Acinetobacter baumannii is one of the ESKAPE group of nosocomial pathogens that are challenging current treatment options. In addition to the major multiply antibiotic resistant global clones, GC1 and GC2, new Acinetobacter baumannii clones such as ST25 are emerging. In GC1 and GC2, most of the antibiotic resistance genes are in resistance islands in the chromosome rather than in plasmids.
D4 was isolated in 2006 from a wound at a Sydney hospital, and was found to be resistant to multiple antibiotics of different classes. It belongs to ST25 (Institut Pasteur Scheme) rather than the predominant clones. To examine the regions responsible for antibiotic resistance, D4 was sequenced using Illumina HiSeq and a de-novo assembly generated. ResFinder 2.1 was used to identify resistance genes. PCR followed by sequencing was used to join contigs containing resistance genes. Most of the D4 resistance phenotype was accounted for by several aminoglycoside resistance genes, aadB, strA-strB, aphA1b, aadA2 genes and a new aadA hybrid gene, and two sulphonamide resistance genes, sul1, sul2. Resistance to 3rd generation cephalosporins was due to blaPER not the ISAba1-ampC configuration found in GC1 and GC2. These genes were found to be located in three resistance islands, two in the chromosome and one in a plasmid. The aadB, strAB, sul1, aadA2, blaPER genes and the aadA hybrid were in a complex class 1 integron, which was part of a 54 kb integrative element, designated A. baumannii genomic resistance island 1, AGI1. AGI1 is distantly related to Salmonella genomic island 1 (SGI1) and Proteus genomic island PGI1. Like SGI1 and PGI1, AGI1 encodes a site-specific recombinase (integrase) at one end and has integrated at the 3'-end of the chromosomal trmE(thdF) gene. The class 1 integron is the preferred location adjacent to a res gene in the island backbone. Hence, AGI1 is a new resistance island type belonging to the same broad family of integrative mobilizable elements as SGI1. These GI have related integrases and, hence, target the same integration site.
The aphA1b gene was part of a 4.5 kb transposon bounded by two IS26. This transposon was adjacent, on one side, to backbone from a Tn6022 that was inserted in the comM gene. The left hand side of Tn6022 and ~ 2 kb of chromosome had been removed via IS26-mediated adjacent deletion. The ISAba1-sul2-CR2-strB-strA-orf4b segment was found in another transposon within a large plasmid and this transposon is related to one of the genomic resistance islands found in GC2 isolates.