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Journal of Clinical Microbiology, December 2004, p. 5767-5773, Vol. 42, No. 12
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.12.5767-5773.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Emergence of Extended-Spectrum-ß-Lactamase (CTX-M-9)-Producing Multiresistant Strains of Salmonella enterica Serotype Virchow in Poultry and Humans in France
François-Xavier Weill,1*
Renaud Lailler,2
Karine Praud,3
Annaëlle Kérouanton,2
Laëtitia Fabre,1
Anne Brisabois,2
Patrick A. D. Grimont,1 and
Axel Cloeckaert3
Centre National de Référence des Salmonella, Unité de Biodiversité des Bactéries Pathogènes Emergentes, Institut Pasteur, INSERM U389, Paris,1
Unité Caractérisation et Epidémiologie Bactérienne, Agence Française de Sécurité Sanitaire des Aliments, Maisons-Alfort,2
Unité BioAgresseurs, Santé et Environnement, Institut National de la Recherche Agronomique, Nouzilly, France3
Received 19 May 2004/
Returned for modification 29 June 2004/
Accepted 5 July 2004

ABSTRACT
During 2002 to 2003, eight
Salmonella enterica serotype Virchow
poultry and poultry product isolates from various sources (chicken
farms, poultry slaughterhouse, or retail store) and one
S. enterica rough strain isolated from human feces were found to produce
extended-spectrum ß-lactamase CTX-M-9. Poultry and
poultry product isolates were recovered from different locations
in the southwest of France. The human rough isolate had sequences
of flagellin genes (
fliC and
fljB) typical of serotype Virchow
and ribotyping and pulsed-field gel electrophoresis (PFGE) patterns
closely similar to those of serotype Virchow strains. PFGE confirmed
the clonal relationship between the poultry isolates, while
the human isolate displayed a pattern with 94% homology. The
blaCTX-M-9 gene was located on a conjugative plasmid and was
shown to be linked to orf513. Plasmid profiling found a very
similar EcoRI restriction pattern in six transconjugants studied,
including transconjugants obtained from the human isolate. A
single hatchery, supplying chicks to the six farms, was identified.
Emergence of extended-spectrum ß-lactamase-producing
S. enterica strains in food animals is a major concern, as such
strains could disseminate on a large scale and lead to antibiotic
therapy difficulties.

INTRODUCTION
Salmonella enterica is a frequent pathogen of animals and humans.
Food-borne diseases caused by this species represent an important
public health problem worldwide. An increase in the ß-lactam
resistance in
Salmonella spp. has been observed during the 1990s
with the emergence of a multiresistant epidemic strain of
S. enterica serotype Typhimurium of phage type DT 104, with chromosomal
integration of the genes coding for resistance to ampicillin,
streptomycin (and spectinomycin), chloramphenicol, sulfonamides,
and tetracycline (
7,
10). The emergence of
Salmonella strains
that are resistant to extended-spectrum cephalosporins have
been reported throughout the world since 1991 (
1,
3,
4,
9,
15,
18,
19,
23,
27,
30). These strains, isolated mostly in hospitalized
patients, produced plasmid-mediated class A extended-spectrum
ß-lactamases belonging to the TEM, SHV, CTX-M, or
PER families. More recently, the emergence of strains of
S. enterica producing plasmidic class C cephamycinase CMY-2 has
been reported in the United States (
14). These strains, belonging
mostly to serotype Newport (known as Newport-MDRAmpC), have
been isolated in food animals, in retail ground meat, and in
humans.
We report here the characterization of nine CTX-M-9 extended-spectrum ß-lactamase-producing multiresistant Salmonella strains isolated in France from 2002 to 2003. The human isolate was recovered from stools of a 4-year-old girl with gastroenteritis in February 2002. The eight poultry and poultry product isolates were recovered in 2003 from various sources (chicken farms, poultry slaughterhouse, or retail store) located in the southwest of France. Molecular characterization of these isolates was done by pulsed-field gel electrophoresis (PFGE) and plasmid fingerprinting. The ß-lactamases were characterized by isoelectric focusing and molecular methods.

MATERIALS AND METHODS
Bacterial strains.
