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Antimicrobial Agents and Chemotherapy, November 2005, p. 4485-4491, Vol. 49, No. 11
0066-4804/05/$08.00+0 doi:10.1128/AAC.49.11.4485-4491.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Novel Acquired Metallo-ß-Lactamase Gene, blaSIM-1, in a Class 1 Integron from Acinetobacter baumannii Clinical Isolates from Korea
Kyungwon Lee,1,2,3
Jong Hwa Yum,2,3
Dongeun Yong,1,2,3
Hyuk Min Lee,1,2
Heung Dong Kim,4
Jean-Denis Docquier,5
Gian Maria Rossolini,5 and
Yunsop Chong1,2*
Department of Laboratory Medicine,1
Research Institute of Bacterial Resistance,2
Brain Korea 21 Project for Medical Sciences,3
Department of Pediatrics, Yonsei University College of Medicine, Seoul 120-752, Korea,4
Department of Molecular Biology, Microbiology Section, University of Siena, Siena I-53100, Italy5
Received 10 March 2005/
Returned for modification 30 May 2005/
Accepted 9 August 2005

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 nonduplicate
isolates of carbapenem-resistant
Pseudomonas spp. and
Acinetobacter spp. isolated at a tertiary-care hospital in Seoul, Korea, 211
(17%) were positive for metallo-ß-lactamase (MBL).
Of these, 204 (96%) had either the
blaIMP-1 or
blaVIM-2 allele.
In addition, seven
Acinetobacter baumannii isolates were found
to have a novel MBL gene, which was designated
blaSIM-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 µg/ml)
and had a multidrug resistance phenotype. Expression of the
cloned
blaSIM-1 gene in
Escherichia coli revealed that the encoded
enzyme is capable of hydrolyzing a broad array of ß-lactams,
including penicillins, narrow- to expanded-spectrum cephalosporins,
and carbapenems. The
blaSIM-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.

INTRODUCTION
Gram-negative bacilli have a propensity to develop and acquire
resistance to multiple antimicrobials. A significant increase
in the prevalence of multidrug-resistant gram-negative bacilli,
even among isolates recovered at admission, was reported (
20).
Carbapenems have been the most successful ß-lactam
antibiotics in evading bacterial resistance (
14). However, carbapenem
resistance, mediated by acquired carbapenemase genes, has been
increasingly reported, particularly for clinical isolates of
Pseudomonas aeruginosa and
Acinetobacter spp. (
7). Although
some enzymes of molecular classes A and D can hydrolyze carbapenems,
metallo-ß-lactamases (MBLs) are the most prevalent
acquired carbapenemases (
5,
14,
18,
24,
27,
28).
Of acquired MBLs, the IMP- and VIM-type enzymes are the most common and exhibit a worldwide distribution (7, 8, 19, 24, 26). Recently, however, two additional types, SPM and GIM, have been reported for P. aeruginosa isolates from Brazil and Germany, respectively (2, 22). In Korea, a prevalence of both IMP-1- and VIM-2-type MBLs has been reported (10, 12). Here we report the detection of a new acquired MBL in clinical isolates of Acinetobacter baumannii from Korea.

