Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7

Abstract

Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is multiresistant to antibiotics. We first sequenced gyrA, gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found that PA7 is a taxonomic outlier. We report here the complete sequence of the 6,588,339 bp genome, which has only about 95% overall identity to other strains. PA7 has multiple novel genomic islands and a total of 51 occupied regions of genomic plasticity. These islands include antibiotic resistance genes, parts of transposons, prophages, and a pKLC102-related island. Several PA7 genes not present in PAO1 or PA14 are putative orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7 appears to be closely related to the known taxonomic outlier DSM1128 (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin type II. Preliminary proteomic studies indicate numerous differences with PAO1, some of which are probably a consequence of a frameshift mutation in the mvfR quorum sensing regulatory gene.

Figure 1. The chromosome of P. aeruginosa PA7.

The outermost two circles indicate positions of CDSs in plus (circle 1) and minus (circle 2) strands colored by functional category: translation, ribosomal structure, and biogenesis (maroon); transcription (navy); DNA replication, recombination and repair (purple); cell division and chromosome partitioning (brown); posttranslational modification, protein turnover, chaperones (aqua); cell envelope biogenesis, outer membrane (teal); cell motility and secretion (blue); inorganic ion transport and metabolism (orange); signal transduction mechanisms (lavender); energy production and conversion (olive); carbohydrate transport and metabolism (light green); amino acid transport and metabolism (dark green); nucleotide transport and metabolism (fuchsia); coenzyme metabolism (pink); lipid metabolism (red); secondary-metabolite biosynthesis, transport, and catabolism (yellow); general function prediction only (dark grey); function unknown (light grey); and no COG (black). Genomic islands or ‘regions of genomic plasticity’ are indicated by green bars in the third circle; these are in the same order as listed in Table 3 (starting from the 0 kbp mark). Moving toward the center, the following three circles map pairwise blastn alignments (expected threshold = 1e−20) between PA7 and previously sequenced P. aeruginosa genomes (circle 4 PAO1 (teal); circle 5 PA14 (aqua); circle 6 LESB58 (orange)). Circle seven shows G+C content (deviation from average), and the eighth circle illustrates G+C skew in green (+) and purple (−). The scale (in kbp) is indicated on the innermost circle. CGview software was used to construct the genome map.

Figure 2. Genomic comparisons of P. aeruginosa strains.

Venn diagram showing the number of P. aeruginosa PA7 predicted proteins with significant similarity (expected threshold = 1e−5) with the predicted products of other P. aeruginosa strains PAO1, PA14 and LESB58. The numbers in parentheses represent the total number of predicted proteins for each genome.

Figure 3. Proteomic comparison of PA7 and PAO1, Condition-level matching using Progenesis PG240 software.

Green, PAO1-specific; pink, PA7-specific, black, PAO1-PA7 match.