The human
S. enterica isolate ROU was received for serotyping
at the French National Reference Center for
Salmonella in February
2002. The eight poultry and poultry product isolates were received
at the Agence Française de Sécurité Sanitaire
des Aliments (French Agency for Food Safety) laboratory between
April and June 2003. Table
2 shows details of the nine isolates
studied.
Escherichia coli J5 (
rif) was used for conjugation
experiments.
E. coli ATCC 25922 was used as a susceptible control
in disk diffusion method and in MIC determinations. Four non-ß-lactamase-producing
strains of
S. enterica serotype Virchow from the Agence Française
de Sécurité Sanitaire des Aliments collection
isolated in poultry in 2003 and
S. enterica serotype Braenderup
H9812 were used as controls and molecular size markers, respectively,
in the PFGE experiment. The reference strains used for automated
ribotyping, 41K of serotype Virchow (6,7:r:1,2), 16K of serotype
Heidelberg (1,4,5,12:r:1,2), 7404/90 of serotype Bsilla (6,8:r:1,2),
1741/76 of serotype Lode (17:r:1,2), 3363/81 of serotype Grandhaven
(30:r:1,2), and 1136/72 of serotype Crossness (67:r:1,2), were
from the World Health Organization Collaborative Centre for
Reference and Research on
Salmonella, Institut Pasteur, Paris,
France.
Serotyping.
Isolates were serotyped on the basis of somatic O and phase
1 and phase 2 flagellar antigens by agglutination tests with
antisera (Bio-Rad, Marnes la Coquette, France, and World Health
Organization Collaborative Centre for Reference and Research
on
Salmonella) as specified by the White-Kauffman-Le Minor scheme
(
21).
Automated ribotyping.
Automated ribotyping was performed with the RiboPrinter microbial characterization system (Qualicon, Wilmington, Del.) according to the manufacturer's instructions. Digestion by restriction endonuclease PstI, gel separation, transfer, and hybridization with a chemiluminescent-labeled DNA probe containing the E. coli rRNA operon were carried out in 8 h.
Pulsed-field gel electrophoresis.
PFGE with XbaI (Amersham Biosciences, Freiburg, Germany) was carried out with a CHEF-DRIII system (Bio-Rad) as described previously (20). The running conditions were 6 V/cm at 14°C for 20 h with pulse times ramped from 2.2 to 63.8 s. BioNumerics software (Applied Maths, Kortrijk, Belgium) was used to compare the PFGE profiles. The bands generated were analyzed by the Dice coefficient and the unweighted pair group method with arithmetic averages.
Antimicrobial susceptibility testing.
Antibiotic susceptibility was determined by the disk diffusion method on Mueller-Hinton (MH) agar according to the guidelines of the Antibiogram Committee of the French Society for Microbiology (28). The following antimicrobials (Bio-Rad) were tested: amoxicillin, amoxicillin-clavulanic acid, ticarcillin, ticarcillin-clavulanic acid, piperacillin, piperacillin-tazobactam, cephalothin, cefamandole, cefoperazone, cefoxitin, ceftriaxone, ceftazidime, cefepime, aztreonam, moxalactam, imipenem, streptomycin, spectinomycin, kanamycin, tobramycin, netilmicin, gentamicin, amikacin, isepamicin, nalidixic acid, pefloxacin, ciprofloxacin, sulfonamides, trimethoprim, chloramphenicol, and tetracycline.
The MICs of the ß-lactams and ciprofloxacin were determined by Etest (AB Biodisk, Solna, Sweden). The extended-spectrum ß-lactamase phenotype was detected with the extended-spectrum ß-lactamase detection Etest strips and the double disk diffusion test (16).
Preparation of crude extracts of ß-lactamase and isoelectric focusing.
Crude extracts of ß-lactamases were obtained by sonication followed by 45 min of ultracentrifugation at 100,000 x g with a Beckman L8-55 M ultracentrifuge. Isoelectric focusing was performed with a PhastSystem apparatus (Amersham-Pharmacia Biotech, Freiburg, Germany) as described previously (31).
PCR amplification and DNA sequencing.
