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Antimicrobial Agents and Chemotherapy, July 1998, p. 1794-1798, Vol. 42, No. 7
National Reference Center for Staphylococci,
Unité des Staphylocoques, Institut Pasteur, 75724 Paris Cedex
15, France
Received 19 November 1997/Returned for modification 20 February
1998/Accepted 14 April 1998
We isolated and sequenced a plasmid, named pIP1714 (4,978 bp),
which specifies resistance to streptogramins A and B and the mixture of
these compounds. pIP1714 was isolated from a Staphylococcus cohnii subsp. cohnii strain found in the environment
of a hospital where pristinamycin was extensively used. Resistance to
both compounds and related antibiotics is encoded by two novel,
probably cotranscribed genes, (i) vatC, encoding a
212-amino-acid (aa) acetyltransferase that inactivates streptogramin A
and that exhibits 58.2 to 69.8% aa identity with the Vat, VatB, and
SatA proteins, and (ii) vgbB, encoding a 295-aa lactonase
that inactivates streptogramin B and that shows 67% aa identity with
the Vgb lactonase. pIP1714 includes a 2,985-bp fragment also found in
two rolling-circle replication and mobilizable plasmids, pUB110 and
pBC16, from gram-positive bacteria. In all three plasmids, the common
fragment was delimited by two direct repeats of four nucleotides (GGGC)
and included (i) putative genes closely related to repB,
which encodes a replication protein, and to
pre(mob), which encodes a protein required for conjugative mobilization and site-specific recombination, and (ii)
sequences very similar to the double- and single-strand origins (dso, ssoU) and the recombination
site, RSA. The antibiotic resistance genes repB
and pre(mob) carried by each of these plasmids
were found in the same transcriptional orientation.
Streptogramins and related
antibiotics are produced by streptomycetes and are classified as A and
B compounds according to their basic primary structure (9).
Compounds of the A group, including streptogramin A (SgA),
pristinamycin IIA (PIIA), virginiamycin M, mikamycin A, and synergistin
A, are polyunsaturated cyclic macrolactones. Compounds of the B group,
including streptogramin B (SgB), pristinamycin IB (PIB), virginiamycin
S, mikamycin B, and synergistin B, are cyclic peptide macrolactones. A
and B compounds are bacteriostatic when used separately, but they can
act in synergy to become bactericidal, mainly against gram-positive
bacteria. Natural mixtures such as pristinamycin (Pt), synergistin,
virginiamycin, and mikamycin are used orally and topically. A
semisynthetic injectable streptogramin (Synercid), consisting of a
mixture of derivatives of A and B compounds (dalfopristin and
quinupristin, respectively), is currently undergoing in vivo clinical
trials and evaluation by the U.S. Food and Drug Administration (see the
entire volumes of the Journal of Antimicrobial Chemotherapy
[volume 30, Suppl. A, 1992, and volume 39 Suppl. A, 1997). In this
study, pristinamycins (PIIA, PIB, and Pt) were used to evaluate the
levels of resistance to A and B compounds and to the synergistic
mixtures of these compounds. The MICs of dalfopristin and quinupristin,
which are the derivatives of Pts, are similar to those of PIIA and PIB, respectively.
Staphylococcal resistance to synergistic mixtures of A and B
compounds (Pt MICs, We have reported on PCR experiments with degenerate primers
corresponding to the conserved motifs III and IV in the
acetyltransferases encoded by vat, vatB, and
satA: a 147-bp DNA fragment was amplified from S. cohnii subsp. cohnii BM10711 (23).
This fragment was used as a probe and hybridized with a plasmid of 5 kb, pIP1714, harbored by BM10711, suggesting that the plasmid carries a
vat-related gene which we named vatC. We report
herein the isolation and sequence of pIP1714. It carries a
vgb-related gene, vgbB, in addition to vatC and a 2,985-bp fragment homologous to part of the
rolling-circle and mobilizable staphylococcal plasmids pUB110
(24) and pBC16 (29), which has also been called
pNS1981 (33).
Bacterial strains and plasmids.
