Acinetobacter baumannii is a gram-negative opportunistic pathogen that causes a range of hospital-acquired infections. Antibiotic resistance is a critical problem in A. baumannii, particularly when resistance genes are acquired by members of successful globally-distributed clones e.g. global clone 1 (GC1). Here, we investigated the evolution of an expanding sub-clade of multiply antibiotic resistant GC1 associated with carbapenem and aminoglycoside resistance.
Twenty-seven strains belonging to a specific clade of GC1 were identified, 3 in our collection and 24 in GenBank, using a range of criteria including the carriage of the Tn6168 transposon, carrying the ISAba1-ampC structure, responsible for resistance to 3rd generation cephalosporins, in a specific chromosomal location, and a specific Outer Core oligoaccharide, OCL3. The genome sequence of the representative of Australian isolates, which was also resistant to carbapenems, was determined using Illumina HiSeq and PacBio long-read technology. A range of bioinformatics tools was used to examine the context of resistance genes, distribution of the chromosomal ISAba1 copies, and phylogeny.
Bayesian analysis showed that the Tn6168/OCL3 clade arose in the late 1990s, from an ancestor that had already acquired resistance to third generation cephalosporins and fluoroquinolones. Between 2000 and 2002, this clade further diverged into distinct sub-clades by insertion of AbaR4 (carrying the oxa23 carbapenem resistance gene) at a specific chromosomal location in one group, and a phage genome in the other. Both subgroups show evidence of ongoing evolution of resistance loci and ISAba1 dispersal. Most concerning, this includes introduction of the armA aminoglycoside resistance gene via AbGRI3, acquired from a GC2 isolate.
Our analysis revealed the complexity of genetic events leading to resistance to multiple antibiotics in the Tn6168/OCL3 clade of GC1. Comparison of IS insertions sites with the dated phylogeny shows ISAba1 first entered this clade in around mid 90s with the cephalosporin resistance transposon Tn6168 and has since expanded in both sub-clades. It also revealed multiple routes for the acquisition of the oxa23 carbapenem resistance gene.