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Journal of Clinical Microbiology, April 2001, p. 1443-1448, Vol. 39, No. 4
Laboratory of Enteric Pathogens1 and
Virus Reference Division,2 Central
Public Health Laboratory, London NW9 5HT, and Veterinary
Laboratories Agency, New Haw, Surrey KT15 3NB,3
United Kingdom
Received 27 November 2000/Returned for modification 20 January
2001/Accepted 3 February 2001
A LightCycler-based PCR-hybridization gyrA mutation
assay (GAMA) was developed to rapidly detect gyrA point
mutations in multiresistant (MR) Salmonella enterica
serotype Typhimurium DT104 with decreased susceptibility to
ciprofloxacin (MIC, 0.25 to 1.0 mg/liter). Ninety-two isolates (49 human, 43 animal) were tested with three individual oligonucleotide
probes directed against an Asp-87-to-Asn (GAC Multiresistant (MR) Salmonella
enterica serotype Typhimurium definitive phage type 104 (DT104)
emerged during the 1990s as the most prevalent MR phage type in England
and Wales. MR DT104 has been responsible for a substantial number of
infections in humans and a wide range of food animals and is now
recognized as a significant health problem in numerous European
countries, North America, the Middle East, South Africa, and southeast
Asia (38). MR DT104 is typically resistant to ampicillin,
chloramphenicol, streptomycin-spectinomycin, sulfonamides, and
tetracylines (resistance type [R type] ACSSpSuT; see Table 1 for
definitions of individual elements of the R types). The ACSSpSuT
resistance genes (blaCARB-2, cmlA, aadA2,
sul1, and tetG) are all clustered together on a segment of the chromosome that is approximately 13 kb in length and includes two class 1 integrons (7, 8).
Since 1988 fluoroquinolones have become the antimicrobials of choice
for extraintestinal salmonella infections. However, an increasing
number of treatment failures have been associated with ciprofloxacin-resistant salmonella, including infections associated with strains with resistance levels below the designated MIC
(27-29, 39, 40). Since 1993, the increasing number of MR
DT104 isolates from humans and animals with additional resistance to
nalidixic acid and decreased susceptibility to ciprofloxacin has become an important issue, particularly as this has followed the licensing of
enrofloxacin for veterinary use. Moreover in a recent food-borne outbreak of MR DT104 with resistance to nalidixic acid and reduced susceptibility to ciprofloxacin in Denmark, four hospitalized patients
did not respond to treatment with ciprofloxacin and there were two
deaths (25). This clearly illustrates the potential risk
that decreased susceptibility to ciprofloxacin can present in the
effective antibiotic therapy of patients with serious salmonella infections, particularly when such strains are already resistant to
several therapeutic antimicrobials.
Bacterial resistance to quinolones is chromosomal in origin and can be
caused by alterations in target enzymes (DNA gyrase and topoisomerase
IV), a decrease in drug permeability, or an active efflux mechanism
(19, 31). Although quinolone resistance can involve a
variety of different mechanisms, mutations within gyrA
resulting in amino acid substitutions in the GyrA subunit of DNA gyrase
play a major role in quinolone resistance in gram-negative bacteria
including Salmonella (19). Point mutations in a
region of the gyrA gene product, between amino acids 67 and
122, termed the quinolone resistance-determining region, have
frequently been detected in salmonella serotypes that are resistant to
nalidixic acid and that exhibit decreased susceptibility to
ciprofloxacin (30, 42). Although several different GyrA
mutations have been identified in Salmonella, Ser-83 and
Asp-87 are most commonly mutated in clinically resistant isolates and
in isolates with decreased susceptibility.
In this study we describe the adaptation of a rapid
LightCycler assay, previously described by Gibson et al.
(14), to detect the GyrA substitutions Ser-83 to Phe
(TCC Bacterial strains.