S. cohnii subsp.
cohnii BM10711 was isolated from a cupboard in Douera
Hospital in Algiers, Algeria (23). It is resistant to
macrolides, lincosamides, streptogramins A and B and their mixture,
0066-4804/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Characterization of a Staphylococcal Plasmid
Related to pUB110 and Carrying Two Novel Genes, vatC and
vgbB, Encoding Resistance to Streptogramins A and B and
Similar Antibiotics
and
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ABSTRACT
Top
Abstract
Introduction
Materials & Methods
Results & Discussion
References
![]()
INTRODUCTION
Top
Abstract
Introduction
Materials & Methods
Results & Discussion
References
2 µg/ml) is always associated with
resistance to A compounds (PIIA MICs,
8 µg/ml) but not necessarily
with resistance to B compounds (1). To date, five genes
encoding resistance to A compounds have been isolated from
staphylococcal and enterococcal plasmids. The genes vat
(6), vatB (2), and satA
(30) encode related acetyltransferases (47.7 to 60.8% amino
acid [aa] identity) which inactivate A compounds. The staphylococcal genes vga (4) and vgaB (3)
encode related ATP-binding proteins (48.3% aa identity) probably
involved in the active efflux of A compounds. The distribution of these
genes and the gene vgb (5), encoding a lactonase
which inactivates B compounds, has been investigated with a collection
of 53 staphylococcal isolates resistant to A compounds (PIIA MICs,
8
µg/ml) (1, 3, 23). Forty-eight staphylococcal isolates
carried vga or a combination of two or three genes:
vgaB-vatB, vga-vat, or vga-vat-vgb.
None of these genes was detected in four Staphylococcus
aureus isolates or in the single Staphylococcus cohnii
subsp. cohnii strain tested (strain BM10711)
(23).
![]()
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials & Methods
Results & Discussion
References
-lactams due to penicillinase production and the presence of the
mecA gene, tetracycline, trimethoprim, sulfonamide, cadmium salts, sodium arsenate, ammonium bromide, and ethidium bromide. The 53 staphylococcal isolates resistant to A compounds screened for the
presence of vatC and vgbB genes include BM10711
(23) and the 52 isolates described previously (1)
(S. aureus, 32 isolates; Staphylococcus
epidermidis, 14 isolates; Staphylococcus haemolyticus,
4 isolates; Staphylococcus simulans, 1 isolate; S. cohnii subsp. urealyticum, 1 isolate). S. aureus RN4220 (22) and Escherichia coli TG1
(16) were used as recipients.
Media. Brain heart infusion broth and agar (Difco Laboratories, Detroit, Mich.) were used for staphylococcal growth. Susceptibility to antimicrobial agents was tested on Mueller-Hinton agar (Sanofi Diagnostics Pasteur, Marnes-la-Coquette, France). Trypticase soy broth or Trypticase soy agar (Difco Laboratories) was used for the detection of PIIA and PIB inactivation. E. coli was grown on Luria-Bertani broth as described previously (2).
Susceptibility to antimicrobial agents. Susceptibility to antimicrobial agents was determined by a disk diffusion assay with commercially available antibiotic disks (Diagnostics Pasteur, Marne-la-Coquette, France) and disks containing 20 µg of PIIA, 40 µg of PIB, 0.2 µmol of cadmium acetate, 0.2 µmol of sodium arsenate, 0.2 µmol of mercuric nitrate, 200 µg of ethidium bromide, 200 µg of acriflavin, 200 µg of propamidine isethionate, or 10 µg of cetyltrimethylammonium bromide.
The MICs of PIIA, PIB, and Pt were determined with serial twofold dilutions of the antibiotics in Mueller-Hinton agar (15).Detection of PIIA or PIB inactivation. Inactivation of PIIA or PIB was investigated by the test described by Gots (17), with Micrococcus luteus ATCC 9341 grown on Trypticase soy agar supplemented with 0.2 µg of PIIA per ml or 2 µg of PIB per ml used as the indicator organism.
DNA isolation and analysis. Total cellular DNA and plasmid DNA were isolated from staphylococcal strains and purified as described previously (12, 32). Plasmid DNA was extracted and purified from E. coli with the QIA-prep Spin plasmid kit from Qiagen (Hilden, Germany).