MATERIALS AND METHODS
Bacterial strains.
A total of 1,234 nonduplicate imipenem-resistant clinical isolates
of
Pseudomonas spp. and
Acinetobacter spp. isolated in 2003-2004
at a tertiary-care hospital in Seoul, Korea, were investigated
in this study. The isolates were identified by conventional
methods (
21) or by using the ATB 32GN system (bioMerieux, Marcy
l'Etoile, France). The phenotypic identification of four randomly
selected VIM-2 MBL-producing
Pseudomonas putida isolates was
confirmed by 16S rRNA sequencing as described previously (
15).
The
Escherichia coli strain XL-1 Blue (Stratagene Inc., La Jolla,
Calif.) was used as the host for expression of the cloned
blaSIM-1 gene.
Susceptibility testing.
Imipenem susceptibility was tested by a disk diffusion method (17). MICs for the SIM-1-producing A. baumannii isolates were determined by an agar dilution method (16) and interpreted according to the guidelines of the Clinical Laboratory Standards Institute (3). MICs for E. coli XL-1(pBC-SIM1) were determined by a broth microdilution method (16).
ß-Lactamase assays.
The Hodge test (9), using MacConkey agar instead of Mueller-Hinton agar, which allows a better performance (unpublished result), was used for screening of carbapenemase production. The imipenem and EDTA-sodium mercaptoacetic acid (SMA) double-disk synergy test (11) and Etest MBL strips (AB BIODISK, Solna, Sweden) were used for screening of MBL production. A spectrophotometric assay was used to measure the MBL activity in crude cell extracts, as described previously (8). Analytical isoelectric focusing of ß-lactamase was performed using the nitrocefin chromogenic substrate (8).
DNA analysis and manipulation methodology.
PCR detection of the blaIMP-1 and blaVIM-2 genes was carried out using the IMP1 and VIM2 primers (Table 1) as described previously (29). SIM primers, which were designed after an analysis of the sequence of the novel MBL gene, were used to detect the presence of the allele in the remaining six non-IMP-, non-VIM-type MBL-producing isolates. PCR was performed with 1 µl of heat-extracted DNA template, 20 pmol of each primer, and PreMix (Bioneer, Cheongwon, Korea) containing 1 U of Taq DNA polymerase in a total volume of 20 µl. A Mastercycler instrument (Eppendorf, Hamburg, Germany) was used with the following reaction conditions: 94°C for 5 min, 25 cycles of 94°C for 30 s, 56°C for 30 s, and 72°C for 45 s, and finally, 72°C for 7 min.
The amplicons generated with primers INT1-F and INT2-R (
13)
were used to analyze the sequence of the new MBL gene and other
gene cassettes. The reactions were carried out in a total volume
of 50 µl, with 5 µl of heat-extracted template DNA,
20 pmol of each primer, and 3 U of LA
Taq (Takara, Shiga, Japan).
The cycling conditions were as follows: 94°C for 12 min
and then 35 cycles of 94°C for 1 min, 56°C for 1 min,
and 72°C for 5 min. The extension time was increased by
5 s for each cycle. Nucleotide sequences were determined for
both strands of DNA by the dideoxy chain-termination method
using an ABI 3700 autosequencer (Perkin-Elmer, Foster City,
Calif.). Three independently generated amplicons were used to
determine the nucleotide sequences. Sequence analysis and comparisons
were performed using programs available at the NCBI (
http://www.ncbi.nlm.nih.gov/)
and ExPASy (
http://www.expasy.org/) servers.
Southern blot hybridization was performed on pulsed-field gel electrophoresis (PFGE)-separated DNA after its transfer to a nylon membrane (Bio-Rad, Hercules, Calif.), using a digoxigenin-labeled blaSIM-1 probe which was prepared according to the reagent manufacturer's instructions (Roche Diagnostics, Mannheim, Germany).
Plasmid pBC-SIM1 was constructed by cloning a PCR amplicon containing the blaSIM-1 gene which was generated with primers SIM1-Exp/f (adding an XbaI restriction site and a ribosome binding site upstream of the blaSIM-1 start codon) and SIM-1-Exp/r (adding a BamHI restriction site downstream of the blaSIM-1 stop codon) (Table 1). PCR was performed in a 50-µl volume, using 3.5 U of the Expand High-Fidelity PCR system (Roche Diagnostics) in the buffer supplied by the manufacturer, with 50 pmol of each primer and 10 ng of A. baumannii YMC 03/9/T104 genomic DNA, under the following cycling conditions: 95°C for 3 min, 30 cycles of 95°C for 1 min, 55°C for 1 min, and 72°C for 2 min, and finally, 72°C for 7 min. The XbaI- and BamHI-digested amplicon was ligated to the pBC-SK(+) plasmid vector (Stratagene), which had been digested with the same enzymes. The authenticity of the cloned blaSIM-1 gene carried by pBC-SIM1 was confirmed by sequencing.
Gene transfer experiments.
Imipenem resistance transfer was tested by the agar mating method (1), using rifampin-resistant P. aeruginosa PAO 4089 and azide-resistant Escherichia coli J53 as recipients and ceftazidime (4 µg/ml) plus rifampin (200 µg/ml) or azide (100 µg/ml) for the selection of transconjugants. Ceftazidime was used for the selection of transconjugants instead of a carbapenem because the SIM-1-producing isolates were inhibited by a relatively low concentration of imipenem.
Genotyping.
PFGE of SmaI-restricted genomic DNAs of the SIM-1-producing A. baumannii isolates was performed using the CHEF-DR II system (Bio-Rad) according to the manufacturer's protocols. The banding patterns were analyzed with UVIband/Map software (UVItech Ltd., Cambridge, United Kingdom) to generate a dendrogram based on the unweighted-pair group method using arithmetic averages from the Dice coefficients.
Nucleotide sequence accession number.
The nucleotide sequence data reported in this paper are listed in the GenBank database under accession number AY887066.

