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Antimicrobial Agents and Chemotherapy, April 2007, p. 1223-1227, Vol. 51, No. 4
0066-4804/07/$08.00+0 doi:10.1128/AAC.01195-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Prevalence of Plasmid-Mediated Quinolone Resistance Determinants QnrA, QnrB, and QnrS among Clinical Isolates of Enterobacter cloacae in a Taiwanese Hospital
Jiunn-Jong Wu,1
Wen-Chien Ko,2
Shu-Huei Tsai,3 and
Jing-Jou Yan3,4*
Departments of Medical Laboratory Science and Biotechnology,1
Internal Medicine,2
Pathology, College of Medicine, National Cheng Kung University,3
Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan, Republic of China4
Received 23 September 2006/
Returned for modification 11 December 2006/
Accepted 15 January 2007

ABSTRACT
The prevalence of three plasmid-mediated quinolone resistance
determinants, QnrA, QnrB, and QnrS, among 526 nonreplicate clinical
isolates of
Enterobacter cloacae collected at a Taiwanese university
hospital in 2004 was determined by PCR and colony hybridization,
and the association of Qnr with the IMP-8 metallo-ß-lactamase
was investigated. Eighty-six (16.3%) of all isolates were
qnr positive, and the
qnrA1-like,
qnrB2-like, and
qnrS1-like genes
were detected alone or in combination in 3 (0.6%), 53 (10.1%),
and 34 (6.5%) isolates, respectively. Among 149 putative extended-spectrum-ß-lactamase-producing
isolates, 59 (39.6%) isolates, all of which were SHV-12 producers,
harbored
qnrA (0.7%; 1 isolate),
qnrB (28.9%; 43 isolates),
or
qnrS (12.1%; 18 isolates). Forty-four (78.6%) of 56 IMP-8
producers carried
qnrB (58.9%; 33 isolates),
qnrS (25.0%; 14
isolates), or both. PCR and sequence analysis revealed that
qnrA1 was located in a complex
sul1-type integron that contains
dhr15,
aadA2,
qacE
1,
sul1,
orf513,
qnrA1,
ampR, and
qacE
1. Conjugation
experiments revealed the coexistence of
qnrB and
blaIMP-8 on
the transferred plasmids and the absence of ß-lactamase
content on the transferred
qnrS-positive plasmids. The transferred
blaIMP-8-positive plasmids with and without
qnrB had very similar
restriction patterns, suggesting the horizontal mobility of
qnrB. Pulsed-field gel electrophoresis showed six major patterns
among the 44
qnr-positive IMP-8-producing isolates. Thus, the
extremely high prevalence of
qnr among the metallo-ß-lactamase-producing
E. cloacae isolates in the hospital may be due mainly to the
intrahospital spread of a few clones and the dissemination of
plasmids containing both
qnrB and
blaIMP-8.

INTRODUCTION
Since the first plasmid-mediated quinolone resistance determinant,
Qnr (later termed QnrA), was described in a
Klebsiella pneumoniae strain from the United States in 1998 (
17), three major groups
of Qnr determinants, QnrA, QnrB, and QnrS, have been identified
in various enterobacterial species (
3-
14,
17,
20,
22,
33,
34).
Qnr determinants may protect DNA gyrase directly from quinolone
inhibition, leading to an 8- to 32-fold increase in MICs of
quinolones (
31).
qnrA has been well known for its worldwide
distribution and is located in complex
sul1-type class 1 integrons
(
12,
16,
20,
22,
28,
33). Such integrons consist of duplicate
qacE
1 and
sul1 genes, which surround a putative recombinase
gene,
orf513 (
23). At least five
qnrB and two
qnrS variants
have been described (
1,
7-
9,
11,
26), among which only
qnrB2 has been found in the complex
sul1-type integron (
7). QnrB and
QnrS have been detected in Asia, Europe, and the United States
(
1,
4,
8,
9,
14,
24).
In Taiwan, qnrS on a plasmid encoding the SHV-2 extended-spectrum ß-lactamase (ESBL) from a K. pneumoniae strain has been described (4), and the presence of qnrA and qnrB has not been reported. The present study was conducted to determine the prevalence of the three groups of Qnr among Enterobacter cloacae isolates in a Taiwanese teaching hospital. An extraordinary high frequency of qnr among E. cloacae isolates with the IMP-8 metallo-ß-lactamase (MBL) was observed, and the emergence of qnrA and qnrB in Taiwan is reported first in this work.