Total DNA was extracted with the InstaGene matrix kit (Bio-Rad) in accordance with the manufacturer's recommendations. The sequences of the primers used in the PCR amplifications are given in Table 1. PCR amplifications of fliC and fljB genes coding the two flagellar phases were performed with the FLIC-F and FLIC-R or FLJB-F and FLJB-R primers (13).
CTX-M-specific PCR analysis was performed with in-house primers
designed on the basis of consensus sequences of various CTX-M
genes; primer forward CTX-M-F (located from positions 209 to
227 with respect to the CTX-M translational starting point),
and primer reverse CTX-M-R (located from positions 750 to 732).
A CTX-M-9 group-specific PCR assay was carried out with primers
CTX-M-9-F and CTX-M-9-R amplifying an 856-bp fragment of
blaCTX-M-9 like (
27). Primers TEM-F and TEM-R were used to amplify a 1,080-bp
fragment of the
blaTEM gene. All amplifications except the quinolone
resistance-determining region of
gyrA and upstream region of
blaCTX-M-9 were performed on 50-µl samples containing
DNA (2.5 µl), primers (50 pmol each), deoxynucleoside
triphosphate (200 µM),
Taq DNA polymerase (1.25 U; Ampli
Taq Gold; Roche) and its buffer, MgCl
2 (2 mM), and dimethyl
sulfoxide (10%). The cycling conditions included 10 min of denaturation
at 94°C (one cycle); 30 s (1 min for
fliC and
fljB) of denaturation
at 94°C, 30 s (1 min for
fliC and
fljB) of annealing at
50°C (53°C for
blaCTX-M consensus,
fliC, and
fljB and
54°C for
blaCTX-M-9) and 1 min (1 min 30 s for
fliC and
fljB) of polymerization at 72°C (35 cycles), followed by
10 min of extension at 72°C.
Amplification of class I integrons with primers 5'-CS (17) and 3'-CS was performed as described previously (31). PCR amplification of the quinolone resistance-determining region of gyrA was carried out with primers STGYRA1 and STGYRA12 as described previously (2). PCR amplification of the upstream region of blaCTX-M-9 was performed with primers ORF513-F and MA-2-R. Amplification was performed on 25-µl samples containing DNA (2.5 µl), primers (20 pmol each), deoxynucleoside triphosphate (200 µM), and Taq DNA polymerase (2.5 U; Taq DNA polymerase, Promega, Charbonnières, France) and its buffer. The cycling conditions included 5 min of denaturation at 94°C (one cycle); 1 min of denaturation at 94°C, 1 min of annealing at 58°C, and 4 min of polymerization at 72°C (35 cycles), followed by 7 min of extension at 72°C.
The purified PCR fragments were sequenced on both strands by Genome Express (Meylan, France) with an ABI 100 DNA sequencer (Applied Biosystems, Foster City, Calif.).
The nucleotide sequence was analyzed with the Lasergene software (Dnastar, Madison, Wis.). The BLASTN program of NCBI (http://www.ncbi.nlm.nih.gov) was used for database searches.
Resistance transfer determination.
A resistance transfer experiment was carried out on liquid media with four selected isolates as described previously (12). E. coli J5 resistant to rifampin was used as the recipient strain. Transconjugants were selected on Drigalski agar supplemented with cefotaxime (2 mg/liter) and rifampin (250 mg/liter).
Plasmid analysis.
Plasmid DNA was purified from E. coli transconjugants by an alkaline lysis procedure (29) and subjected to 0.8% agarose gel electrophoresis. The molecular sizes of plasmids were determined with Taxotron software (Institut Pasteur, Paris, France) by reference to plasmids of known sizes (RP4, 54 kb, and pIP173, 126 kb) mixed with a supercoiled DNA ladder (Invitrogen, Groningen, The Netherlands). DNA restriction fragment length polymorphisms were analyzed by agarose gel electrophoresis of plasmid DNA cleaved with EcoRI and PstI (Roche, Mannheim, Germany).

RESULTS
Serotyping of Salmonella isolates.
The eight poultry and poultry product isolates belonged to serotype
Virchow (6,7:r:1,2), while the human isolate ROU could not be
serotyped due to autoagglutination (rough strain). PCR amplification
of the
fliC and
fljB genes encoding the two flagellar phases
from isolate ROU and subsequent sequencing identified sequences
99% identical to the H-1(r) gene (EMBL accession no.
