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Antimicrobial Agents and Chemotherapy, September 2005, p. 3743-3748, Vol. 49, No. 9
0066-4804/05/$08.00+0     doi:10.1128/AAC.49.9.3743-3748.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

BEL-1, a Novel Clavulanic Acid-Inhibited Extended-Spectrum ß-Lactamase, and the Class 1 Integron In120 in Pseudomonas aeruginosa

Laurent Poirel,1 Laura Brinas,1,2 Annemie Verlinde,3 Louis Ide,3 and Patrice Nordmann1*

Service de Bactériologie-Virologie, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, Faculté de Médecine Paris-Sud, Université Paris XI, Le Kremlin-Bicêtre, France,1 Area de Bioquimica y Biologia Molecular, Universidad de La Rioja, 26006 Logrono, Spain,2 Department of Microbiology, Heilig Hartziekenhuis Roeselare, Wilgenstraat 2, 8800 Roeselare, Belgium3

Received 16 April 2005/ Returned for modification 31 May 2005/ Accepted 1 July 2005


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ABSTRACT
 
Screening by a double-disk synergy test identified a Pseudomonas aeruginosa isolate that produced a clavulanic acid-inhibited expanded-spectrum ß-lactamase (ESBL). Cloning and sequencing identified a novel ESBL, BEL-1, weakly related to other Ambler class A ESBLs. ß-Lactamase BEL-1 hydrolyzed significantly most expanded-spectrum cephalosporins and aztreonam, and its activity was inhibited by clavulanic acid, tazobactam, cefoxitin, moxalactam, and imipenem. This chromosome-encoded ESBL gene was embedded in a class 1 integron containing three other gene cassettes. In addition, this integron was bracketed by Tn1404 transposon sequences at its right end and by P. aeruginosa-specific sequences at its left end.


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INTRODUCTION
 
Clavulanic acid-inhibited Ambler class A extended-spectrum ß-lactamases (ESBLs) are rarely reported in Pseudomonas aeruginosa. To date, there have been five reports of TEM- and SHV-type ESBLs in P. aeruginosa (SHV-2a, SHV-5, TEM-4, TEM-24, and TEM-42), and three non-TEM-, non-SHV-type ESBLs have also been reported in that species (PER-1, VEB-like, and GES-like ß-lactamases) (35). The blaPER-1 ß-lactamase gene is most widespread in Turkey (33), VEB-1 is most widespread in Southeast Asia (9), and GES-like ß-lactamases have been identified in French, Greek, and South African isolates (8, 16, 26). Interestingly, GES-2, a point mutant derivative of GES-1 that was identified in South Africa, possessed an ability to hydrolyze not only expanded-spectrum cephalosporins but also imipenem (27).

The genetic vehicles that carry ESBL genes are variable. The blaTEM genes are part of Tn1, Tn2, and Tn3 transposon structures (19), blaSHV genes are part of IS26-related transposon structures, and blaPER-1 is part of a peculiar composite transposon, Tn1213, made of two different insertion sequence elements belonging to the IS4 family (21). The blaVEB and blaGES genes are in the form of gene cassettes integrated into class 1 integrons (22, 24). In addition, a peculiar genetic organization involving 135-bp repeated elements (Re) bracketing a blaVEB-1a gene cassette has been recently identified in a P. aeruginosa isolate from India (2).

This study characterized a novel ESBL whose gene was identified in a class 1 integron.


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MATERIALS AND METHODS
 
Bacterial strains. P. aeruginosa clinical isolate 51170 was identified with the API-20 NE system (bioMérieux, Marcy l'Etoile, France). Escherichia coli DH10B was the host for cloning experiments, and in vitro-obtained, rifampin-resistant P. aeruginosa PU21 was used as a recipient strain for transformation experiments (25).