MATERIALS AND METHODS
Bacterial isolates.
A total of 526 nonreplicate clinical isolates of
E. cloacae consecutively collected in 2004 at National Cheng Kung University
Hospital were analyzed for the presence of
qnr genes. Each isolate
was obtained from a single patient.
Detection of qnr genes.
The qnrA, qnrB, and qnrS genes were detected by PCR with the primer sets shown in Table 1 and colony hybridization with a DIG DNA labeling and detection kit (Roche Applied Science, Mannheim, Germany) according to the manufacturer's instructions. qnrB-CS-1A and qnrB-CS-1B are consensus primers chosen from regions with high levels of sequence homology to the qnrB genes known in April 2006. Both strands of amplicons were sequenced with the same primers for PCR amplification, and all PCR experiments were performed at least twice. The qnr probes were prepared by using PCR products as the templates.
Susceptibility testing.
Isolates were screened for the production of ESBLs and MBLs
by the double-disk synergy test and the 2-mercaptopropionic
acid double-disk potentiation method, respectively, as described
previously (
32,
35). MICs of amikacin, ampicillin, aztreonam,
cefepime, cefotaxime, ceftazidime, cephalothin, ciprofloxacin,
gentamicin, imipenem, and nalidixic acid were determined by
the agar dilution method according to CLSI (formerly NCCLS)
guidelines (
19).
ß-Lactamase characterization.
The expression of ß-lactamases was detected by isoelectric focusing (IEF) using an LKB Multiphor apparatus (GE Healthcare Life Sciences, Hong Kong) as described previously (18, 36). The presence of blaSHV (21), blaTEM (15), and bla genes related to blaCTX-M-1 (29), blaCTX-M-9 (29), and blaIMP-2 (36) was detected by PCR and nucleotide sequencing with previously reported oligonucleotide primers (Table 1).
PFGE.
Pulsed-field gel electrophoresis (PFGE) analysis of XbaI-digested genomic DNA was performed using a CHEF-DR 3 apparatus (Bio-Rad Laboratories, Hercules, CA) according to the instruction manual. PFGE patterns were interpreted according to criteria described previously by Tenover et al. (30). The patterns were considered to belong to the same type if there was a difference of no more than three bands.
Conjugation experiments and plasmid analysis.
Conjugation experiments were performed by the liquid mating-out assay using streptomycin-resistant Escherichia coli C600 as the recipient as described previously (25, 36). Transconjugants were selected on tryptic soy agar plates containing 512 µg of streptomycin (Sigma Chemical Co., St. Louis, MO) per ml and 8 µg of nalidixic acid (Sigma) per ml or 2 µg of ceftazidime (Glaxo Group Research, Greenford, United Kingdom) per ml. Plasmid DNA samples extracted from transconjugants were digested with the endonuclease EcoRI (Roche Applied Science). The resulting fragments were loaded onto a 0.8% agarose gel and then subjected to Southern hybridization with the digoxigenin-labeled qnr probes. The sizes of transferred plasmids were estimated by adding up restriction fragments.
Structure analysis of the qnrA-containing integron.
A qnrA-positive isolate was randomly selected for structure analysis of the qnrA-containing integron. PCR was performed with the primer pair Int1-6A and qnrA-1B and the primer pair Int1-6A and qacE-2B to amplify nucleotide sequences upstream and downstream, respectively, of qnrA (Table 1). Both strands of PCR products were sequenced by gene walking with custom sequencing primers. Nucleotide and amino acid sequences were analyzed and compared by use of the BLAST computer program (National Center for Biotechnology Information).
Nucleotide sequence accession number.
The nucleotide sequence of the qnrA-positive integron from isolate EB715/04 has been submitted to the GenBank database and assigned accession number DQ989302.

