrobial susceptibility testing, results may not reflect the overall resistance exhibited by the P. aeruginosa population in the CF lung.…”

Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung

“…A recent study has suggested that a mixture of strains influenced traits such as drug response in ways that were difficult to predict from the study of single strains (9). Clinical isolates of P. aeruginosa, even from the same respiratory sample, can have striking differences in phenotypes, including colony morphology, quorum-sensing regulation, and motility (9)(10)(11)(12)(13), and recent data highlight that there is gene expression diversity even among phenotypically similar strains (9). Given the significant limitations of the aforementioned laboratory approaches, novel methods for directly interrogating population-level microbial gene expression in the CF lung are needed to provide accurate information about the growth and virulence of P. aeruginosa in the CF airway.…”