Susceptibility testing. Antibiotic-containing disks were used for routine antibiograms by the disk diffusion assay (Sanofi-Diagnostic Pasteur, Marnes-la-Coquette, France) as previously described (20). The double-disk synergy test was performed with disks containing ceftazidime or cefepime and ticarcillin-clavulanic acid on Mueller-Hinton agar plates, and the results were interpreted as described previously (10). MICs were determined by an agar dilution technique with Mueller-Hinton agar (Sanofi-Diagnostic Pasteur) with an inoculum of 104 CFU per spot as described previously (10). All plates were incubated at 37°C for 18 h at ambient atmosphere. MICs of ß-lactams were determined alone or in combination with fixed concentrations of clavulanic acid (2 µg/ml), tazobactam (4 µg/ml), and sulbactam (4 µg/ml). MIC results were interpreted according to the guidelines of the National Committee for Clinical Laboratory Standards (17).

PCR and hybridization experiments. Total DNA of P. aeruginosa 51170 was extracted as described previously (20). This DNA was used as a template under standard PCR conditions (30) with a series of primers designed for detection of the following class A ß-lactamase genes and their extended-spectrum derivatives found in enterobacterial and P. aeruginosa isolates: blaTEM, blaSHV, blaPER-1/2, blaVEB, and blaGES (9, 22). Southern hybridizations were performed as described by Sambrook et al. (30) using the ECL nonradioactive labeling and detection kit (Amersham Pharmacia Biotech, Orsay, France).

Cloning experiments, recombinant plasmid analysis, and DNA sequencing. Total DNA of P. aeruginosa isolate 51170 was partially digested by the Sau3AI restriction enzyme, ligated into the BamHI site of plasmid pBK-CMV, and transformed into reference strain E. coli DH10B as previously described (20). Recombinant plasmids were selected on Trypticase soy agar plates containing amoxicillin (50 µg/ml) and kanamycin (30 µg/ml). The cloned DNA fragments of several recombinant plasmids, including pBEL-1, were sequenced on both strands with an Applied Biosystems sequencer (ABI 3100; Applied Biosystems, Foster City, Calif.). The entire sequence provided in this study was made of sequences of several plasmids that contained overlapping cloned fragments. The nucleotide and deduced amino acid sequences were analyzed and compared to sequences available over the Internet at the National Center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov).

Genetic support. Transformation experiments were performed with P. aeruginosa 51170 and in vitro-obtained, rifampin-resistant P. aeruginosa strain PU21 as previously described (25). Extraction of plasmid DNA from P. aeruginosa 51170 was attempted with the QIAGEN plasmid DNA maxi kit (QIAGEN, Courtaboeuf, France) and by the Kieser method (12). To search for a chromosomal location of the ß-lactamase gene, we used the endonuclease I-CeuI (Amersham Phamacia Biotech) (14), which digests a 26-bp sequence in rrn genes for the 23S large-subunit rRNA, and separated the fragments by pulsed-field gel electrophoresis as previously described (23). Hybridization was performed with two different probes, a 1,504-bp PCR-generated probe specific for 16S and 23S rRNA genes (9) and a 448-bp probe specific for the blaBEL-1 gene generated with internal primers BEL-A (5'-CGACAATGCCGCAGCTAACC-3') and BEL-B (5'-CAGAAGCAATTAATAACGCCC-3').

ß-Lactamase purification and isoelectric focusing (IEF) analysis. Cultures of E. coli DH10B(pBEL-1) were grown overnight at 37°C in 4 liters of Trypticase soy broth containing amoxicillin (100 µg/ml) and kanamycin (30 µg/ml). ß-Lactamase was purified by ion-exchange chromatography. Briefly, the ß-lactamase extract was sonicated, cleared by ultracentrifugation, treated with DNase, and dialyzed against 20 mM Bis-Tris buffer (pH 8). This extract was loaded onto a Q-Sepharose column, and the ß-lactamase-containing fractions were eluted with a linear 0 to 0.5 mM NaCl gradient. The fractions containing the highest ß-lactamase activity were dialyzed against 20 mM Bis-Tris buffer (pH 5.5) and subsequently reloaded onto the preequilibrated Q-Sepharose column. The ß-lactamase activity was recovered in the flowthrough, and then the extract was concentrated using an ultrafiltration filter tip (Sartorius, Göttingen, Germany). The purity of the enzyme was estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis (30).

IEF analysis was performed with an ampholine polyacrylamide gel (pH 3.5 to 9.5) as described previously (20), using a purified ß-lactamase extract from a culture of E. coli DH10B(pBEL-1). The focused ß-lactamases were detected by overlaying the gel with 1 mM nitrocefin (Oxoid, Dardilly, France) in 100 mM phosphate buffer (pH 7.0).