Restriction endonucleases were obtained from Amersham International (Little Chalfont, United Kingdom) or from Pharmacia (Uppsala, Sweden) and were used according to the manufacturers' instructions. Native or digested DNA was analyzed by 0.7% (wt/vol) agarose gel electrophoresis, and the DNA fragments amplified by PCR were separated by electrophoresis in 4% (wt/vol) Nusieve agarose gels (FMC Products, Rockland, Maine) as described previously (2).PCR. DNA was amplified by PCR as described previously (2). The samples were subjected to a precycle of 3 min at 95°C and 2 min at 60°C and then 30 cycles of 20 s at 72°C, 20 s at 95°C, and 20 s at 60°C, followed by a final cycle of 1 min at 72°C.
The oligonucleotides used as primers were as follows: oligonucleotide O, 5'-ATGAATTCGCAAAATCAGCAAGG-3' (the underlined sequence is the EcoRI site); oligonucleotide P, 5'-TCGTCTCGAGCTCTAGGTCC-3' (the underlined sequence is the SacI site); oligonucleotide Q, 5'-CAGCAGTCTAGATCAGAGTGG-3' (the underlined sequence is the XbaI site); and oligonucleotide R, 5'-CATACGGATCCATCTTTTCC-3' (the underlined sequence is the BamHI site). The EcoRI and SacI sites in oligonucleotides O and P, respectively, were introduced to facilitate manipulation of the DNA fragment amplified with primer pair O-P. The XbaI and BamHI sites in oligonucleotides Q and R are present in the vgbB sequence. Primer pair O-P was designed to amplify a 581-bp DNA fragment from the vatC gene (this study), and primer pair Q-R was designed to amplify a 729-bp DNA fragment from the vgbB gene (this study).Blotting and hybridization. Hybridization of the DNA transferred onto Hybond-N+ membranes (Amersham International) was performed under stringent conditions as described previously (8).
DNA cloning and transformation. Standard methods were used for DNA cloning (32). E. coli was transformed by the method of Hanahan (19) with selection on Luria-Bertani agar containing 100 µg of ampicillin per ml. S. aureus RN4220 was transformed by electroporation as described previously (2).
DNA sequencing. An automated 373A DNA sequencer (Applied Biosystems, Inc.) and the protocol described by the manufacturer were used for sequencing. The sequencing reaction was performed by PCR amplification in a final volume of 20 µl with 500 ng of plasmid DNA, 10 pmol of primer, and 9.5 µl of a dye terminator premix. After heating at 94°C for 2 min, the reaction was carried out as follows: 25 cycles of 30 s at 94°C and 30 s at 55°C and then 4 min at 60°C (9600 thermal cycler; Perkin-Elmer). Excess dye terminators were removed with Quick Spin columns (Boehringer Mannheim). The samples were dried in a vacuum centrifuge and dissolved in 4 µl of a deionized mixture (5/1; vol/vol) of formamide and 50 mM EDTA (pH 8). The samples were loaded onto the sequencer and run for 12 h in a 4.5% denaturing acrylamide gel.
For the sequencing of vatC, the following primers were used: 5'-GAAATGGTTGGGAGAAGCATACC-3', 5'-AATCGGCAGAATTACAAACG-3', 5'-CAGCAATCGCGCCCGTTTG-3', and 5'-CGTTCCCAATTTCCGTGTTACC-3'. For the sequencing of vgbB, the following primers were used: 5'-GTTTCTATGCTGATCTGAATC-3', 5'-GGTCTAAATGGCGATATATGG-3', 5'-GTCGTTTGTAATTCTGCCGATT-3', and 5'-TTCGAATTCTTTTATCCTACC-3'.Sequence analysis. The aa sequence was analyzed with the Genetics Computer Group package. The aa sequences of vatC and vgbB were compared by using the program TFastA with those deduced from nucleotide sequences in the GenBank-EMBL Data Library. The aa sequences were aligned according to the algorithm in the Clustal V package.
Nucleotide sequence accession number. The sequence of plasmid pIP1714 described in this paper has been deposited in the GenBank-EMBL Data Library under accession no. AFO15628.
