Evading host defences: Genome sequence analysis of the environmental Acinetobacter baumannii NCIMB8209 strain indicates extensive insertion sequence-mediated genome remodelling with loss of exposed cell structures and defensive mechanisms

VIALE, ALEJANDRO M.; ESPARIZ, MARTIN; DÍAZ MILOSLAVICH, J.I.; SERAVALLE, JOANA L.; SHUMAN, HOWARD A.; GUILLERMO REPIZO

Frankfurt

Simposio; 12th International Symposium on the Biology of Acinetobacter; 2019

Goethe University Frankfurt

Acinetobacter baumannii currently represents an important opportunistic pathogen of obscure reservoirs outside the clinical setting. Here we traced the origins of the collection strain Acinetobacter sp. NCIMB8209 to an isolate first reported in 1944 in the U.S.A. NCIMB8209 was isolated from the enriched microbiota responsible for the aerobic decomposition of guayule, a resinous desert shrub. Whole-genome sequencing analysis indicated the presence of a 3.9 Mb chromosome and a plasmid of 134 kb. Phylogenetic analysis based on core genes and a chromosomal blaOXA-51-type gene confirmed NCIMB8209 affiliation to A. baumannii. The NCIMB8209 chromosome contains 7 genomic islands (GI) and 5 regions encompassing phage-related genes. Remarkably, 93 insertion sequences (IS) were found in its genome, 15 of them correspond to novel mobile elements. No antimicrobial resistance islands were identified, agreeing with a general antimicrobial susceptibility phenotype including to folate synthesis inhibitors. In contrast to its companion, the environmental strain NCIMB8208/DSM30011 [1], NCIMB8209 displayed low virulence in both the Galleria mellonella and Caenorhabditis elegans infection models. Moreover, this strain lacks GIs providing defences against biological aggressors such as Type 6 secretion systems and corresponding toxin genes. NCIMB8209harbours many genes linked to persistence and virulence in pathogenic A. baumannii strains, but many of them encoding external structures are interrupted by IS. Searching for catabolic genes and metabolic assays revealed several clusters involved in the degradation of plant defence substances, pointing to alternative environmental niche(s) for this species. These results suggest that the disruption in NCIMB8209 of exposed structures likely recognized by host defences most probably resulted from the adaptation of this particular A. baumannii strain to a specific environmental niche. Moreover, they also indicated that the reported genetic plasticity of A. baumannii represents an intrinsic characteristic of this species, having evolved prior to its adaptation to the clinical environment.[1] Repizo GD, Viale AM, Borges V, Cameranesi MM, Taib N, Espariz M, Brochier-Armanet C, Gomes JP, Salcedo SP. The environmental Acinetobacter baumannii isolate DSM30011 reveals clues into the pre-antibiotic era genome diversity, virulence potential, and niche range of a predominant nosocomial pathogen. Genome Biol Evol. 9 (2017), 2292-2307