The putative location of the signal peptide cleavage site has been determined by using software available on the SignalP 3.0 server (http://www.cbs.dtu.dk/services/SignalP/).

Kinetic measurements. Purified ß-lactamase was used for kinetic measurements performed at 30°C with 100 mM sodium phosphate (pH 7.0) with an ULTROSPEC 2000 UV spectrophotometer (Amersham Pharmacia Biotech). Fifty percent inhibitory concentrations (IC50s) were determined for clavulanic acid, tazobactam, sulbactam, cefoxitin, moxalactam, and imipenem. Various concentrations of these inhibitors were preincubated with the purified enzyme for 3 min at 30°C to determine the concentrations that reduced the hydrolysis rate of 100 µM benzylpenicillin by 50%.

The specific activity of the purified ß-lactamase from E. coli DH10B(pBEL-1) was obtained as described previously (24). One unit of enzyme activity was defined as the activity which hydrolyzed 1 µmol of benzylpenicillin per min per mg of protein. The total protein content was measured with the DC protein assay kit (Bio-Rad, Ivry-sur-Seine, France).

Nucleotide sequence accession number. The nucleotide sequences reported in this work have been deposited in the GenBank nucleotide sequence database under accession no. DQ089809.


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RESULTS
 
Properties of P. aeruginosa isolate 51170. P. aeruginosa isolate 51170 was isolated in May 2004 at the Heilig Hartziekenhuis, Roeselare, Belgium, from a scrotal swab of a 72-year-old man hospitalized for a dissecting aneurism of the left arteria renalis. He did not have any history of recent travel or hospitalization elsewhere. P. aeruginosa 51170 was resistant to ticarcillin and ceftazidime; had reduced susceptibility to piperacillin, cefepime, cefpirome, and aztreonam; and was susceptible to imipenem according to disk diffusion susceptibility testing. Double-disk synergy testing was positive with clavulanate-ceftazidime and clavulanate-aztreonam combinations (data not shown). P. aeruginosa 51170 was also resistant to aminoglycosides, fluoroquinolones, rifampin, chloramphenicol, and tetracycline and remained susceptible to fosfomycin and colistin.

Cloning and sequencing of the ß-lactamase gene. Preliminary attempts to detect by PCR several Ambler class A ESBL-encoding genes failed (data not shown). Using total DNA of P. aeruginosa 51170 as a template in cloning experiments, several recombinant plasmids, including pBEL-1, were obtained. Sequence analysis of a ca. 10-kb cloned fragment of pBEL-1 revealed an 852-bp-long open reading frame encoding a 283-amino-acid preprotein. This protein was a ß-lactamase designated BEL-1 (for Belgium extended ß-lactamase) with the STFK, SDN, and KTG structural elements characteristic of the active site of Ambler class A ß-lactamases (Fig. 1) (1, 15). The G+C content of blaBEL-1 was 48.4%, a value which differs significantly from the G+C content of P. aeruginosa genes (60.1 to 69.5%). BEL-1 was distantly related to other class A ß-lactamases. Indeed, the highest percentages of amino acid identity were 50% with ESBL GES-1 and 40% with ESBLs CTX-M-2, CTX-M-3, and CTX-M-8. ß-Lactamase BEL-1 shared 36% identity with ESBL BES-1, 35% with SHV-1, 34% with TEM-1, and only 21 and 19% with ESBLs PER-1 and VEB-1, respectively. The position of the leader peptide cleavage site would be between amino acids 20 and 21 (Ala and Asp, respectively) (Fig. 1).



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  		FIG. 1. Comparison of the amino acid sequence of ß-lactamase BEL-1 to those of the most closely related ESBLs. Bolded amino acids are conserved residues. Numbering of ß-lactamases is according to the nomenclature of Ambler et al. (1). The omega loop region is shaded in gray (3). The putative position of the leader peptide cleavage site for BEL-1 is indicated by a vertical arrow.

ß-Lactam susceptibility. MICs of ß-lactams for P. aeruginosa 51170 and for E. coli DH10B(pBEL-1) indicated the expression of a clavulanic acid-inhibited ß-lactamase that hydrolyzed expanded-spectrum cephalosporins but did not confer significant reduced susceptibility to carbapenems (Table 1).


