Variants of Tn, a Novel Tn Family Transposon Carrying the Metallo-β-Lactamase and 14 Copies of the Amikacin Resistance Genes Found in Acinetobacter baumannii.

Carbapenem resistance in Acinetobacter baumannii is primarily due to the global spread of two main clones that carry , , and However, new carbapenem-resistant clones are emerging that are also resistant to a wide range of antibiotics. Strains belonging to ST85 (Institut Pasteur) carry the metallo-β-lactamase carbapenem resistance gene. Here, we completed the genome sequence of an ST85 strain, Cl300, recovered in 2015 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. Cl300 is highly resistant to meropenem and amikacin, and consistent with this, a copy of the carbapenem and 14 copies of the amikacin resistance genes were found in the genome. Cl300 also contains the sulfonamide and the (E) macrolide resistance genes. All copies and are in a novel 76-kb Tn family transposon designated Tn. Like Tn, Tn is bounded by 29-bp inverted repeats with additional TnsB binding sites at each end. Several variants of Tn were found in a set of diverse strains, including ST85 strains as well as members of global clones 1 and 2. and (E) are in a 13.0-kb pseudocompound transposon (PCT) bounded by IS. ST85s represent a diverse group of strains, particularly in their antibiotic resistance gene content and the K and OC surface polysaccharide loci. Acquisition of Tn by members of global clones indicates the significance of this transposon in spreading two clinically significant resistance genes, and . To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other clones, it is associated with the carriage of the gene. Here, we completed the genome sequence of an ST85 strain and showed that and 14 copies of the amikacin resistance genes are in Tn, a novel Tn family transposon. Analysis of all publicly available ST85s predicted that all strains in the main lineage carry a variant of Tn. Variants of Tn were also found in other clones, including GC1 and GC2. Tn is an important mobile element given that it carries two clinically important resistance genes ( and ) and has spread to other clones. Therefore, outbreaks caused by ST85s should be studied and tracked.