RESULTS AND DISCUSSION
MBL production in carbapenem-resistant Pseudomonas spp. and Acinetobacter spp.
Of 1,234 nonduplicate imipenem-resistant clinical strains isolated
in 2003-2004 at a tertiary-care hospital, 211 (17%) were positive
for carbapenemase and MBL production by the Hodge test and the
imipenem and EDTA-SMA double-disk synergy test, respectively
(Table
2). PCR analysis of the MBL producers revealed the presence
of a
blaVIM-2 allele in 157 (74%) isolates and of a
blaIMP-1 allele in 47 (22%) isolates, but 7 (4%)
A. baumannii isolates
yielded negative results for both genes. MBL activities were
detectable in crude extracts of these isolates by a spectrophotometric
assay (data not shown). With these isolates, the imipenem and
EDTA-SMA double-disk synergy test was clearly positive only
when the two disks were placed 15 mm (edge-to-edge) apart from
each other, due to a relatively large imipenem inhibition zone,
while the Etest for MBL was not informative due to the relatively
low imipenem MICs for these isolates (8 to 16 µg/ml) (Table
3).
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TABLE 3. Clinical features of patients and characteristics of A. baumannii isolates with blaSIM-1 cassette-carrying class 1 integrons
|
Identification of a new MBL determinant.
The new MBL determinant and the integron content of the first
non-IMP- and non-VIM-type MBL-producing isolate (YMC 03/9/T104)
were investigated by sequencing, using PCR products obtained
with the INT1-F and INT2-R primers (
13). This analysis revealed
the presence of two class 1 integrons, with one containing two
gene cassettes (
arr-3 and
aacA4) and the other containing four
gene cassettes (Fig.
1). The first cassette of the latter integron
carried a new MBL gene, which we designated
blaSIM-1 (for
Seoul
imipenemase).
The SIM-1 enzyme is a new subclass B1 MBL (
4) whose closest
relatives are the IMP-type enzymes (69% identity with IMP-12
and 64% identity with IMP-9), while the other MBLs are more
divergent (Fig.
2 and
3). The theoretical molecular weight and
pI of the mature SIM-1 protein are 25,439 and 7.28, respectively,
considering the presence of an 18-amino-acid leader peptide
(
http://www.cbs.dtu.dk/services/SignalP/). The
attC (59-base
element) recombination site of the
blaSIM-1 cassette was 88
bp long and not related to those of known
blaIMP cassettes but
was very similar (90% identity) to that of a cassette (
ypar13)
of the
Pseudomonas alcaligenes In
55044 superintegron (
23), suggesting
that the source of the
blaSIM-1 cassette could be a similar
element. It was interesting that the other cassettes carried
arr-3, a rifampin ADP ribosyltransferase gene, and
catB3, a
chloramphenicol acetyltransferase gene, which are rarely found
in MBL-encoding integrons (
6).
Using the SIM primers, the
blaSIM-1 gene was also detected in
the remaining six isolates. The structures of the
blaSIM-1-containing
class 1 integrons were apparently identical in these isolates,
according to the results of PCR mapping using the INT1-F and
INT-2R primers in combination with the SIM1-R and SIM1-F primers,
respectively, and of partial sequencing of the amplicons (data
not shown).
Repeated attempts failed to transfer ceftazidime resistance from each of the seven isolates to either P. aeruginosa or E. coli recipient cells by conjugation. In a Southern blot analysis of SmaI-restricted and PFGE-separated genomic DNAs, a blaSIM-1 probe recognized a band of approximately 300 kb in all seven isolates (data not shown). This suggested that the blaSIM-1 gene was located on the chromosome. Further studies are required to ascertain the chromosomal or plasmid location of the blaSIM-1 gene.
Functional characterization of SIM-1.
