A Novel Insertion Sequence, ISAba10, Inserted into ISAba1 Adjacent to the bla OXA-23 Gene and Disrupting the Outer Membrane Protein Gene carO in Acinetobacter baumannii

ABSTRACT We investigated an outbreak caused by carbapenem-resistant Acinetobacter baumannii carrying the bla OXA-23 gene. A novel insertion sequence (IS), named ISAba10, was found to be inserted into the ISAba1 element preceding the bla OXA-23 gene in a group of isolates showing higher carbapenem MICs. The presence of ISAba10 was associated with increased OXA-23 expression, likely by providing additional promoter sequences. ISAba10 was also inserted into the carO outer membrane protein gene in most of these isolates.

Insertion sequences (ISs) may enhance ␤-lactamase gene expression by providing promoters. ISAba1 has frequently been found upstream of the ADC AmpC ␤-lactamase and OXA carbapenemase genes in A. baumannii (16). ISAba2, ISAba3, and ISAba4 elements have also been found to precede the bla OXA-58 and the bla OXA-23 genes in clinical isolates of A. baumannii (2,15,17).
In this work, we investigated an outbreak of carbapenemresistant A. baumannii and identified a new IS that could be involved in carbapenem resistance by multiple mechanisms.
Consecutive nonreplicate carbapenem-resistant A. baumannii isolates were recovered from 23 patients hospitalized at a tertiary care hospital in Korea between May and July 2007. All isolates showed positive results with the modified Hodge test, suggesting carbapenemase production, but negative results with the EDTA-sodium mercaptoacetic acid double-disk synergy test for the screening of MBLs (6). All isolates were nonsusceptible to multiple drugs, including ampicillin, cefox-itin, ceftazidime, cefotaxime, cefepime, levofloxacin, amikacin, gentamicin, and tobramycin, by the CLSI disk diffusion method (3). SmaI macrorestriction anaylsis of 23 isolates exhibited genetic similarities of 70% to 100% by the unweighted pair group method with arithmetic average method (data not shown) (8,18). Thirteen of the isolates (group I) showed identical SmaI macrorestriction patterns (Table 1).
Genes encoding known carbapenemases were investigated as described previously (20). The naturally occurring bla OXA-66 gene, a member of the bla OXA-51 cluster, was detected in all 23 A. baumannii isolates. Furthermore, 20 of the 23 isolates showed positive results in PCR experiments for the detection of the bla OXA-23 gene. I-CeuI mapping experiments showed that a probe specific for bla OXA-23 hybridized with an approximately 500-kb I-CeuI chromosomal fragment that was also recognized by a probe specific for 16S rRNA genes, revealing a chromosomal location of the bla OXA-23 gene, as observed in recent studies (8,11). Genes encoding OXA-24-like and OXA-58-like carbapenemases or MBLs such as IMP-1-like, VIM-2like, and SIM-1 were not detected in any of the isolates.
PCR experiments detected ISAba1 upstream of the bla OXA-23 gene in all the bla OXA-23 -positive isolates (19,20). However, the PCR product from 13 isolates (group I) was about 2.5 kb, which was larger than the expected size (1.4 kb), suggesting the insertion of additional DNA. Direct sequencing of PCR products showed the presence of a novel IS, named ISAba10, inserted at the 167th nucleotide from the right inverted repeat of the ISAba1 element. Although insertion of ISAba10 disrupted the ISAba1 element, promoter sequences for the bla OXA-23 gene within ISAba1 remained intact. The new ISAba10 element was 1,023 bp long, contained a 927-bp open reading frame (ORF) encoding a putative transposase, and was bounded by imperfect 18-bp inverted repeat sequences, which are common to members of the IS903 group (Fig. 1). A 9-bp duplication (5Ј-TGTTTGCTT-3Ј) flanked ISAba10 at the predicted insertion site. Amino acid sequence alignment using an online tool (http://www-is.biotoul.fr) showed that the ORF of the ISAba10 element shared some similarities to the transposases of ISs such as ISGNB1-1 (identity, 55%), ISJsp1 (52%), ISRusp5 (51%), ISAba7 (48%), and ISAba5 (45%) in the IS903 group.
The remaining seven bla OXA-23 -positive isolates (group II) carried an intact ISAba1 upstream of the bla OXA-23 -like gene. In all group I and group II isolates, bla OXA-66 was not preceded by the ISAba1 element, while in the three bla OXA-23negative isolates (group III) the bla OXA-66 gene was preceded by ISAba1.
Notably, group I isolates showed two to eight times higher MICs (32 to 64 mg/liter) for both imipenem and meropenem, compared to group II isolates, by agar dilution. Real-time quantitative PCR experiments with the primers and probes listed in Table 2 showed 2-to 5-fold higher bla OXA-23 gene expression in group I isolates than in group II isolates (Table  1) (8). Based on this, we speculated that the ISAba10 element may play a role in higher-level carbapenem resistance by conferring additional promoter sequences to the bla OXA-23 gene. Analyses using the online tool BPROM (Softberry, Inc., Mount Kisco, NY) suggested the presence of a putative promoter within the ISAba10 element (Fig. 1).  Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) experiments were performed as previously described (7). A. baumannii ATCC 19606 was used as a reference strain. All group I isolates, except one (isolate SC0701), lacked the 29-kDa CarO-like OMP, while the other OMPs, such as 33to 36-and 43-kDa porins, were apparently similar to the wildtype strain (data not shown). In the 12 isolates lacking the 29-kDa CarO-like protein, PCR experiments for the carO gene yielded a PCR product about 1.7 kb in size, which was larger than the expected size (741 bp), suggesting the insertion of additional DNA (9). Direct amplicon sequencing confirmed the presence of the ISAba10 element within the carO gene in these isolates. ISAba10 inserted at the 204th base from the carO gene start codon (Fig. 1).
Disruption of the carO gene by the ISAba1, ISAba125, or ISAba825 element has previously been described (13,16). Loss of the CarO OMP likely plays a role in carbapenem resistance in A. baumannii. Interestingly, however, the isolate SC0701, which carried the intact carO gene, exhibited similar MIC levels for imipenem and meropenem compared to the other 12 clonally related group I isolates. Our results suggest that, under similar conditions, loss of the CarO OMP had only a minor effect on carbapenem resistance in A. baumannii.
Nucleotide sequence accession numbers. The nucleotide sequence data reported in this paper are available in the GenBank nucleotide database under accession numbers FJ998184 and GQ379223. We thank Young Hee Suh and Eun Hee Jeon for laboratory assistance.