RESULTS
Prevalence of qnr genes.
The
qnrA,
qnrB, and
qnrS genes were detected in 3 (0.6%), 53
(10.1%), and 34 (6.5%) of the isolates, respectively, by PCR
and colony hybridization and were found to belong to the
qnrA1,
qnrB2, and
qnrS1 alleles by subsequent sequencing of all PCR
products. Since four isolates carried both
qnrS and
qnrB, the
prevalence of any
qnr gene was 86 (16.3%) of all isolates.
Association of qnr with MBL and ESBL production.
Among the 526 E. cloacae isolates, the phenotypic screening tests suggested MBL and ESBL production in 56 (10.6%) and 149 (28.3%) isolates, respectively. Presumptive ESBLs were detected in 46 (82.1%) of the 56 putative MBL producers. The prevalence of the three qnr genes among putative ESBL, MBL, non-ESBL, and non-MBL producers is shown in Table 2. Overall, 44 (78.6%) of the 56 putative MBL producers and 59 (39.6%) of the 149 putative ESBL producers carried any of the three qnr genes.
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TABLE 2. Distribution of qnrA, qnrB, and qnrS among ESBL-producing, MBL-producing, and non-ESBL- and non-MBL-producing E. cloacae isolates
|
The ß-lactamase contents of all putative MBL producers
and all
qnr-positive ESBL-producing isolates were determined
according to the results of IEF and PCR experiments (
2,
36).
The IMP-8-type MBL (pI 8.2) was detected in all 56 putative
MBL producers, and the SHV-12-type ESBL (pI 8.2) was detected
in all 59
qnr-positive ESBL producers. Moreover, the TEM-1-type
narrow-spectrum ß-lactamase (pI 5.4) was detected
in all MBL producers and 11 of the 25 non-MBL-producing ESBL
producers, and a pI 8.0 ß-lactamase that might represent
the chromosomal AmpC ß-lactamase of
E. cloacae was
detected in all test isolates. The
blaCTX-M genes were not detected
by PCR. Accordingly, one of the three
qnrA1-like-positive isolates
expressed SHV-12; 43 (81.1%) and 33 (62.3%) of the 53
qnrB2-like-positive
isolates and 18 (52.9%) and 14 (41.2%) of the 34
qnrS1-like-positive
isolates produced SHV-12 and IMP-8, respectively.
PFGE.
The 44 qnr-positive IMP-8-producing isolates gave six major patterns, designated patterns I to VI, and various subtypes were observed in patterns I to IV and VI (Fig. 1). Among the 14 qnrS-positive MBL producers, all 11 isolates that were negative for qnrB belonged to pattern II; the remaining 3 isolates that were positive for qnrB belonged to three different patterns. The 33 qnrB-positive isolates belonged to five major patterns, patterns I and III to VI, and 18 of them belonged to pattern IV.
Conjugation experiments and plasmid analysis.
The results of conjugation experiments and plasmid analysis
for the 56 IMP-8-producing isolates are shown in Fig.
2 and
Table
3. Five
qnrS-positive transconjugants were obtained and
revealed no ß-lactamase activity in the IEF analysis.
All
qnrS-positive plasmids showed the same restriction pattern
and were about 7 kb in size. Eight
qnrB-positive transconjugants
were obtained, and
blaTEM-1,
blaSHV-12, and
blaIMP-8 were found
to be cotransferred with
qnrB. blaIMP-8-positive plasmids that
were negative for any
qnr gene were also obtained from 4 of
12
qnr-negative and 11 of 14
qnrS-positive isolates; these conjugable
plasmids were all greater than 150 kb in size and gave 12 restriction
patterns, designated B1 to B12. With only one to three band
differences, the
qnrB-positive plasmids with patterns B3 to
B5 were very similar to the
qnrB-negative plasmids with patterns
B6 to B8. The
qnrB probe hybridized with a 2.4-kb restricted
fragment in all
qnrB-positive plasmids.
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TABLE 3. Restriction patterns of conjugative plasmids and transferred resistance genes in conjugation experiments
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Susceptibility testing.
Of the 86
qnr-positive isolates, 100% and 43.0% were nonsusceptible
(resistant or intermediately resistant) to nalidixic acid (MIC,
32 to >256 µg/ml; MIC
90, >256 µg/ml) and ciprofloxacin
(MIC, 0.13 to 32 µg/ml; MIC
90, 16 µg/ml), respectively,
and 86.0% were nonsusceptible to ceftazidime, 97.8% to cefotaxime,
33.7% to cefepime, 77.9% to aztreonam, 9.3% to imipenem, 75.6%
to gentamicin, and 3.5% to amikacin. Eight imipenem-nonsusceptible
isolates were all MBL producers. Among the 86
qnr-positive isolates,
the 69 isolates that were positive for IMP-8 and/or SHV-12 had
remarkably higher rates than the 17 isolates that were negative
for MBL and ESBL in nonsusceptibilities to ceftazidime (100%
versus 29.4%), cefepime (40.6% versus 5.9%), aztreonam (85.5%
versus 47.1%), and gentamicin (89.9% versus 17.6%).
The five qnrS-positive and eight qnrB-positive transconjugants revealed decreased susceptibilities to nalidixic acid (MIC, 16 to 32 µg/ml) and ciprofloxacin (MIC, 0.25 to 0.5 µg/ml). All qnrB-positive transconjugants revealed resistance or decreased susceptibilities to extended-spectrum cephalosporins, imipenem, and gentamicin; all qnrS-positive transconjugants showed no decreased susceptibilities to ampicillin, cephalothin, extended-spectrum cephalosporins, and aminoglycosides (data not shown).
Structure of the qnrA1-containing integron.
Primers Int1-6A and qnrA-1B generated an approximately 5.8-kb amplicon and primers qnrA-1A and qacE-2B generated an approximately 2-kb amplicon from a qnrA-positive strain, EB715/04. Nucleotide sequencing revealed that qnrA1 was located in a complex sul1-type integron that contains dhr15, aadA2, qacE
1, sul1, orf513, qnrA1, ampR, and qacE
1. The integron and In36 of an E. coli isolate from the People's Republic of China differed only by the first gene cassette, which is the dhr16 cassette in In36 (33).