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RESULTS AND DISCUSSION |
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Isolation of plasmids pIP1714 and pIP1742 harbored by S. cohnii subsp. cohnii BM10711. Two plasmids harbored by BM10711 were introduced separately by electroporation into recipient strain S. aureus RN4220. pIP1714 was found in a transformant selected on brain heart infusion agar supplemented with 10 µg of PIIA per ml, and pIP1742 was found in a transformant selected on brain heart infusion agar supplemented with 20 µg of PIB per ml. Plasmid pIP1714 conferred resistance to PIIA (MIC, 32 µg/ml) and PIB (MIC, 16 µg/ml), whereas pIP1742 conferred constitutive resistance to macrolides, lincosamides, and PIB (MIC, 64 µg/ml). The ability of the transformants carrying each of these two plasmids to inactivate PIIA and PIB was tested by the microbiological test described by Gots (17). The transformant harboring pIP1714 inactivated PIIA and PIB, whereas neither of these two antibiotics was inactivated by the transformant containing pIP1742.
Sequence of pIP1714. Cleavage of pIP1714 with HindIII generated a single fragment of 5 kb which was ligated into the HindIII site of pOX7 (14), giving pIP1715. The sequence of the HindIII insert (4,978 nucleotides [nt]) in pIP1715 was determined (Fig. 1) and is registered in the GenBank-EMBL Data Library under accession no. AFO15628. Four putative genes were detected, and all were in the same transcriptional orientation. Two of these genes are the same as the repB and pre(mob) genes in pUB110 (24) and pBC16 (29). One other gene is similar to the gene vgb (69.5% nt sequence identity) and was named vgbB, and the fourth gene is similar to the genes vat, vatB, and satA (71.7, 62.2, and 64.1% nt sequence identities, respectively) and was named vatC.
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60.2 kJ/mol. The G+C content of the gene is 38.9%. It encodes a 295-aa protein with a calculated molecular mass of
32.7 kDa. VgbB is very similar to the staphylococcal Vgb lactonase
which inactivates B compounds (5) (67.0% identical aa and
81.9% similar aa). The common aa are distributed throughout the
peptide chain (data not shown). No significant similarities were
detected between the two SgB lactonases, Vgb and VgbB, and other
peptide sequences in data banks. The molecular masses of Vgb and VgbB
are similar to that of a lactonase in Actinoplanes missouriensis which inactivates virginiamycin B components (35 kDa) (20).
The putative gene vatC (636 nt) extends from an ATG start
codon at nt 1307 to 1309 to the stop codon at nt 1943 to 1945. The start codon is preceded 10 nt upstream by an 8-nt putative RBS (TGGGAGTG). The free energy of association of the most
stable structure between the putative RBS and the 3' terminus of the 16S rRNA calculated as described by Tinoco et al. (34) is
44.3 kJ/mol. The G+C content of the gene is 36.3%. It encodes a
212-aa protein with a calculated molecular mass of 23.6 kDa; the
sequence of this protein is similar to those of the three known SgA
acetyltransferases with similar molecular masses: Vat (24.3 kDa; 69.8%
identical aa and 83.5% similar aa), VatB (23.3 kDa; 58.2% identical
aa and 77.4% similar aa), and SatA (23.3 kDa; 66.0% identical aa and 80.1% similar aa). These four SgA acetyltransferases have in common 48 identical aa and a repeated sequence of an isoleucine patch (13) also found in the peptide sequences of several
homotrimer acetyltransferases which modify various substrates
(25).
Putative
35 and
10 promoter sequences are present upstream from the
vgbB gene but not upstream from the contiguous
vatC gene, suggesting that the two genes may be coordinately
transcribed. The reason why the staphylococcal vat-related
genes (vat, vatB, and vatC) are
regularly downstream from another gene encoding resistance to
streptogramins (vgb, vgaB, and vgbB,
respectively) and with which they appear to be cotranscribed remains
unclear.
The region of pIP1714 located between nt 1984 and 4968 is the same as
or very similar to regions in five rolling-circle replication and
mobilizable plasmids (3.7 to 4.6 kb) previously isolated from strains
belonging to gram-positive species: pUB110 from S. aureus (24), pBC16 from Bacillus cereus (29),
pNS1981 from Bacillus subtilis (33), pTB913 from
thermophilic Bacillus (27), and pIP823 from
Listeria monocytogenes (7). These plasmids carry various antibiotic resistance genes. The similar regions include the
replication pUB110-repB gene (24), recombination
and mobilization pre(mob) genes (35),
dso and ssoU sequences consisting of
double-strand and single-strand replication origins, respectively
(10, 11, 18, 35), and RSA sites corresponding to
the origin transfer by mobilization (35). The similar
regions of the six plasmids are delimited by two direct repeats (GGGC;
see Fig. 2). In pUB110 and pNS1981, several inverted repeats
overlapping part of the GGGC repeats were observed (31).
