Habitat‐associated skew of clone abundance in the Pseudomonas aeruginosa population

Abstract

The population structure of the cosmopolitan Pseudomonas aeruginosa was investigated by genotyping 2921 isolates from 1448 independent habitats with a custom-made 58 binary marker microarray. Of 323 identified clone types, 109 clones made up 82% of the population. The 20 most frequent clones had an absolute share of 44% indicating that the P. aeruginosa population is dominated by few epidemic clonal complexes. The frequency distribution of common clones was different between inanimate habitats and human niches. The three most abundant clones in the environment were rare among isolates from human infection. Conversely, disease-associated isolates either belonged to ubiquitous clones such as C and PA14 or to clones that were uncommon in the environment. The P. aeruginosa population consists of major clones that are just as versatile in their habitat and geographic origin as the whole species and of minor clones with preference for a peculiar niche.

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

“…The analyzed P. aeruginosa strains were selected from the Hannover strain collection (23). The 361 isolates (see Table S1 in the supplemental material) had been retrieved from respiratory tract specimens of 258 people with cystic fibrosis (CF) regularly seen at 30 CF centers in 12 European countries.…”

“…Hence, we became interested to know if and to what extent the global P. aeruginosa population in lungs of patients (CF lungs) carries mutations in these genes. 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).…”

“…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.…”

Environmental Pseudomonads Inhibit Cystic Fibrosis Patient-Derived Pseudomonas aeruginosa

“…aeruginosa when sampling for pseudomonads, which is reflected in other studies that specifically probe for P. aeruginosa using selective media (43–45) or molecular techniques (46–48); this suggests that this species represents a minority of community-derived Pseudomonas populations (i.e., closely related isolates that cluster as distinct phylogenetic groups). Instead, we observe these environments to be dominated by non-aeruginosa Pseudomonas groups (22, 26, 27, 46) whose abundances suggest the possession of traits that are advantageous to survival in that ecological habitat.…”

Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14

“…Correspondingly, genome diversity is significantly lower within clones than between clones. Here, we report on the intraclonal genome diversity of the two most common clones in the global population of the opportunistic pathogen Pseudomonas aeruginosa (Wiehlmann et al ., 2007; 2015).…”