Acinetobacter baumannii that are extensively-antibiotic resistant (XAR) or pan-resistant pose an increasingly significant treatment challenge. Most Australian XAR A. baumannii belong to global clone 2 (GC2), one of the globally disseminated clones. We previously showed that two chromosomally located genomic islands, AbGRI1 and AbGRI2, contain most of the antibiotic resistance genes in GC2 isolates, though their structures are not conserved.
Whole genome sequencing was performed on 78 XAR A. baumannii isolates from 8 hospitals in Sydney, Brisbane and Canberra. 70 of these isolates had an identical AbGRI1, while 8 had a minor variant. This indicated that this collection of Australian isolates was closely related, sharing a common ancestor. The position of two mobile elements in AbGRI1, ISAba17 and Tn2006, containing the oxa23 carbapenem resistance gene, appears specific to the Australian isolates differentiating them from AbGRI1 variants seen in other countries.
However, there were 7 variants of AbGRI2, mainly caused by IS26-mediated deletion. These deletions often removed the gene responsible for gentamicin resistance, but a subgroup of isolates regained this resistance via a different gene on a plasmid. All of the variants could be derived from the largest, AbGRI2-1, providing further evidence that the isolates have diverged from a common ancestor. Some variants were unique to a single hospital, while others were observed in multiple hospitals, and cities. It was possible to track different sublineages of the Australian GC2s based on the different structures of AbGRI2. Combining this data with an analysis of each isolates plasmid content provided further insight into the spread of these sublineages between hospitals.
While the whole genome approach used here is not yet practical for routine hospital screening, a simple PCR based strategy for the detection of AbGRI1 and AbGRI2 was developed that can be applied for rapid characterization of isolates in future outbreaks.