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Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major

Luca Freschi1, Claire Bertelli2,3, Julie Jeukens1

  • 1Institute for Integrative and Systems Biology (IBIS), University Laval, Québec City, QC G1V 0A6, Canada.

FEMS Microbiology Letters
|June 14, 2018
PubMed

Insights

This study sequenced Pseudomonas aeruginosa isolates, revealing genetic diversity and adaptations in cystic fibrosis infections. Two main groups of P. aeruginosa were identified, each potentially utilizing different mobile gene pools.

Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Pseudomonas aeruginosa is a significant opportunistic pathogen, particularly in cystic fibrosis (CF) infections.
  • An international reference panel of P. aeruginosa isolates was established for coordinated research.
  • Genome sequencing of this panel aims to further characterize the pathogen's population structure and adaptive mechanisms.

Purpose of the Study:

  • To perform whole-genome sequencing and analysis of 33 P. aeruginosa isolates and 7 reference genomes.
  • To characterize the genetic diversity and population structure of the reference panel.
  • To identify adaptive mutations and mobile genetic elements within P. aeruginosa.

Main Methods:

  • Whole-genome sequencing of 40 P. aeruginosa strains.
  • Core genome single nucleotide variant (SNV) phylogeny for population structure analysis.
  • Analysis of genomic islands (GIs), prophages, and regions of genome plasticity (RGPs).
  • Prediction of resistomes using the Resistance Gene Identifier (RGI) method and the Comprehensive Antibiotic Resistance Database (CARD).

Main Results:

  • Panel strains represent a wide distribution within the P. aeruginosa population.
  • Common CF-associated mutations (e.g., in mucA, mexA) were found in chronic respiratory isolates.
  • 37 unique resistomes were predicted across the 40 analyzed strains.
  • Phylogenetic analysis based on GIs and RGPs supported the subdivision of P. aeruginosa into two major groups.
  • Each major group may utilize distinct mobile gene pools.

Conclusions:

  • The reference panel provides a diverse resource for studying P. aeruginosa.
  • Genomic plasticity, including GIs and prophages, plays a significant role in P. aeruginosa evolution and adaptation.
  • The observed subdivision into two main groups suggests distinct evolutionary trajectories and mobile genetic element acquisition strategies.

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