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  		TABLE 1. MICs of ß-lactams for P. aeruginosa clinical isolate 51170, E. coli DH10B harboring recombinant plasmid pBEL-1 expressing ß-lactamase BEL-1, and reference strain E. coli DH10B

Biochemical properties of BEL-1. IEF analysis showed that P. aeruginosa 51170 and E. coli DH10B(pBEL-1) had ß-lactamase activities with a pI value of 7.1, corresponding to that of BEL-1 (data not shown). ß-Lactamase activity with a pI value of 8.5 was also detected for P. aeruginosa 51170, corresponding to the chromosomal cephalosporinase of P. aeruginosa. The specific activity of the purified ß-lactamase BEL-1 was 43 U mg of protein–1. Its overall recovery was 80% with 70-fold purification. The purity of the enzyme was estimated to be more than 95% according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis (data not shown). Kinetic parameters of BEL-1 showed its broad-spectrum activity against most ß-lactams, including expanded-spectrum cephalosporins and aztreonam but excluding cephamycins and carbapenems (Table 2). Analysis of the relative hydrolysis rates of BEL-1 showed that ceftriaxone was five- to sixfold more hydrolyzed than benzylpenicillin, and cefotaxime was also a good substrate. Although ceftazidime was well hydrolyzed, its kinetic parameters could not be determined precisely. This was due to a very high Km value (>700 µM) reflecting a very low affinity of BEL-1 for ceftazidime, as is commonly observed with many ESBLs (4, 22, 24). IC50 determinations performed with benzylpenicillin as a substrate showed that BEL-1 activity was very well inhibited by clavulanic acid (0.1 µM) and exhibited lower susceptibility to sulbactam (2.2 µM) and tazobactam (3 µM). It was also, but to a lesser extent, inhibited by moxalactam (7 µM). In addition, BEL-1 activity was inhibited by imipenem (2 µM), as observed for VEB-1 and GES-1 (22), and by cefoxitin (9 µM), as observed for VEB-1 (24).


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  		TABLE 2. Kinetic parameters of purified ß-lactamase BEL-1a

Genetic environment of blaBEL-1. Sequence analysis of the inserts of several recombinant plasmids harboring the blaBEL-1 gene revealed that it was in the form of a gene cassette located in a class 1 integron structure named In120 (Fig. 2). The blaBEL-1 gene cassette has a perfect core site (GTTAGAC) and an inverse core site (GTCTAAC), and the length of its 59-be sequence is 63 bp, including nonperfect internal 2L (CCTAAGC) and 2R (GCTTGGC) sequences separated by 23 bp. This 59-be element did not show identity with any other known 59-be element.



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  		FIG. 2. Genetic environment of the blaBEL-1 gene. Open reading frames are indicated by horizontal arrows and 59-be elements by white circles. The inverted repeats of ISPa7 are indicated by triangles. The IRt end of In120 is indicated by a black vertical rectangle. This overall map is not to scale.

Four gene cassettes were identified in In120, with the blaBEL-1 gene cassette being at the second position (Fig. 2). Upstream of blaBEL-1, the aacA4 aminoglycoside resistance gene encoding a 6'-N-acetyltransferase was found. Downstream of blaBEL-1, a gene cassette encoding the putative small drug resistance protein SMR-2 was identified. This 105-amino-acid protein likely belongs to the SugE-type efflux protein subfamily known to confer resistance to toxic quaternary ammonium compounds (6). An identical gene cassette was identified recently in another integron together with the metallo-ß-lactamase blaVIM-1 gene (32) and with a blaGES-like positive isolate (34). Downstream of the smr2 gene cassette, the aadA5 gene cassette was identified that encodes an aminoglycoside-3'-adenylyltransferase conferring resistance to streptomycin and spectinomycin (36).

Analysis of the 5'-end sequence of the integron showed that the P1 promoter sequences were located in the structural integrase gene, but no secondary (P2) promoter was identified (7, 13). Thus, the gene cassettes located in that integron are under the control of weak promoter sequences.