X04505)
and the H-2(1, 2) gene (GenBank accession no.
U17177), respectively,
indicating that isolate ROU possesses at least the same flagellar
phases as the Virchow isolates.
Automated ribotyping.
To determine if human isolate ROU, untypeable by conventional serotyping (rough), could derive from serotype Virchow, automated ribotyping was performed on isolate ROU, on poultry isolate 2731, on the reference strain of serotype Virchow, and on reference strains of serotypes Heidelberg, Bsilla, Lode, Grandhaven, and Crossness, which possess the same flagellar antigens (r:1,2) but different O antigens. Isolates ROU and 2731 displayed the same pattern, which differed from that of the Virchow reference strain by a single band (Fig. 1). The patterns obtained with the other reference strains were quite different (Fig. 1 and data not shown).
PFGE.
The clonal relatedness of the nine CTX-M-9-producing
S. enterica isolates and four non-ß-lactamase-producing
S. enterica serotype Virchow isolates was assessed by PFGE with XbaI (Fig.
2). Eight distinct profiles were observed among the 12 strains
and five among the nine CTX-M-9-producing isolates (Table
2 and Fig.
2). Two separate clusters (similarity < 82%) were
found after cluster analysis of these fingerprints (Fig.
2).
All the CTX-M-9-producing isolates and non-ß-lactamase-producing
isolate 4298 belonged to the main cluster, with a genetic similarity
of about 91%.
Antimicrobial susceptibility.
All nine isolates were resistant to amoxicillin, ticarcillin,
piperacillin, cephalothin, cefamandole, and ceftriaxone and
remained apparently in vitro susceptible to piperacillin-tazobactam,
cefoxitin, ceftazidime, and imipenem by the disk diffusion method.
The isolates were also resistant to aminoglycosides (streptomycin,
spectinomycin, and, for most isolates, kanamycin), sulfamethoxazole-trimethoprim,
nalidixic acid, and tetracycline (Table
2). An extended-spectrum
ß-lactamase-producing phenotype was detected with
the double disk diffusion test and Etest strips (data not shown).
The MICs of the ß-lactams determined by Etest in five
selected isolates are shown in Table
3. The selected isolates
showed decreased susceptibilities to ceftriaxone (MICs of 8
to 16 mg/liter) and slightly decreased susceptibilities to ceftazidime
(MICs of 1 to 2 mg/liter). The five isolates showed decreased
susceptibilities to ciprofloxacin (MIC of 0.25 mg/liter) (Table
3).
Isoelectric focusing.
Seven isolates produced two ß-lactamases with isoelectric
points of 5.4 and 7.9, while isolate 3464 b produced only pI
7.9 ß-lactamase (Table
2).
Characterization of ß-lactamase genes, quinolone resistance-determining region of gyrA, and class I integrons.
CTX-M consensus PCR performed on all the isolates gave the expected PCR product of 540 bp. Sequence analysis of the PCR product from isolate ROU revealed 100% homology with the blaCTX-M-9a sequence (GenBank accession number AF252621). To confirm the presence of blaCTX-M-9 in all the isolates, a CTX-M-9 group-specific PCR assay was carried out, and all the isolates gave the expected PCR product of 856 bp (Table 2). Sequencing of PCR products and deduced amino acid sequence analysis from isolates ROU, 2731, 3464b, and 4300 confirmed that the ß-lactamase was CTX-M-9 (Table 2). It was consistent with the identification of a pI 7.9 ß-lactamase by isoelectric focusing. A TEM-specific PCR assay gave the expected 1,080-bp fragment in all but one isolate, 3464b (Table 2). DNA sequencing of the PCR product from isolate ROU confirmed that the ß-lactamase was TEM-1 (Table 2). It was consistent with the production of a pI 5.4 ß-lactamase.
The PCR amplifications of the quinolone resistance-determining region of gyrA in two isolates tested (ROU and 2437) revealed identical single mutations leading to the amino acid substitution Ser83Phe, reported to be involved in quinolone resistance.