The functional properties of SIM-1 were investigated by expression of the enzyme in E. coli XL-1 Blue and testing of the susceptibility of this strain to several ß-lactams. The E. coli XL-1(pBC-SIM1) strain produced an EDTA-inhibitable carbapenemase (Table 4), and analytical isoelectric focusing of a crude extract revealed the presence of a ß-lactamase band with a pI of 7.2 (consistent with the theoretical value calculated for the mature SIM-1 protein [see above]). Compared to the host strain, XL-1(pBC-SIM1) exhibited decreased susceptibility to a broad array of ß-lactams, including penicillins, narrow- to expanded-spectrum cephalosporins, and carbapenems (Table 4), indicating that SIM-1 has a broad overall substrate specificity. Only the MICs of aztreonam and piperacillin were unchanged, suggesting that SIM-1 is not active against these compounds.
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TABLE 4. MICs of ß-lactams for E. coli XL-1 (pBC-SIM1), expressing the SIM-1 enzyme, and for the E. coli host containing only the cloning vector pBC-SK
|
Clonal relatedness of SIM-1-producing isolates and clinical features of patients.
PFGE of SmaI-restricted genomic DNAs showed that the SIM-1-producing
isolates belonged to two quite different clusters (Fig.
4).
The first SIM-1-producing
A. baumannii isolate was from a sputum
specimen from a patient with pneumonia, while the remaining
six were from urines from patients with urinary tract infections.
All patients had underlying diseases, and all but one were inpatients.
The single outpatient, however, had a long history of ambulatory
treatment due to several comorbidities. The six patients had
been in the hospital for 3 to 30 days before the isolation of
a SIM-1-producing isolate (Table
3). Only the first patient
had received meropenem therapy for 12 days before the isolation
of the SIM-1-producing isolate. The other patients had received
other antimicrobial agents, except for one pediatric patient,
who did not receive any antimicrobial agents during the 4 days
of hospitalization preceding the isolation of the SIM-1-producing
isolate. This suggests that the acquisition of SIM-1-producing
A. baumannii was not strictly related to the use of carbapenems.
The first four SIM-1-producing isolates were detected sporadically,
from different settings, during a period of 14 months (September
2003 to November 2004), while the last three isolates were detected
over a period of 11 days from patients in the same ward, suggesting
the occurrence of a small outbreak. Of the two clonal lineages
of SIM-1-producing isolates, one was represented by the sporadic
isolates, and the other was represented by those involved in
the outbreak in the pediatric ward (Table
3; Fig.
4).
All isolates were susceptible to ciprofloxacin but resistant or intermediate to other antimicrobial agents, including expanded-spectrum cephalosporins, ampicillin-sulbactam, and all aminoglycosides tested (Table 3). Levofloxacin was used in one patient, and isepamycin was used in the other patients. All patients eventually recovered from the infection.
In conclusion, a novel acquired MBL gene, blaSIM-1, was detected in seven clinical isolates of A. baumannii from Korea, where VIM-2- and IMP-1-type MBL-producing P. aeruginosa and Acinetobacter spp. have been prevalent. SIM-1 is encoded by a class 1 integron-borne gene cassette and is more closely related to IMP-type enzymes than to other MBLs. The presence of apparently the same integron in isolates belonging to different clonal lineages indicates that horizontal transfer of this gene has occurred and suggests that further spread of the resistance may occur in the future.

ACKNOWLEDGMENTS
This work was supported in part by the Brain Korea 21 Project
for Medical Sciences, Yonsei University, in 2004.
We thank Myung Sook Kim for collecting the isolates and Yonghee Suh and Chasoon Lee for screening the MBL-producing isolates.

FOOTNOTES
* Corresponding author. Mailing address: Department of Laboratory Medicine, Yonsei University College of Medicine, 134 Shinchondong, Seodaemunku, Seoul 120-752, Korea. Phone: 82-2-222-82446. Fax: 82-2-313-0908. E-mail:
whonetkor{at}yumc.yonsei.ac.kr.


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Antimicrobial Agents and Chemotherapy, November 2005, p. 4485-4491, Vol. 49, No. 11
0066-4804/05/$08.00+0 doi:10.1128/AAC.49.11.4485-4491.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
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