Acinetobacter variabilis represents a diverse species with novel regions associated with antibiotic resistance and surface polysaccharides.

Acinetobacter variabilis is an opportunistic pathogen found in both clinical and environmental settings with the potential to harbour and disseminate clinically significant antibiotic resistance genes. Here, we sequenced the complete genome of NGH-QLD-N1, an A. variabilis isolate recovered from a blood sample of a patient at Nambour General Hospital located on the Sunshine Coast region of Queensland, Australia. The assembly was used as a reference to assess the diversity in available A. variabilis genome sequences and investigate the genomic context of surface polysaccharide biosynthesis genes and antibiotic resistance determinants in relation to the priority pathogen, Acinetobacter baumannii. Phylogenetic analysis revealed substantial diversity in the species, with a distinct NGH-QLD-N1 subclade containing multiple strains with important resistance determinants. We identified a novel transposon related to the Tn6022 family, designated Tn6929, that interrupted comM and identified multiple structural variants in A. variabilis genomes. Notably, some variants carried bla NDM and aphA6 in ISAba14-bounded regions, suggesting acquisition from diverse bacterial hosts. We also identified several integrative conjugative elements (ICEs) variants integrated into the chromosomal thyA gene, which differed in backbone structure and resistance gene content from our previously described A. baumannii ICE. The capsule and outer core loci for surface carbohydrate structures also had similar arrangements to those found in A. baumannii. This study provides a new understanding of the diversity of mobile genetic elements and ICEs carrying resistance genes, and surface polysaccharides associated with virulence, across the Acinetobacter genus.