PCR amplification of class I integrons was performed in all the isolates. They all gave a PCR product of 1.5 kb (data not shown). The DNA sequences of 1.5 kb of the PCR products from isolates ROU and 2731 were 100% identical to the corresponding sequence of In36 (GenBank accession no. AY259085) and 99% identical to the corresponding sequence of In60 (25). Two different gene cassettes were detected. The first one contained the dfrA16 gene cassette, encoding resistance to trimethoprim. The second gene cassette contained an aadA2 gene, encoding resistance to streptomycin and spectinomycin. Analysis of the upstream region of blaCTX-M-9 by PCR with primers ORF513-F and MA-2-R showed that the nine isolates had the expected 2,700-bp regions between orf513 and blaCTX-M-9, as described for In60, a complex integron carrying blaCTX-M-9, identified in E. coli and S. enterica serotype Virchow in Spain (data not shown).
Resistance transfer determination and plasmid analysis.
A resistance transfer experiment was carried out on liquid media with E. coli J5 (rif) as the recipient strain. E. coli transconjugants pROU-1, p2437-1, p2731-1, p3279-1, p3464b-1, and p4300-1 were obtained for all the isolates tested, ROU, 2437, 2731, 3279, 3464b, and 4300, respectively. They expressed ß-lactamases with pIs of 5.4 and 7.9, except p4300-1, which expressed only a pI 7.9 ß-lactamase. The MICs of ceftazidime and ceftriaxone were lower for the transconjugants than for the parental strains (MICs of ceftazidime were 0.125 versus 1 to 2 mg/liter and the MICs of ceftriaxone were 2 versus 8 to 16 mg/liter) (Table 3). Other resistance determinants, including streptomycin, spectinomycin, kanamycin (except p4300-1), tetracycline, and sulfamethoxazole-trimethoprim, were cotransferred to transconjugants with cefotaxime resistance. Extraction of plasmids isolated from all the transconjugants revealed single plasmids larger than 126 kb (data not shown). Plasmid DNAs extracted from all the transconjugants were compared by restriction endonuclease analysis (EcoRI and PstI). All the plasmids had a very similar fingerprint (Fig. 3 and data not shown).

DISCUSSION
CTX-Ms are extended-spectrum ß-lactamases that are
generally more active against cefotaxime (and ceftriaxone) than
ceftazidime but are inhibited by clavulanic acid. CTX-Ms form
a growing family that comprises at least 40 enzymes belonging
to six groups (
4). The CTX-M-9 group includes nine plasmid-mediated
enzymes (CTX-M-9, CTX-M-13, CTX-M-14, CTX-M-16, CTX-M-17, CTX-M-19,
CTX-M-21, CTX-M-27, and Toho-2). CTX-M-9 was first reported
in a human isolate of
E. coli in Spain in 1996 (
24). Since then,
this extended-spectrum ß-lactamase has been sporadically
identified in Spain (
22,
24), France (
26), Turkey (U. G. Bahar,
T. Demiray, E. Kandirali, N. Apaydin, and A. Mert, Abstr. 13th
Eur. Congress Clin. Microbiol. Infect. Dis., abstr. P580, 2003),
Brazil (
5), and China (
11), mostly from
E. coli isolated in
hospitalized patients. In the genus
Salmonella, CTX-M-9 has
only been reported in Spain within serotype Virchow (
27). Simarro
et al. (
27) described four cases of gastroenteritis caused by
CTX-M-9-producing isolates of
S. enterica serotype Virchow from
1997 to 1998. The source of these infections was not investigated.
In our study, we report a dual emergence in France of CTX-M-9-producing multiresistant strains of S. enterica serotype Virchow in poultry (and in a poultry-derived retail meat) and of an S. enterica rough strain in a human. This rough strain could derive from serotype Virchow because it possessed the same flagellar genes and close ribotyping and PFGE patterns. The reports of extended-spectrum ß-lactamases in the genus Salmonella mostly described nosocomial outbreaks. Exchange of mobile genetic elements carrying extended-spectrum ß-lactamase genes, such as plasmids and transposons, between enteric bacteria frequently encountered in hospitals and selected by traces of extended-spectrum cephalosporins used in humans has been suggested to explain the hospital outbreaks.
