Abstract
The genomes of Pseudomonas aeruginosa isolates of the new sequence type ST-1146, three environmental (P37, P47 and P49) and one clinical (SD9) isolates, with differences in their antibiotic susceptibility profiles have been sequenced and analysed. The genomes were mapped against P. aeruginosa PAO1-UW and UCBPP-PA14. The allelic profiles showed that the highest number of differences were in “Related to phage, transposon or plasmid” and “Secreted factors” categories. The clinical isolate showed a number of exclusive alleles greater than that for the environmental isolates. The phage Pf1 region in isolate SD9 accumulated the highest number of nucleotide substitutions. The ORF analysis of the four genomes assembled de novo indicated that the number of isolate-specific genes was higher in isolate SD9 (132 genes) than in isolates P37 (24 genes), P47 (16 genes) and P49 (21 genes). CRISPR elements were found in all isolates and SD9 showed differences in the spacer region. Genes related to bacteriophages F116 and H66 were found only in isolate SD9. Genome comparisons indicated that the isolates of ST-1146 are close related, and most genes implicated in pathogenicity are highly conserved, suggesting a genetic potential for infectivity in the environmental isolates similar to the clinical one. Phage-related genes are responsible of the main differences among the genomes of ST-1146 isolates. The role of bacteriophages has to be considered in the adaptation processes of isolates to the host and in microevolution studies.
Highlights
Pseudomonas aeruginosa is a Gram negative, aerobic, rodshaped, gammaproteobacterium with polar inserted flagella
A P. aeruginosa chromosome is often described as a mosaic structure of a conserved core genome frequently interrupted by the inserted portions of the accessory genome
Protein clustering analysis was initially performed with strains P37, P47, P49 and SD9 and later including two P. aeruginosa reference genomes, PAO1-UW (NC_002516.2)(PAO1) and UCBPP-PA14 (NC_008463.1) (PA14), using the Cd-hit program available at Cd-hit home page [26]
Summary
Pseudomonas aeruginosa is a Gram negative, aerobic, rodshaped, gammaproteobacterium with polar inserted flagella Environmental isolates of this ubiquitous bacterium are highly versatile and adapt to a large variety of natural ecosystems, water is considered to be the primary habitat of this microorganism [1], [2]. P. aeruginosa can cause a wide range of opportunistic infections in animals and humans [3] The colonisation of this broad spectrum of habitats results from the ability to exploit many different nutrition sources and the high potential to adapt to new (or changing) environmental conditions [4]. A P. aeruginosa chromosome is often described as a mosaic structure of a conserved core genome frequently interrupted by the inserted portions of the accessory genome. The ongoing acquisition of new foreign DNA, the mobilization of prophages, larger or smaller deletion events, mutations of single nucleotides and even chromosomal inversions [8], [11]–[15], are potentially affecting portions of the core and the accessory genome, and these processes continuously modify the genome and modulate the phenotype of a P. aeruginosa strain, differentiating the strains from each other
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