Five MR S. enterica serotype
Typhimurium DT104 strains with known gyrA mutations were
selected as controls for the LightCycler GAMA protocol
(33). These included P3801900 (Asp-87 to Asn), P4111690
(Asp-87 to Asn), P3424780 (Asp-87 to Gly), P4156400 (Asp-87 to Gly),
and P3749380 (Ser-83 to Phe). P3343110 was included as a
quinolone-sensitive DT104 strain with no gyrA mutations.
Mutations in the gyrA gene in 49 human and 43 animal MR
DT104 isolates were investigated. The human isolates were from patients
in England and Wales in 1999 and were epidemiologically unrelated. The
animal strains were isolated in 1999 and 2000 and came from a variety of sources (Table 1).
0095-1137/01/$04.00+0 DOI: 10.1128/JCM.39.4.1443-1448.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Use of a LightCycler gyrA Mutation Assay
for Rapid Identification of Mutations Conferring Decreased
Susceptibility to Ciprofloxacin in Multiresistant Salmonella
enterica Serotype Typhimurium DT104 Isolates
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ABSTRACT
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
AAC) mutation, an
Asp-87-to-Gly (GAC
GGC) mutation, and a Ser-83-to-Phe (TCC
TTC)
mutation. Strains homologous to the probes could be distinguished from
strains that had different mutations by their probe-target melting
temperatures. Thirty-seven human and 30 animal isolates had an
Asp-87-to-Asn substitution, 6 human and 6 animal isolates had a
Ser-83-to-Phe substitution, and 5 human and 2 animal isolates had an
Asp-87-to-Gly substitution. The remaining six strains all had
mismatches with the three probes and therefore different
gyrA mutations. The sequencing of gyrA from
these six isolates showed that one human strain and two animal strains
had an Asp-87-to-Tyr (GAC
TAC) substitution and two animal strains had a Ser-83-to-Tyr (TCC
TAC) substitution. One animal strain had no
gyrA mutation, suggesting that this isolate had a different mechanism of resistance. Fifty-eight of the strains tested were indistinguishable by several different typing methods including antibiograms, pulsed-field gel gel electrophoresis, and plasmid profiling, although they could be further subdivided according to
gyrA mutation. This study confirmed that MR DT104 with
decreased susceptibility to ciprofloxacin from humans and food animals
in England and Wales may have arisen independently against a background of clonal spread of MR DT104.
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INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
TTC), Asp-87 to Gly (GAC
GGC), and Asp-87 to Asn
(GAC
AAC) in strains of MR DT104 from humans and animals. This
LightCycler gyrA mutation assay (GAMA) involves real-time
PCR followed by the detection of mutations using oligonucleotide probes
and thermal analysis. We have subsequently applied GAMA to investigate
the type and frequency of gyrA mutations in 92 isolates from
humans and animals that were resistant to nalidixic acid and that had
reduced susceptibility to ciprofloxacin. These strains were
additionally characterized using pulsed-field gel electrophoresis
(PFGE), plasmid profiling, and a long-PCR assay to detect the ACSSpSuT
resistance gene cluster.
![]()
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
TABLE 1.
Antibiograms (R types) of 92 MR DT104 isolates from
humans and animals
Phage typing and antimicrobial susceptibility tests. Isolates were phage typed by the method of Callow (9) as extended by Anderson (2) and assigned to phage types in accordance with the scheme of Anderson et al. (3). Resistance to ampicillin, chloramphenicol, gentamicin, kanamycin, neomycin, streptomycin, spectinomycin, sulfonamides, tetracyclines, trimethoprim, low-level ciprofloxacin, high-level ciprofloxacin, nalidixic acid, and furazolidone was determined using a breakpoint method in Iso-Sensitest agar (12). The final concentrations (in micrograms per milliliter) of the antibacterial drugs were as follows: ampicillin, 8; chloramphenicol, 8; gentamicin, 4; kanamycin, 8; neomycin, 8; streptomycin, 16; spectinomycin, 64; sulfonamides, 64; tetracyclines, 8; trimethoprim, 2; low-level ciprofloxacin, 0.125; high-level ciprofloxacin, 1; nalidixic acid, 16; furazolidone, 8.
