Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains

Abstract

The nosocomial pathogen Acinetobacter baumannii acquired clinical significance due to the rapid development of its multi-drug resistant (MDR) phenotype. A. baumannii strains have the ability to colonize several ecological niches including soil, water, and animals, including humans. They also survive under extremely harsh environmental conditions thriving on rare and recalcitrant carbon compounds. However, the molecular basis behind such extreme adaptability of A. baumannii is unknown. We have therefore determined the complete genome sequence of A. baumannii DS002, which was isolated from agricultural soils, and compared it with 78 complete genome sequences of A. baumannii strains having complete information on the source of their isolation. Interestingly, the genome of A. baumannii DS002 showed high similarity to the genome of A. baumannii SDF isolated from the body louse. The environmental and clinical strains, which do not share a monophyletic origin, showed the existence of a strain-specific unique gene pool that supports niche-specific survival. The strains isolated from infected samples contained a genetic repertoire with a unique gene pool coding for iron acquisition machinery, particularly those required for the biosynthesis of acinetobactin. Interestingly, these strains also contained genes required for biofilm formation. However, such gene sets were either partially or completely missing in the environmental isolates, which instead harbored genes required for alternate carbon catabolism and a TonB-dependent transport system involved in the acquisition of iron via siderophores or xenosiderophores.

Fig 1. Circular map of the chromosome.

Circle 1 (outer to inner) represents the total 3251 CDS in the genome. Genes present on the positive and negative strands are depicted in red and green colour, respectively. Circles 3, 4 and 5 represent GC content, GC skew, and dinucleotide bias, respectively. The tRNA (black) and rRNA (red) coding genes and the genomic islands (blue) are shown in the outermost discontinuous circle.

Fig 2. Phylogenetic tree.

Core genome-derived phylogenetic tree of 78 A. baumannii strains. The position of DS002 in the phylogenetic tree is highlighted with a blue background and dotted clade line.

Fig 3. Pan genome analysis.

Panel A indicates the pan and core genome curves. Panel B shows the frequency distribution of gene families within genomes. The number of new genes added to each genome is depicted in panel C. The COG and KEGG distribution of the representative proteins in the core, accessory, and unique genome are shown in panels D, and E respectively.

Fig 4. Heat map showing LS-BSR analysis of genes involved in carbon catabolism.

Genes extensively discussed in the text as well as the strain DS002 are highlighted in red font.

Fig 5. Heat map showing LS-BSR analysis of genes involved in virulence.

Genes extensively discussed in the text as well as the strain DS002 are highlighted in red font.

Fig 6. Heat map showing LS-BSR analysis of genes involved in resistance.

Genes extensively discussed in the text as well as the strain DS002 are highlighted in red font.

Fig 7. Heat map showing LS-BSR analysis of genes involved in iron acquisition.

Genes extensively discussed in the text as well as the strain DS002 are highlighted in red font.

Fig 8. Genomic Island.

The genetic map indicates the genomic island (30Kb) identified in the genome of DS002 with putative iron acquisition machinery. Genes coding a TonB transport system and hypothetical proteins are shown with dark green and blue arrows, respectively. The genetic map also indicates the presence of tnsB, tnsC_1, tnsC_2, tnsE_1 encoding a transposase (red), along with uvrD (grey), racE (light blue) and recF2 (yellow) encoding DNA helicase, racemase, and a DNA replication/repair protein, respectively.