Acinetobacter baumannii NCIMB8209: A rare environmental strain displaying extensive insertion sequence-mediated genome remodeling resulting in the loss of exposed cell structures and defensive mechanisms

Abstract

Acinetobacter baumannii represents nowadays an important nosocomial pathogen of poorly defined reservoirs outside the clinical setting. Here we conducted whole-genome sequencing analysis of the Acinetobacter sp. NCIMB8209 collection strain, isolated in 1943 from the aerobic degradation (retting) of desert guayule shrubs. NCIMB8209 contained a 3.75 Mb chromosome and a plasmid of 134 kb. Phylogenetic analysis based on core genes indicated NCIMB8209 affiliation to A. baumannii, a result supported by the identification of a chromosomal blaOXA-51-like gene. Seven genomic islands lacking antimicrobial resistance determinants, 5 regions encompassing phage-related genes and, notably, 93 insertion sequences (IS) were found in this genome. NCIMB8209 harbors most genes linked to persistence and virulence described in contemporary A. baumannii clinical strains, but many of them encoding components of surface structures are interrupted by IS. Moreover, defense genetic islands against biological aggressors such as type 6 secretion systems or crispr/cas are absent from this genome. These findings correlate with a low capacity of NCIMB8209 to form biofilm and pellicle, low motility on semisolid medium, and low virulence towards Galleria mellonella and Caenorhabitis elegans. Searching for catabolic genes and concomitant metabolic assays revealed the ability of NCIMB8209 to grow on a wide range of substances produced by plants including aromatic acids and defense compounds against external aggressors. All the above features strongly suggest that NCIMB8209 has evolved specific adaptive features to a particular environmental niche. Moreover, they also revealed that the remarkable genetic plasticity identified in contemporary A. baumannii clinical strains represents an intrinsic characteristic of the species. IMPORTANCEAcinetobacter baumannii (Ab) is an ESKAPE opportunistic pathogen, with poorly defined natural habitats/reservoirs outside the clinical setting. Ab arose from the Acb complex as the result of a population bottleneck, followed by a recent population expansion from a few clinically-relevant clones endowed with an arsenal of resistance and virulence genes. Still, the identification of virulence traits and the evolutionary paths leading to a pathogenic lifestyle has remained elusive, and thus the study of non-clinical ("environmental") Ab isolates is necessary. We conducted here comparative genomic and virulence studies on Ab NCMBI8209 isolated in 1943 from the microbiota responsible of the decomposition of guayule, and therefore well differentiated both temporally and epidemiologically from the nowadays predominant multidrug-resistant strains. Our work provides insights on the adaptive strategies used by Ab to escape from host defenses, and may help the adoption of measures aimed to limit its further dissemination.