Detection of gyrA mutations using a LightCycler GAMA. Briefly, GAMA involves amplification of a region of the gyrA gene (encompassing the nucleotides between codons 71 and 102) coupled with simultaneous detection of product formation by the LightCycler software (Roche Diagnostics Ltd., Lewes, United Kingdom), as the double-stranded DNA-specific fluorophore Sybr Green 1 (SG1) (BioGene, Cambridge, United Kingdom) is incorporated into the PCR amplicons. The level of SG1 fluorescence increases as the amount of PCR product doubles with each cycle and is measured by channel 1 (wavelength, 530 nm) of the LightCycler. The PCR product is then denatured, and a single gyrA mutation-specific oligonucleotide probe labeled with fluorophore Cy5 anneals to its target. Hybridization of the probe to the target DNA strand leads to an increase in Cy5 fluorescence as a result of fluorescence resonance energy transfer (FRET) between SG1 and Cy5 (14); this is measured by channel 3 (710 nm). The temperature is then increased, and the probe and target dissociate. Increasing the temperature stepwise to 94°C causes the Cy5 fluorescence to decrease as the probe and target dissociate and Cy5 and SG1 are no longer in close enough proximity for FRET to occur. If the specific mutation is not present, the mismatch of the probe with the target destabilizes the hybrid, so the decrease in fluorescence will occur at a melting temperature (Tm) lower than that for a hybrid where there are no mismatches.
A 96-bp fragment of gyrA was amplified with primers gyrAF (5'-GGTGACGTAATCGGTAAATA-3') and gyrAR (5'-CAGCATGTAACGCAGCGA-3'), purchased from MWG Biotech UK Ltd. (Milton Keynes, United Kingdom) and based on the sequence of gyrA from S. enterica serotype Typhimurium NCTC 74 (17). The PCR and hybridization reaction were carried out in a 20-µl volume containing 1× buffer (10× buffer is 500 mM Tris-HCl, 20 mM MgCl2, and 5 µg of bovine serum albumin/ml), 20 ng of template DNA extracted using the DNeasy DNA extraction kit (Qiagen, Crawley, United Kingdom), 200 µM (each) deoxynucleoside triphosphate (Boehringer Mannheim, Lewes, United Kingdom), 0.5 µM forward primer (gyrAF), 0.2 µM reverse primer (gyrAR), 0.8 U of platinum Taq (Life Technologies, Paisley, United Kingdom), 1 mM MgCl2, a 1/10,000 dilution of SG1 (BioGene), and a 0.5 µM concentration of the probe complementary to either the Asp-87-to-Asn (GAC
AAC)
mutation (gyrAPI
[Cy5-5'-GGTGTTATACACTGCGGAAT-3'-biotin]), the
Ser-83-to-Phe (TCC
TTC) mutation (gyrAPII
[Cy5-5'-GGTGTCATACACTGCGAAAT-3'-biotin]), or
the Asp-87-to-Gly (GAC
GGC) mutation (gyrAPIII
[Cy5-5'-GGTGCCATACACTGCGGAAT-3'-biotin]) where bases
complementary to specific point mutations are shown in bold. The
labeled probes were also synthesized by MWG Biotech. The 3' end of each
probe is blocked with biotin to prevent the probes from behaving as
primers. Forward and reverse primers were added in unequal
concentrations in order to favor the amplification of the strand to
which the probe bound. Table 2 lists the
PCR amplification and probe melting conditions.