Analysis of the right end of this integron showed that the 3' conserved segment made of the qacE{Delta}1, sul1, and orf5 genes was flanked by an incomplete set of tni genes as identified in In0, In2, In5, and In31 and considered defective derivatives of Tn402-like transposable elements (Fig. 2) (5). The tniA allele of the Tn402-tni module was flanked by the IRt end of the transposon (Fig. 2).

Genetic environment of In120. Analysis of the 5' end of In120 showed that an ISPa7 element was present 107 bp downstream of the int1 integrase gene, as observed in integrons carrying the blaIMP-13 or the blaVIM-1 metallo-ß-lactamase gene cassette identified in P. aeruginosa in Italy (29, 32) and in blaOXA-2-containing integron In78 from P. aeruginosa from India (2). As found in the latter integrons, the transposase gene of ISPa7 was transcribed in the same orientation as that of the integrase gene (Fig. 2). ISPa7 is 1,669 bp long, possesses 17-bp inverted repeats, and belongs to the ISNCY family (http://www-is.biotoul.fr/). A same target site duplication made of GGCC was observed at both ends of ISPa7 that could suggest that this element had been integrated separately. However, analysis of the sequences present at the right end of ISPa7 did not identify specific sequences of the 5' end of Tn402. Immediately upstream of the direct repeat generated by ISPa7 transposition, sequences very similar to that of P. aeruginosa strain UCBP-PA14 were identified (GenBank, unfinished genome sequence) (Fig. 2). Indeed, two open reading frames were identified, consisting of a 159-amino-acid putative protein-S-isoprenylcysteine methyltransferase (only one amino acid substitution) and a thioredoxin reductase (100% identity). Thus, it is likely that the sequences flanking the 5' end of In120 corresponded to sequences of the chromosome of P. aeruginosa isolate 51170.

Analysis of the 3' end of Tn402-borne integron In120 identified part of transposon Tn1404 (18). Detailed analysis showed that In120-containing Tn402 had been inserted inside the res resolution site of Tn1404 (Fig. 2). This transposon had been identified in tetracycline-resistant P. aeruginosa isolates recovered from Michigan apple orchards (31). In the latter case, integration of a class 1 integron at the same location in the res site had been also observed. The sequences specific for Tn1404, particularly the tnpA gene encoding the transposase and the tetracycline resistance determinant, were not identified by PCR in P. aeruginosa 51170 (data not shown).

Genetic support of the ESBL determinant. Since no conjugation experiments were possible due to the lack of resistance markers available, direct transformation of putative plasmid DNA from P. aeruginosa 51170 to P. aeruginosa PU21 was attempted but remained unsuccessful. In addition, analysis of the plasmid content of P. aeruginosa 51170 did not identify any plasmid (data not shown), indicating a probable chromosomal location of the blaBEL-1 gene. Using the I-CeuI technique, we showed that the DNA probe for rRNA hybridized with all the fragments from the two P. aeruginosa strains, but hybridization with a DNA probe internal to the blaBEL-1 gene gave a single signal for P. aeruginosa 51170 only (Fig. 3). This signal corresponded to a large fragment that cohybridized with the rRNA probe, therefore corresponding to a chromosomal fragment. The latter result was in agreement with the identification of P. aeruginosa-specific sequences in the immediate vicinity of integron In120.



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  		FIG. 3. (A) PFGE profiles of I-CeuI-digested whole-cell DNAs of reference strain P. aeruginosa PU21 (lane 1) and P. aeruginosa 51170 (lane 2). Lane M is for bacteriophage lambda concatemers used as molecular size markers (Bio-Rad). Southern hybridization performed with specific probes for the (B) 16S-23S rRNA gene of P. aeruginosa and for (C) the blaBEL-1 gene are shown. Horizontal arrow indicates position of hybridization with the blaBEL-1 probe.


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DISCUSSION
 
This report identified a novel ESBL that had weak amino acid identity with other ESBLs but had similar biochemical properties. ß-Lactamase BEL-1 is a novel example of a non-TEM-, non-SHV-type ESBL in P. aeruginosa.

The relatively low-level MICs of expanded-spectrum ß-lactams for the BEL-1-producing P. aeruginosa isolate may be explained in part by a lack of strong promoter sequences in the 5'-CS sequence of the blaBEL-1-positive integron. This result strengthens the idea that ESBLs may be difficult to detect in P. aeruginosa and may therefore be clinically underestimated (35).

