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

Abstract

Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within-clone single nucleotide sequence diversity of 8 × 10(-6) for clone C and 2 × 10(-5) for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.

Figure 1

Clone C NN2 genome atlas.

Figure 2

Intraclonal genome diversity of the clonal complexes C and PA14. A and B. SNP‐based phylogenetic trees of the clonal complexes C (A) and PA14 (B). C. Conservation of the core genome. Normalized distribution of the length of 100% pairwise conserved sequence (‘haplotype’) in 58 clone C (n = 33 800 haplotypes), 42 clone PA14 (n = 9510) and 20 clonally unrelated P. aeruginosa strains (n = 3 779 224). D. Comparison of intraclonal versus. interclonal sequence diversity: Plot of the ratio of synonymous to non‐synonymous SNPs versus the total number of SNPs per strain. Clone C, clone PA14 and clonally unrelated strains (reference: strain PAO1 genome) are differentiated by symbol. The dotted line indicates the expectancy value of random mutation. E. Diversity of the accessory genome. Box‐plot presentation of the similarity of the accessory genome within and between clonal complexes. For each strain, a global score of relatedness was evaluated, whereby the two strains were assessed of whether they were concordant (assigned value: +1) or discordant (assigned value: −1) for the presence or absence of each RGP or genomic island known from eight completely sequenced P. aeruginosa genomes (PAO1, PA14, PACS2, PA7, LESB58, C3719, 2192). Please note the large overlap of scores of the intraclonal comparisons (C_C; PA14_PA14) with those of interclonal comparisons of 20 unrelated strains (20_20).