The Birth and Demise of the IS--IS Composite Transposon: the Vehicle for Transferable Colistin Resistance

The origin and mobilization of the ~2,609-bp DNA segment containing the mobile colistin resistance gene continue to be sources of uncertainty, but recent evidence suggests that the gene originated in species. Moreover can be mobilized as an IS-flanked composite transposon (Tn), but many sequences have been identified without IS or with just a single copy (single ended). To further clarify the origins and mobilization of , we employed the Geneious R8 software suite to comprehensively analyze the genetic environment of every complete structure deposited in GenBank as of this writing (September 2017) both with and without associated IS ( = 273). This revealed that the 2,609-bp structure was likely mobilized from a close relative of a novel species of containing a chromosomal region sharing >96% nucleotide identity with the canonical sequence. This chromosomal region is bounded by AT and CG dinucleotides, which have been described on the inside ends (IE) of all intact Tn described to date and represent the ancestral 2-bp target site duplications (TSDs) generated by IS transposition. We further demonstrate that all structures with just one IS copy or with no IS copies were formed by deletion of IS from the ancestral Tn, likely by a process related to the "copy-out-paste-in" transposition mechanism. Finally, we show that only the rare examples of single-ended structures that have retained a portion of the excised downstream IS including the entire inverted right repeat might be capable of mobilization. A comprehensive analysis of all intact sequences in GenBank was used to identify a region on the chromosome of a novel species with remarkable homology to the canonical structure and that likely represents the origin of this important gene. These data also demonstrate that all structures lacking one or both flanking IS were formed from ancestral composite transposons that subsequently lost the insertion sequences by a process of abortive transposition. This observation conclusively shows that mobilization of occurs as part of a composite transposon and that structures lacking the downstream IS are not capable of mobilization.