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DNA sequencing. DNA sequencing was performed by amplifying a fragment of the gyrA gene using the primers P1 (5'-TGTCCGAGATGGCCTGAAGC-3') and P2 (5'-TACCGTCATAGTTATCCACG-3'), previously described by Griggs et al. (17). These primers surround the nucleotides between codons 37 and 151 of gyrA and therefore include all bases previously detected as mutation hot spots. PCR was performed in a 50-µl volume with the Hybaid (Ashford, United Kingdom). MultiBlock system. Reaction mixtures contained 1× MgCl2-free buffer (Life Technologies), 0.5 µM (each) primer, 2.5 U of Taq DNA polymerase (Life Technologies), 200 µM (each) deoxynucleoside triphosphate (Boehringer Mannheim), 1.5 mM MgCl2, and approximately 25 ng of template DNA. After an initial denaturation (3 min at 94°C), 25 cycles of amplification were performed as follows: denaturation at 94°C for 1 min, annealing at 55°C for 1 min, and DNA extension at 72°C for 1 min. Finally DNA was extended at 72°C for 10 min for 1 cycle. The 347-bp products were purified using the QIAquick PCR purification kit (Qiagen), and the sequencing reactions were performed using the P1 and P2 primers and the CEQ dye terminator cycle sequencing kit (Beckman Coulter, High Wycombe, United Kingdom). The purified sequencing reaction samples were run on the CEQ 2000 DNA sequencer using the DTSC-2 method (Beckman Coulter DTCS sequencing protocol).
PFGE. Chromosomal DNA was prepared by the method described by Powell et al. (32). DNA contained in the agarose plug was digested with 40 U of XbaI (New England BioLabs, Hitchin, United Kingdom). DNA fragments were resolved on 1% agarose gels (PFGE certified; Bio-Rad, Hemel Hempstead, United Kingdom) and run in 0.5% Tris-borate-EDTA on the contour-clamped homogeneous electric field DRII apparatus (Bio-Rad). The conditions for electrophoresis were 180 V for 44 h with a pulse time from 6 to 72 s. Gels were then stained with ethidium bromide (0.5 µg/ml) and visualized under UV light (312 nm). A mixture of lambda DNA HindIII fragments and lambda concatamers was used as a size standard (New England BioLabs).
Plasmid analysis. Plasmid DNA was isolated by the method of Kado and Liu (22) and run on a 0.6% agarose gel with Escherichia coli K-12 strain 39R861 as the plasmid molecular mass marker (35). Plasmid sizes were determined with reference to plasmids carried in E. coli 39R861.
Long PCR of ACSSpSuT resistance gene cluster. A 10,041-bp fragment of the ACSSpSuT resistance gene cluster was amplified using primers XLF (5'-TCAGAGGTGCTAAGCGTCATTGAG-3') and XLR (5'-GCTTGATGCTCACTCCACACAACT-3') based on the sequence of the antibiotic resistance gene cluster from S. enterica serotype Typhimurium DT104 isolate H3380 (8) and annealed to aadA2 and blaCARB-2, respectively. XLF and XLR were purchased from MWG Biotech. The reaction was performed on the Hybaid MultiBlock system in 100-µl volumes. The reaction mixtures contained 1× 3.3 XL buffer (PE Biosystems, Warrington, United Kingdom), 200 µM (each) deoxynucleoside triphosphate (Boehringer Mannheim), 30 pM (each) primer, 0.9 mM magnesium acetate, 4 U of rTth DNA polymerase XL (PE Biosystems), and 75 ng of template DNA. After an initial denaturation (1 min at 95°C), 30 cycles of amplification were performed as follows: denaturation at 95°C for 1 min, annealing at 59°C for 1 min, and DNA extension at 72°C for 10 min. Finally DNA was extended at 72°C for 10 min for 1 cycle.
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RESULTS |
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Susceptibilities to antimicrobials. All MR DT104 isolates were resistant to six or more antibiotics, including nalidixic acid (>16 mg/liter). All strains exhibited low-level resistance to ciprofloxacin (MIC, 0.25 to 1.0 mg/liter). The antibiograms are summarized in Table 1.
Type and frequency of gyrA mutations in MR DT104 using
GAMA and DNA sequencing.
Table 3
shows the mean Tms of the three probes with the
gyrA PCR products from MR DT104 quinolone-resistant control
strains with known gyrA mutations and one
quinolone-sensitive DT104 strain. The Tms of
strains which had nucleotide mismatches with the three probes were
consistently lower than the Tms of the strains
where there was 100% homology between probe and target.
