Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain

Matthew P. Moore, Iain L. Lamont, David Williams, Steve Paterson, Irena Kukavica-Ibrulj, Nicholas P. Tucker, Dervla T.D. Kenna, Jane F. Turton, Julie Jeukens, Luca Freschi, Bryan A. Wee, Nicholas J. Loman, Stephen Holden, Susan Manzoor, Peter Hawkey, Kevin W. Southern, Martin J. Walshaw, Roger C. Levesque, Joanne L. Fothergill, Craig Winstanley*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

The Liverpool epidemic strain (LES) is an important transmissible clonal lineage of Pseudomonas aeruginosa that chronically infects the lungs of people with cystic fibrosis (CF). Previous studies have focused on the genomics of the LES in a limited number of isolates, mostly from one CF centre in the UK, and from studies highlighting identification of the LES in Canada. Here we significantly extend the current LES genome database by genome sequencing 91 isolates from multiple CF centres across the UK, and we describe the comparative genomics of this large collection of LES isolates from the UK and Canada. Phylogenetic analysis revealed that the 145 LES genomes analysed formed a distinct clonal lineage when compared with the wider P. aeruginosa population. Notably, the isolates formed two clades: one associated with isolates from Canada, and the other associated with UK isolates. Further analysis of the UK LES isolates revealed clustering by clinic geography. Where isolates clustered closely together, the association was often supported by clinical data linking isolates or patients. When compared with the earliest known isolate, LESB58 (from 1988), many UK LES isolates shared common loss-of- function mutations, such as in genes gltR and fleR. Other loss-of- function mutations identified in previous studies as common adaptations during CF chronic lung infections were also identified in multiple LES isolates. Analysis of the LES accessory genome (including genomic islands and prophages) revealed variations in the carriage of large genomic regions, with some evidence for shared genomic island/ prophage complement according to clinic location. Our study reveals divergence and adaptation during the spread of the LES, within the UK and between continents.

Original languageEnglish
Article number000511
JournalMicrobial Genomics
Volume7
Issue number3
DOIs
Publication statusPublished - 2021

Bibliographical note

Funding Information:
We acknowledge funding from the UK Cystic Fibrosis Trust (grant RS34) to support the studentship of M. P. M. R. C. L. was supported by Cystic Fibrosis Canada. I. L. would like to acknowledge funding support from Cystic Fibrosis New Zealand, the New Zealand Lotteries Board (Health) and the NHMRC (Australia).

Publisher Copyright:
© 2021 The Authors.

Keywords

  • Cystic fibrosis
  • Genomics
  • Prophage
  • Pseudomonas aeruginosa

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