Comparative analysis of Acinetobacters: three genomes for three lifestyles

Abstract

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.

Figure 1. Comparison of gene content of A. baylyi ADP1, A. baumannii AYE and A. baumannii SDF chromosomes.

Putative orthologs are defined as genes showing a minimum of 40% identity and a ratio of 0.8 of the length of the smallest protein, or as two genes included in a synteny group. The intersections between the three circles give the number of genes found in the 2 or 3 compared species. Genes outside these areas are specific to the corresponding organism. The total number of annotated genes is also given under each species name. Figures in brackets indicate the number of pseudogenes.

Figure 2. Gene content comparison of the three Acinetobacter chromosomes according to nine functional categories.

The proportions of specific genes which have no ortholog in the two other strains are indicated by light colors. Genes having an ortholog in at least one of the other 2 species were regarded as non specific (dark colors). Absolute gene count for each subclass is reported in boxes at bars bottom. Two genes were considered as orthologs when their respective product shares more than 40% identity over more than 80% of their length.

Figure 3. Circular representation of the three Acinetobacter genomes (ADP1, left; AYE, middle; SDF, right).

Circles display from the outside in: (1) GC deviation (mean GC content in a 1kb window–overall mean GC). Red areas indicate that deviation is higher than 1.5 SD. (2) Location of various genomic regions. (3) Gene specificity (grey, Acinetobacter spp. core genome; green, A. baumannii core genome; red, strain specific genes). (4) GC skew (G+C/G−C using a 1kb sliding window). (5) Pseudogenes (yellow), ISs (pink), tRNA (green) and rDNA (blue).