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

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

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.

Citation

Darch, S. E., McNally, A., Harrison, F., Corander, J., Barr, H. L., Paszkiewicz, K., Holden, S., Fogarty, A. W., Crusz, S. A., & Diggle, S. P. (2015). Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection. Scientific Reports, 5, Article 7649. https://doi.org/10.1038/srep07649

• Journal Article Type: Article
• Acceptance Date: Nov 27, 2014
• Publication Date: Jan 12, 2015
• Deposit Date: Feb 24, 2016
• Publicly Available Date: Feb 24, 2016
• Journal: Scientific Reports
• Electronic ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 5
• Article Number: 7649
• DOI: https://doi.org/10.1038/srep07649
• Public URL: https://nottingham-repository.worktribe.com/output/743403
• Publisher URL: http://www.nature.com/articles/srep07649
• Contract Date: Feb 24, 2016