Phylogroup-specific variation shapes the clustering of antimicrobial resistance 
genes and defence systems across regions of genome plasticity in Pseudomonas 
aeruginosa

Botelho, João; Tüffers, Leif; Fuss, Janina; Buchholz, Florian; Utpatel, Christian; Klockgether, Jens; Niemann, Stefan; Tümmler, Burkhard; Schulenburg, Hinrich

doi:10.1016/j.ebiom.2023.104532

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Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa

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Botelho, João
Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Schulenburg, Hinrich
Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Botelho, J., Tüffers, L., Fuss, J., Buchholz, F., Utpatel, C., Klockgether, J., et al. (2023). Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa. EBioMedicine, 90: 104532. doi:10.1016/j.ebiom.2023.104532.

Cite as: https://hdl.handle.net/21.11116/0000-000D-4D40-5

Abstract

Background

Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named
A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new
P. aeruginosa genomes.

Methods

In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa
clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for
this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a
phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR)
genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and
“masked” (RGP-free) genomes, and to what extent this variation differs among the phylogroups.

Findings

We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number
of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence
systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from
phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, interand intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events.
Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for
functional analyses.

Interpretation

Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups,
which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the
differential distribution of other defence systems and AMR genes.