Another source of contamination with extended-spectrum ß-lactamase-producing strains of S. enterica could be through the food chain, as seen with ceftriaxone-resistant Newport-MDRAmpC strains (14). Very few studies evoked this way of infection with extended-spectrum ß-lactamase-producing Salmonella strains. Cardinale et al. (9) described the dual emergence of SHV-12-producing S. enterica serotype Keurmassar in humans and in a poultry product in Senegal. Extensive use of antimicrobial agents as feed additives for farm animals (especially in the poultry industry) has been suggested as an essential factor for the emergence of multiresistant Salmonella strains (9). In a second report, the authors also suspected transmission through the food chain for TEM-52-producing strains of S. enterica of various serotypes isolated in France during the period 2002 to 2003 (32). This is a major concern because food animals represent a large reservoir for dissemination of such resistant strains to humans, leading to important therapeutical difficulties, especially in children, for whom extended-spectrum cephalosporins are the treatment of choice.
CTX-M-14, which belongs to the CTX-M-9 group, but also SHV-12 and CMY-2 have been separately identified in three fecal isolates of healthy chickens in Spain in 2000 to 2001 among 120 recovered at the slaughterhouse level (8). The authors could not explain the emergence of such strains, as the use of extended-spectrum cephalosporins is very unusual in chickens. In 2001, dissemination of cephalosporin-resistant E. coli (carrying blaCTX-M-9 or blaCMY-2) among summer camp attendees in Spain was attributed to food or water (22). During a survey in Spain in 2001, CTX-M-14 has been identified in E. coli from 17 patients, of whom five (among 14 documented) never had contact with the hospital environment before isolation of the strain (6).
In our study, CTX-M-9 was found in only eight isolates among 247 isolates of S. enterica serotype Virchow of nonhuman origin collected by the Agence Française de Sécurité Sanitaire des Aliments network in 2003. CTX-M-9-producing human isolates are also extremely rare, as only one isolate has been identified among 1,200 Salmonella sp human isolates tested in 2002 and among 140 S. enterica serotype Virchow human isolates tested from 1997 to 2002. A single hatchery, located in the southwest of France, supplying chicks to the six farms (Table 1) was identified in our study. It is now important to conduct a more detailed investigation to determine the step of the supply chain where the contamination occurred (hatchery or breeding company). It is also important to know the nature of the antimicrobial agents used. Extended-spectrum cephalosporins are not adequate for use as growth promoters in chicken farms but could be used for therapeutical purposes in reproductive chickens.
We can speculate that the selective pressure may lead to the emergence of plasmid-mediated extended-spectrum ß-lactamases harbored by enteric bacteria which could subsequently be transferred to Salmonella spp. The finding that tetracycline, streptomycin, or sulfamethoxazole-trimethoprim resistance genes reside on the same plasmid as blaCTX-M-9 raises the possibility that the use of these common antibiotics could coselect this extended-spectrum ß-lactamase phenotype.
In conclusion, our investigation documented that Salmonella spp. producing the CTX-M-9 extended-spectrum ß-lactamase have been identified in poultry and poultry product in France. Active surveillance of antimicrobial use in animal husbandry is important to reduce selective pressure and subsequent dissemination of multiresistant Salmonella spp. to humans.

ACKNOWLEDGMENTS
We thank all the corresponding laboratories of the French National
Reference Center
Salmonella network and the French Food Safety
Agency
Salmonella Network, I. Castellanos (Laboratoire Vétérinaire
Départemental de la Dordogne, France), I. Thiese (Laboratoire
Vétérinaire Départemental du Tarn-et-Garonne,
France), and M. Kretz (Service de Pédiatrie, Hôpitaux
Civils de Colmar, France) for their collaboration.

FOOTNOTES
* Corresponding author. Mailing address: Centre National de Référence des
Salmonella, Unité de Biodiversité des Bactéries Pathogènes Emergentes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France. Phone: 33-(0)1 45 68 83 45. Fax: 33-(0)1 5 68 88 37. E-mail:
fxweill{at}pasteur.fr.


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Journal of Clinical Microbiology, December 2004, p. 5767-5773, Vol. 42, No. 12
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.12.5767-5773.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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