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. 2018 Jul 1;10(7):1852-1857.
doi: 10.1093/gbe/evy139.

Comparative Genomics of Nonoutbreak Pseudomonas Aeruginosa Strains Underlines Genome Plasticity and Geographic Relatedness of the Global Clone ST235

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Comparative Genomics of Nonoutbreak Pseudomonas Aeruginosa Strains Underlines Genome Plasticity and Geographic Relatedness of the Global Clone ST235

Holger Brüggemann et al. Genome Biol Evol. .
Free PMC article

Abstract

Pseudomonas aeruginosa is an important opportunistic pathogen in hospitals, responsible for various infections that are difficult to treat due to intrinsic and acquired antibiotic resistance. Here, 20 epidemiologically unrelated strains isolated from patients in a general hospital over a time period of two decades were analyzed using whole genome sequencing. The genomes were compared in order to assess the presence of a predominant clone or sequence type (ST). No clonal structure was identified, but core genome-based single nucleotide polymorphism (SNP) analysis distinguished two major, previously identified phylogenetic groups. Interestingly, most of the older strains isolated between 1994 and 1998 harbored exoU, encoding a cytotoxic phospholipase. In contrast, most strains isolated between 2011 and 2016 were exoU-negative and phylogenetically very distinct from the older strains, suggesting a population shift of nosocomial P. aeruginosa over time. Three out of 20 strains were ST235 strains, a global high-risk clonal lineage; these carried several additional resistance determinants including aac(6')Ib-cr encoding an aminoglycoside N-acetyltransferase that confers resistance to fluoroquinolones. Core genome comparison with ST235 strains from other parts of the world showed that the three strains clustered together with other Brazilian/Argentinean isolates. Despite this regional relatedness, the individuality of each of the three ST235 strains was revealed by core genome-based SNPs and the presence of genomic islands in the accessory genome. Similarly, strain-specific characteristics were detected for the remaining strains, indicative of individual evolutionary histories and elevated genome plasticity.

Figures

<sc>Fig</sc>. 1.
Fig. 1.
—(A) Phylogenomic comparison of the 20 P. aeruginosa strains isolated in a Brazilian hospital over a time period of two decades. The phylogenetic relation was reconstructed by a core genome alignment and the comparison of high-quality SNPs. Two reference strains with closed genomes were added, PAO1 and UCBPP-PA14. The three ST235 strains (HIAE_PA17, HIAE_PA19 and HIAE_PA20) are closely related, as well as the two ST244 strains (HIAE_PA11 and HIAE_PA13), and the two ST253 strains (HIAE_PA21 and the reference strain UCBPP-PA14). There is also some relatedness between the strains HIAE_PA05 (ST498) and HIAE_PA07 (ST252). The branch length indicates the individuality of each strain. (B) Phylogenomic analysis of all previously sequenced strains of P. aeruginosa and the 20 strains isolated from Brazil. Only strains with complete genomes were analyzed, altogether 124 strains, together with the here sequenced 20 strains (in red, strains isolated between 1994 and 1998; in blue, strains isolated between 2011 and 2016). The analysis revealed that most strains, except three (belonging to group 3, nodes in black), grouped into two clades: 45 strains formed group 2 (clade in orange), and 96 strains formed group 1 (clade in purple). (C) Core genome SNP analysis of ST235 strains and the phylogenomic reconstruction. Phylogenetic analyses based on SNPs located in the core genome of all publicly available ST235 strains. In red, the three ST235 strains sequenced in this study; in orange, strains from the same clade (they are all strains isolated in South America). The respective clade is highlighted in green. (D) Visualization of genome comparison of the 20 Brazilian strains. A BRIG genome comparison analysis was performed with all strains isolated in this study and the two strains PAO1 and UCBPP-PA14. The analysis was carried out with HIAE_PA17 as the reference genome. Differences regarding the flexible genome can be seen.

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