Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection

Sophie E Darch,Helen L Barr,Konrad Paszkiewicz,Stephen Holden,Freya Harrison,Jukka Corander,Andrew Fogarty,Shanika A Crusz,Stephen P Diggle,Alan Mcnally

doi:10.1038/srep07649

Abstract

The Cystic Fibrosis (CF) lung harbors a complex, polymicrobial ecosystem, in which Pseudomonas aeruginosa is capable of sustaining chronic infections, which are highly resistant to multiple antibiotics. Here, we investigate the phenotypic and genotypic diversity of 44 morphologically identical P. aeruginosa isolates taken from a single CF patient sputum sample. Comprehensive phenotypic analysis of isolates revealed large variances and trade-offs in growth, virulence factors and quorum sensing (QS) signals. Whole genome analysis of 22 isolates revealed high levels of intra-isolate diversity ranging from 5 to 64 SNPs and that recombination and not spontaneous mutation was the dominant driver of diversity in this population. Furthermore, phenotypic differences between isolates were not linked to mutations in known genes but were statistically associated with distinct recombination events. We also assessed antibiotic susceptibility of all isolates. Resistance to antibiotics significantly increased when multiple isolates were mixed together. Our results highlight the significant role of recombination in generating phenotypic and genetic diversification during in vivo chronic CF infection. We also discuss (i) how these findings could influence how patient-to-patient transmission studies are performed using whole genome sequencing, and (ii) the need to refine antibiotic susceptibility testing in sputum samples taken from patients with CF.

Highlights

Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection
The Cystic Fibrosis (CF) lung harbors a complex, polymicrobial ecosystem, in which Pseudomonas aeruginosa is capable of sustaining chronic infections, which are highly resistant to multiple antibiotics
Recent studies examining diversity within P. aeruginosa populations isolated from the CF lung have described significant variation in antibiotic susceptibility profiles in isolates which vary in morphological appearance

Summary

Introduction

Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection. Recent studies have examined the diversity of P. aeruginosa populations isolated from individual patients at a single time point[14] These suggest that considerable phenotypic variation exists at any given time and Pulsed-Field Gel Electrophoresis (PFGE) is suggestive of some level of genetic variation[14]. Despite these studies, it is still not clear how such diversity arises and how this impacts on clinically important factors such as identifying transmission events between patients and performing reliable antibiotic susceptibility testing. Recent studies examining diversity within P. aeruginosa populations isolated from the CF lung have described significant variation in antibiotic susceptibility profiles in isolates which vary in morphological appearance. No study has conducted a detailed examination of a single, morphologically homogeneous population of P. aeruginosa, nor has any study provided a comprehensive map at the genome level of phenotypic variation within an extant CF lung population

Methods

Results

Conclusion