Similar inverted repeats were also found in pIP1714, pBC16, pTB913, and
pIP823, and those in pUB110 and pTB913 carrying the same antibiotic
resistance genes (aadD and ble) exhibit the best
matches (Fig. 2). These direct GGGC
repeats and the multiple inverted, more or less perfect repeats including part of the GGGC sequences may be subject to site-specific breakage and joining, making this fragment available as a cassette to
pick up antibiotic resistance genes and thus to trigger their transfer
between gram-positive species via conjugative mobilization and/or
interplasmid recombination (10, 18, 26-28).
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Distribution of the vgbB and vatC genes among 53 independent wild-type isolates resistant to the synergistic mixtures of A and B compounds. Plasmids pIP1740 and pIP1741 were used as probes in hybridization experiments under stringent conditions. pIP1740 is pUC18 carrying, between the EcoRI and SacI sites, a vatC intragenic fragment of 581 bp amplified with the primer pair O-P and cleaved with the same enzymes. pIP1741 consists of the vgbB intragenic fragment of 729 bp amplified with the primer pair Q-R and cleaved with XbaI and BamHI inserted between the XbaI and BamHI sites of pUC18. The 53 staphylococcal isolates analyzed included S. cohnii subsp. cohnii BM10711 harboring pIP1714, which was used as a positive control. Both probes gave a strong positive signal with BM10711, whereas none of the 52 other isolates contained hybridizing nucleotide sequences.
The habitat of S. cohnii subsp. cohnii is human skin, where it produces small and transient populations (21). The presence of BM10711 on the top of a cupboard in a trauma ward of the Douera Hospital in Algiers therefore probably resulted from human contamination. Ptr S. cohnii subsp. urealyticum strains, usually found on humans and other primates, were isolated from the same environment (sheet, tray, needle) (23). The detection of Ptr S. cohnii strains in all the environmental samples of the hospital ward may result from their ability to persist because of an intrinsic resistance to environmental stresses and/or because of the substantial prevalence in this species of plasmids carrying streptogramin resistance genes. None of the Ptr staphylococci isolated from the pus of seven patients suffering from osteomyelitis and hospitalized in the same ward of Douera Hospital were S. cohnii species. The strains from these patients were S. aureus (six patients) and S. epidermidis (one patient), and the single Ptr staphylococcal strain isolated from a nurse's hands was S. haemolyticus (23). The presence of Ptr S. cohnii strains on the skin flora of the patients treated with Pt cannot be ruled out, but because this species is rarely responsible for infectious diseases, the probability of finding such strains in pus samples is low. Note that in this ward, Pt was used extensively both by oral administration for the long-term treatment of chronic osteomyelitis and by inappropriate direct application of the powder to wounds. In Douera Hospital, the prevalence of Ptr staphylococci was higher (20%) than that elsewhere in Algeria (4.5%) and that in most French hospitals (
5%).
The relatively high prevalence of these strains was mostly a result of
the independent selection of staphylococci of various taxa or types
harboring diverse genes and plasmids conferring resistance to the
mixtures of A and B compounds.
Conclusions. The multiplicity of plasmids and genes conferring resistance to A and B compounds and to their mixtures, including quinuspristin-dalfopristin, must be kept in mind when administering these antibiotics for therapy or using them as additives in animal feed.
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ACKNOWLEDGMENTS |
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We are grateful to Olivier Chesneau for valuable discussions and Catherine Tran for secretarial assistance.
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FOOTNOTES |
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* Corresponding author. Mailing address: National Reference Center for Staphylococci, Unité des Staphylocoques, Institut Pasteur, 75724 Paris Cedex 15, France. Phone: (33) 01 45 68 83 63. Fax: (33) 01 40 61 31 63. E-mail: nelsolh{at}pasteur.fr.
Present address: Laboratoire Central de Bactériologie,
Hôpital Cantonal Universitaire, Geneva, Switzerland.
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