DISCUSSION
The present study demonstrated the high prevalence (16.3%) of
plasmid-mediated quinolone resistance among
E. cloacae isolates
in a Taiwanese university hospital. The prevalence rates of
qnr among putative ESBL producers (39.6%) and MBL producers
(78.6%) were much higher than that among putative non-ESBL and
non-MBL producers (4.6%) (Table
2). The high prevalence of
qnr among
E. cloacae isolates, and extended-spectrum-cephalosporin-resistant
or ESBL-producing isolates in particular, has also been described
in several reports (
6,
22,
26). Three Qnr groups were all detected,
and QnrA and QnrB are described for the first time in Taiwan
in this report. Among all isolates,
qnrB was the most prevalent
(10.1%), followed by
qnrS (6.5%); however,
qnrS was the most
prevalent among the putative non-ESBL and non-MBL producers.
qnrA was uncommon (0.6%) in this study, and the low rates of
qnrA have been observed in most surveillance studies (
10,
12,
16,
20,
27). The
qnrA1 gene of our isolate is also located in
a complex
sul1-type integron, which is different from In
36 of
an
E. coli isolate from the People's Republic of China only
in the first gene cassette (
33).
Only one qnrA1-positive isolate from Australia has been reported to express an MBL (IMP-4), and this is the first report of the association of qnrB and qnrS with genes encoding MBLs. IMP-8 is an IMP-2 variant that is unique in Taiwan (36). The coexistence of the qnrB2-like gene and blaIMP-8 on the same plasmids and only five major PFGE patterns among the 33 qnrB-positive IMP-8-producing isolates suggest that the high prevalence of qnrB among MBL producers was due to the horizontal transfer of plasmids containing both qnrB and blaIMP-8 and the intrahospital spread of several clones. The high prevalence of qnrS among MBL producers may be due mainly to intrahospital spread or nosocomial outbreaks of an E. cloacae clone that carried qnrS and blaIMP-8 on different plasmids.
Previous studies showed that qnr-positive strains frequently expressed ESBLs, such as SHV-2 (4), SHV-7 (34), SHV-12 (11, 26), CTX-M-9 (22), CTX-M-14 (5), CTX-M-15 (11), and VEB-1 (16), and QnrA has also been linked to genes encoding plasmid-mediated cephalosporinases (20, 27, 34). All our qnr-positive ESBL-producing isolates carried blaSHV-12. The qnrB2-like gene was more prevalent than the qnrS1-like gene among the 149 putative ESBL producers (28.9% versus 12.1%) (Table 2). The prevalence rate of qnrS among the non-MBL-producing ESBL producers was very close to that among the non-MBL- and non-ESBL-producing isolates (4.9% versus 4.1%). Among the 18 qnrS-positive ESBL producers, 13 (72.2%) isolates were also MBL producers. Moreover, 46 of the 56 MBL producers carried blaSHV-12, and the coexistence of blaSHV-12 and blaIMP-8 on the transferred plasmids was observed as described previously (36). Thus, the finding that qnrS was common among the ESBL producers may result from the clonal spread of E. cloacae isolates that harbored plasmids with both blaSHV-12 and blaIMP-8.
Although the qnrS1 gene first reported in Taiwan was identified on a plasmid encoding the SHV-2-type ESBL (4), all transferable qnrS-positive plasmids in our isolates appeared to contain no ß-lactamase gene. The restriction patterns of the transferred qnrB-positive, blaIMP-8-positive plasmids were very similar to those of qnrB-negative, blaIMP-8-positive plasmids (Fig. 2), suggesting the occurrence of horizontal mobility of the qnrB2-like gene. The qnrB2 gene has been located in a complex sul1-type integron of a Salmonella enterica serovar Keurmassar strain (7). The association of qnrS and qnrB with integrons was not found in our isolates by PCR mapping (unpublished data). The genetic mechanisms responsible for the mobility of the two qnr genes in Taiwan need further studies.

ACKNOWLEDGMENTS
This work was supported by grant NSC89-2314-B-006-031 from the
National Science Council, Taiwan.

FOOTNOTES
* Corresponding author. Mailing address: Department of Pathology, National Cheng Kung University Hospital, 138 Sheng-Li Road, Tainan 70428, Taiwan, Republic of China. Phone: 886-6-2353535, ext. 2634. Fax: 886-6-2766195. E-mail:
jingjou{at}mail.ncku.edu.tw 
Published ahead of print on 22 January 2007. 

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Antimicrobial Agents and Chemotherapy, April 2007, p. 1223-1227, Vol. 51, No. 4
0066-4804/07/$08.00+0 doi:10.1128/AAC.01195-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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