Compared to GES-1, BEL-1 shared most of the amino acids known to be critical for class A ß-lactamases, such as Cys69, Glu104, Thr220, Cys238, and Ala240 (11). BEL-1 possesses a serine residue at position 237 that has been shown to be responsible for activity against expanded-spectrum cephalosporins. Indeed, in combination with some other residues, Ser237 is especially responsible for the hydrolysis of oxyimino ß-lactams (15). As observed for GES-1, BEL-1 only slightly increases the MIC of cefotaxime once expressed in E. coli. However, the MIC of aztreonam is significantly increased when BEL-1 is expressed, which is not observed with GES-1.

BEL-1 was well inhibited by clavulanic acid, whereas its IC50 for tazobactam was 20-fold higher, indicating that tazobactam was a poor inhibitor of BEL-1 activity. BEL-1 is the second example of an ESBL that exhibits selective resistance to tazobactam after that of BES-1 (4). This property could be related to the presence of an alanine residue at position 276 replacing the usual arginine residue at that position in class A ß-lactamases. The IC50 of imipenem for BEL-1 was similar to the values of other class A ß-lactamases like GES-1 and VEB-1, underlining that inhibition by imipenem is a property shared at least by several class A ß-lactamases, since it is not commonly evaluated. This property could be related to the presence of residues Cys69 and Cys238 forming a disulfide bridge and enhancing binding of imipenem, as observed for GES-1 and for carbapenem-hydrolyzing class A ß-lactamases SME-1, NMC-A, and KPC-1. In addition, it is interesting that moxalactam was also a good inhibitor of BEL-1 activity, due to a high affinity of the enzyme for this substrate, as observed for TEM-52 (28).

Analysis of the surrounding sequences of blaBEL-1 showed that this gene was part of a gene cassette structure. The features of this mobile element entity were identified, including the core and inverse core sites, as well as the presence of a 59-be element. Interestingly, analysis of this overall structure indicated that acquisition of the resistance genes may have occurred by successive steps. It is likely that the primary Tn1404 transposon structure had been truncated by the insertion of In120 since the right end of the integron was identified in the resolution site of Tn1404. Then, due to the fact that an ISPa7 element was present in the left end of In120 (as already observed for other integrons), the latter insertion sequence was at the origin of an integration process involving sequences located at its left end (Fig. 2). This In120-Tn1404 structure was likely plasmid borne to enter the bacteria, and it targeted the chromosome of the P. aeruginosa recipient strain. Thus, this overall mechanism of acquisition likely corresponds to cointegration of a plasmid into the chromosome.

The blaBEL, blaVEB, and blaGES ß-lactamase genes encode class A ESBLs which all have been identified in P. aeruginosa and were located in class 1 integrons. It remains to evaluate whether the blaBEL-1 gene, as observed for the blaVEB and blaGES genes, has been disseminated among other gram-negative isolates, especially members of the family Enterobacteriaceae. This report underlines the variety of ESBL genes in P. aeruginosa, most of them being integron encoded and all of them still from unknown reservoirs. We believe that in many cases the environment-borne P. aeruginosa species may capture antibiotic resistance genes from other environmental species before exchanging those genes with members of the family Enterobacteriaceae.


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ACKNOWLEDGMENTS
 
This work was funded by a grant from the Ministère de l'Education Nationale et de la Recherche (UPRES-EA3539), Université Paris XI, Paris, France, and by the European Community (6th PCRD, LSHM-CT-2003-503-335). L.P. is a researcher from the INSERM, Paris, France.

We thank C. Torres for constant interest in the work of L.B.


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FOOTNOTES
 
* Corresponding author. Mailing address: Service de Bactériologie-Virologie, Hôpital de Bicêtre, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre cedex, France. Phone: 33-1-45-21-36-32. Fax: 33-1-45-21-63-40. E-mail: nordmann.patrice{at}bct.ap-hop-paris.fr. Back


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Antimicrobial Agents and Chemotherapy, September 2005, p. 3743-3748, Vol. 49, No. 9
0066-4804/05/$08.00+0     doi:10.1128/AAC.49.9.3743-3748.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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