Novel acquired metallo-beta-lactamase gene, bla(SIM-1), in a class 1 integron from Acinetobacter baumannii clinical isolates from Korea

Abstract

Carbapenem resistance mediated by acquired carbapenemase genes has been increasingly reported, particularly for clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. Of 1,234 non-duplicate isolates of carbapenem-resistant Pseudomonas spp. and Acinetobacter spp. isolated at a tertiary-care hospital in Seoul, Korea, 211 (17%) were positive for metallo-beta-lactamase (MBL). Of these, 204 (96%) had either the bla(IMP-1) or bla(VIM-2) allele. In addition, seven Acinetobacter baumannii isolates were found to have a novel MBL gene, which was designated bla(SIM-1). The SIM-1 protein has a pI of 7.2, is a new member of subclass B1, and exhibits 64 to 69% identity with the IMP-type MBLs, which are its closest relatives. All SIM-1-producing isolates exhibited relatively low imipenem and meropenem MICs (8 to 16 microg/ml) and had a multidrug resistance phenotype. Expression of the cloned bla(SIM-1) gene in Escherichia coli revealed that the encoded enzyme is capable of hydrolyzing a broad array of beta-lactams, including penicillins, narrow- to expanded-spectrum cephalosporins, and carbapenems. The bla(SIM-1) gene was carried on a gene cassette inserted into a class 1 integron, which included three additional cassettes (arr-3, catB3, and aadA1). The strains were isolated from sputum and urine specimens from patients with pneumonia and urinary tract infections, respectively. All patients had various underlying diseases. Pulsed-field gel electrophoresis of SmaI-digested genomic DNAs showed that the strains belonged to two different clonal lineages, indicating that horizontal transfer of this gene had occurred and suggesting the possibility of further spread of resistance in the future.

FIG. 1.

Structure of the variable region of the bla_SIM-1-containing class 1 integron from isolate YMC 03/9/T104. Large arrows indicate the resistance genes carried by the gene cassettes and their transcriptional direction. The gray box indicates the attI site, open boxes indicate the attC sites (59-base elements) of the gene cassettes, and hatched boxes indicate the partially sequenced 5′ and 3′ conserved sequences. The locations of primers (described in Table 1) used to map the integron and determine its sequence are also shown (small arrows).

FIG. 2.

Unrooted tree showing the relationships between SIM-1 and other subclass B1 MBLs. The shaded triangle indicates the sequence variability observed within the IMP lineage. Accession numbers for the sequences are as follows: IMP-1, AAB30289; CcrA, P25910; BcII, P04190; VIM-1, CAB46686; BlaB, CAA65601; JOHN-1, AAK38324; EBR-1, AAN32638; IND-1, AAD20273; CGB-1, AAL55263; MUS-1, AAN63647; TUS-1, AAN63648; SPM-1, CAD37801; and GIM-1, CAF05908.

FIG. 3.

Amino acid sequence comparison between SIM-1 and representatives of the other four types of acquired MBLs. Residues conserved in all proteins are shown in bold. The residues known to be involved in metal binding are indicated by asterisks. Numbering is according to the updated BBL scheme (4). Accession numbers are the same as those in the legend to Fig. 2.

FIG. 4.

PFGE patterns of SmaI-digested genomic DNAs from SIM-1-producing isolates of A. baumannii. The patterns of the first four isolates are quite different from those of the last three isolates.