Carbapenem-resistant Acinetobacter baumannii isolate HUMC1 (USA, 2009), which is hypervirulent and extensively antibiotic resistant, has been used in many experimental studies. The complete sequence of the chromosome and two plasmids was determined, and the causes of the resistance phenotype were investigated. HUMC1 (ST2:ST1839:KL22:OCL3) is an unusual global clone 2 (GC2) isolate that lacks an AbGRI1 type resistance island interrupting the comM gene. However, a version of AbGRI2, which is present together with AbGRI1 in the oldest known GC2 isolate, and versions of AbGRI3 and the less common AbGRI4 were found in the chromosome. The oxa23 carbapenem resistance gene is carried by two copies of Tn2006. The remaining resistance gene complement is distributed among the three AbGRI, which each carry a sul1 type class 1 integron remnant bounded by IS26 with a gene cassette conferring resistance to useful aminoglycosides; aacC1 (gentamicin) in AbGRI2, aacA4 (gentamicin and tobramycin) in AbGRI3, and aadB (gentamicin and tobramycin) in AbGRI4. The armA gene (amikacin, gentamicin, tobramycin) was also in AbGRI3. The likely source of AbGRI4 was traced to an ST406 lineage. It was imported into HUMC1 or its ancestor, surrounded by a 23 Kbp ST406 segment that is not normally present in GC2 and incorporated into the chromosome by recombination in homologous flanking regions. The segment carrying AbGRI4 has also been acquired by the ST499 and ST229 lineages. The HUMC1 features highlight the importance of class 1 integrons, insertion sequences IS26 and ISAba1, and homologous recombination in the evolution of resistance in this species.
Importance: HUMC1 is a carbapenem-resistant Acinetobacter baumannii isolate belonging to the dominant globally disseminated GC2 clonal complex that is often used in experimental studies as a highly virulent and extensively antibiotic-resistant representative of the species. However, its resistance gene complement had not been examined. The complete genome reported here revealed that HUMC1 carries multiple genes conferring resistance to aminoglycoside antibiotics within chromosomally located resistance islands, including AbGRI4, which is not widespread in GC2 isolates. AbGRI4 appears to have been acquired from an ST406 type co-circulating with GC2 in the USA. The ST499 clonal group, also co-circulating in the USA, has also acquired AbGRI4 from the same source. HUMC1 is also unusual because it lacks an AbGRI1 resistance island found in the comM gene in most current GC2 isolates and in the earliest currently available GC2 isolates from Europe. Hence, it may represent a form that is a precursor of those isolates.
Keywords: AbGRI4; Acinetobacter baumannii; aminoglycoside resistance; carbapenem resistance; global clone 2.