Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment

Abstract

SummaryThe population genomics of Pseudomonas aeruginosa was analysed by genome sequencing of representative strains of the 15 most frequent clonal complexes in the P. aeruginosa population and of the five most common clones from the environment of which so far no isolate from a human infection has been detected. Gene annotation identified 5892-7187 open reading frame (ORFs; median 6381 ORFs) in the 20 6.4-7.4 Mbp large genomes. The P. aeruginosa pangenome consists of a conserved core of at least 4000 genes, a combinatorial accessory genome of a further 10 000 genes and 30 000 or more rare genes that are present in only a few strains or clonal complexes. Whole genome comparisons of single nucleotide polymorphism synteny indicated unrestricted gene flow between clonal complexes by recombination. Using standardized acute lettuce, Galleria mellonella and murine airway infection models the full spectrum of possible host responses to P. aeruginosa was observed with the 20 strains ranging from unimpaired health following infection to 100% lethality. Genome comparisons indicate that the differential genetic repertoire of clones maintains a habitat-independent gradient of virulence in the P. aeruginosa population.

Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

“…This observation is in line with other studies that found the isolation source of a bacterial strain not to be predictive for its performance in another habitat (Alonso et al, 1999;Grosso-Becerra et al, 2014). For instance, Hilker and colleagues found no correlation between original habitat and virulence in different test systems for clinical and environmental clones of P. aeruginosa (Hilker et al, 2015). In general, fluorescent pseudomonads might be quite ubiquitous and probably possess an arsenal of traits allowing them to easily switch niches and to conquer the habitat they encounter.…”

Molecular Epidemiology of Mutations in Antimicrobial Resistance Loci of Pseudomonas aeruginosa Isolates from Airways of Cystic Fibrosis Patients

“…The sequencing of the PCR-amplified DNAs of the CF strain panel revealed 1,908 different sequence variants (SNPs) (see Table S3 in the supplemental material) compared to the PA14 reference genome; i.e., nucleotide substitutions occurred at least once at 7.1% of the sites (Table 1). A portion consisting of 796 SNPs (41.7% of total) had already been observed in the P. aeruginosa pangenome of the 20 most common clones in the P. aeruginosa population (24). The average sequence diversity of the concatenated 17 loci between an individual CF isolate and the PA14 reference was determined to be 0.81%, which fits with the global sequence diversity of the core genome of 0.85% between the PAO1 and PA14 reference genomes (24).…”

“…The 21 49-strain pools were then subjected to amplicon sequencing. The obtained sequences of the CF strain panel were compared with those of the PA14 reference genome and the 20 most common clone types (24) in order to identify those sequence variants of the CF data set which had already been detected in other habitats and thus are not specific for the niche of the CF airway.…”

“…A large collection of more than 350 independent CF isolates collected from 30 CF centers (23) was investigated by amplicon sequencing of the spectrum of mutations. Single nucleotide substitutions (SNPs) were queried as to whether they represent already-known polymorphisms in the P. aeruginosa pangenome (24). Close to 60% of the more than 1,900 detected SNPs were not present in the pangenome of the 20 most frequent P. aeruginosa clones (23,24).…”

“…Single nucleotide substitutions (SNPs) were queried as to whether they represent already-known polymorphisms in the P. aeruginosa pangenome (24). Close to 60% of the more than 1,900 detected SNPs were not present in the pangenome of the 20 most frequent P. aeruginosa clones (23,24). The large proportion of more than 300 singular yet-undescribed mutations indicates strong diversifying selection in these loci that promotes an advantage to P. aeruginosa to persist in CF lungs and to withstand the strong and continuous antimicrobial pressure.…”