The Environmental Acinetobacter baumannii Isolate DSM30011 Reveals Clues into the Preantibiotic Era Genome Diversity, Virulence Potential, and Niche Range of a Predominant Nosocomial Pathogen

Abstract

Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A. baumannii genomes revealed the presence of 12 unique accessory chromosomal regions in DSM30011 including five encompassing phage-related genes, five containing toxin genes of the type-6 secretion system, and one with an atypical CRISPRs/cas cluster. No antimicrobial resistance islands were identified in DSM30011 agreeing with a general antimicrobial susceptibility phenotype including folate synthesis inhibitors. The marginal ampicillin resistance of DSM30011 most likely derived from chromosomal ADC-type ampC and blaOXA-51-type genes. Searching for catabolic pathways genes revealed several clusters involved in the degradation of plant defenses including woody tissues and a previously unreported atu locus responsible of aliphatic terpenes degradation, thus suggesting that resinous plants may provide an effective niche for this organism. DSM30011 also harbored most genes and regulatory mechanisms linked to persistence and virulence in pathogenic Acinetobacter species. This strain thus revealed important clues into the genomic diversity, virulence potential, and niche ranges of the preantibiotic era A. baumannii population, and may provide an useful tool for our understanding of the processes that led to the recent evolution of this species toward an opportunistic pathogen of humans.

Keywords: CRISPRs/cas; comparative genomics; preantibiotic era bacterium; virulence factors.

Fig. 1.

—Maximum Likelihood phylogenetic analysis of Acinetobacter baumannii strains accompanied by the association coefficient for each pair of strains. (A) The ML phylogeny was computed based on 351 concatenated core gene sequences (full tree is shown in supplementary fig. S2, Supplementary Material online). Numbers at nodes correspond to bootstrap values (100 replicates of the original data set). The scale bar below corresponds to evolutionary distance (average number of the substitutions per site). CCI (in blue) and CCII (in green) correspond to subclusters formed by A. baumannii species assigned to epidemic clonal complexes CCI and CCII, respectively. (B) The table corresponds to the S_AB association coefficient computed for each pair of strains as twice the number of shared gene families between the two strains divided by the number of gene families contained in the two strains, considering all the gene families (see Methods for details).

Fig. 2.

—Linear comparison of the genomes of A. baumannii strains DSM30011, AB031, and ATCC17978 inferred using Mauve. Each block corresponds to a DNA fragment of the chromosome distinctively colored for clarity. The degree of conservation is indicated by the vertical bars inside the blocks. Their position relative to the genome line denotes colinear and inverted regions. Putative prophage insertions (Ph1-3) are indicated below the DSM30011 genome (see supplementary table S6, Supplementary Material online for details). DNA inversions (Inv1-2) and the insertion of Tn6021 within comM in ATCC17978 are also shown (see text for details).

Fig. 3.

—Genomic features of A. baumannii DMS30011. (A) Genome map. The two outermost circles denote the positions of protein (blue) and RNA (red) coding sequences on the plus (circle 1) and minus (circle 2) strands. Circle 3 (black) indicates the GC content. Circle 4 denotes positive (green) and negative (purple) GC-skew. The different accessory gene clusters (AGC I–XII) characteristic of DSM30011 (see table 2 for details) are indicated by red boxes. The CGView software (Stothard and Wishart 2005) was used to construct the genome map. (B) Schematic representation of the genomic region encompassing Tn6018-like region and IS1236/ISAcsp3 mobile elements. (C) Schematic representation of the CRISPR-cas cluster. This locus (designated as subtype IF-c) is compared against a group of Acinetobacter strains bearing a locus with a similar genetic organization and also against A. baumannii AYE, the reference strain for the subtype IF-b. (D) Content and organization of catabolic loci in DSM30011 as compared with A. baylyi (Barbe etal. 2004). This figure follows and complements the schematical representation of catabolic loci elaborated by Di Nocera etal. (2011; see fig. 4 therein). Equivalent catabolic loci between the two strains are indicated by similar shades, and those present only in DSM30011 (liu, tau, pen, and atu) are indicated by open boxes. The composition of catabolic islands A–D in DSM30011 is indicated.

Fig. 4.

—A. baumannii DSM30011 major polysaccharides. (A) Scheme showing the genetic organization of K and OC locus. Genes are colored according to the code used in supplementary table S12, Supplementary Material online. (B) Proposed biosynthetic pathways for sugars precursors of the main exopolysaccharides. Glc, d-glucose; GlcA, d-glucuronic acid; GlcN, 2-amino-2-deoxy-d-glucose; GlcNAc, 2-acetamido-2-deoxy-d-glucose; GlcNAcA, 2-acetamido-2-deoxy-d-glucuronic acid; Gal, d-galactose; GalA, d-galacturonic acid; GalNAc, 2-acetamido-2-deoxy-d-galactose. *The genes coding for these enzymes are located outside the K or OC gene clusters.