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Long PCR. Ninety-one of the MR DT104 isolates (R-types: ACSSpSuTNxCpL, ACSSpSuTTmNxCpL, and ACNeKSSpSuTNxCpL) produced a 10,041-bp fragment and were therefore positive for the ACSSpSuT gene cassette. Only one animal isolate was negative for long PCR; this strain was of R type SSpSuTNxCp.
PFGE and plasmid profiling.
Four distinct patterns, which
differed from each other by at least two band differences, were
generated by PFGE (Fig. 1). The PFGE
profiles of 49 human and 37 animal isolates were designated XTm-1, the
predominant profile type for MR DT104 (33). The profiles of the remaining six animal isolates were designated either XTm18, XTm46, or XTm47 (Fig. 1; Table 4). Twenty plasmid profiles were identified (Table 4). Isolates contained between one and five plasmids
ranging from 1.0 to 120 MDa. A 60-MDa plasmid was the most frequently
identified plasmid type, present in 46 human and 43 animal isolates
(Table 4).
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DISCUSSION |
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In recent years the emergence of quinolone resistance in humans and food-producing animals has been a disturbing feature of salmonella infections in several European countries, including the United Kingdom, Germany, and Denmark (1, 18, 24, 36). In England and Wales fluoroquinolone resistance in human salmonella isolates was extremely rare up until 1994 (12, 36), despite the widespread use of ciprofloxacin in humans since 1987 (4). However, following the introduction of enrofloxacin for veterinary use in the United Kingdom in 1993 and its subsequent use in food-producing animals (28), decreased susceptibility to ciprofloxacin has rapidly developed, particularly among MR DT104 isolates of R type ACSSpSuT. In 1998 16% of human MR DT104 isolates were of R type ACSSpSuTNxCpL (37). A considerable increase in nalidixic acid resistance has also been observed among MR DT104 isolates from food-producing animals, especially turkeys (10). Studies in several other European countries have also shown that the incidence of quinolone-resistant salmonellae has increased substantially in the years following the approval of quinolones in livestock (1, 21, 23, 24).
In the present study we have described a LightCycler-based GAMA for the detection of three gyrA point mutations in MR DT104 with resistance to nalidixic acid and decreased susceptibility to ciprofloxacin. Eighty-six of 92 isolates possessed either an Asp-87-to-Asn, an Asp-87-to-Gly, or a Ser-83-to-Phe substitution when tested by GAMA. Although the method could not determine the gyrA mutation for the remaining six strains, it did dramatically reduce the requirement for DNA sequencing and the time taken to determine the presence of specific mutations. The procedure can be completed in less than 1 h following the extraction of DNA. Additionally, diluted cells can also be used in place of DNA (results not shown), thus decreasing further the length of time it takes to perform the test. Thus GAMA is a useful technique for rapidly screening large numbers of isolates in epidemiological investigations involving strains with decreased susceptibility to ciprofloxacin. GAMA has recently been applied to confirm the source and clonal identity of MR DT104 strains associated with a large outbreak involving unpasteurized milk (41). As the quinolone resistance-determining region of the gyrA gene appears to be highly conserved among salmonella serotypes (30), GAMA could also be used to investigate the frequency of different gyrA mutations in such organisms. Furthermore the method could be adapted to rapidly demonstrate gyrA mutations in a wide range of bacteria including Campylobacter spp. and E. coli (11, 34). In a clinical context GAMA could be applied to confirm decreased susceptibility to ciprofloxacin not detectable using the current susceptibility breakpoints of both the British Society for Antimicrobial Chemotherapy (5) and the National Committee for Clinical Laboratory Standards (26). Rapid identification of such strains may be useful in the management of serious salmonella infections.
In total 67 of 92 isolates (73%) had an Asp-87-to-Asn substitution. We therefore conclude that Asp-87 to Asn is the most common mutation giving rise to decreased susceptibility to ciprofloxacin in MR DT104 from both humans and animals. These findings are in agreement with two previous studies that have both identified Asp-87 to Asn as a common mutation among MR DT104 isolates (25, 33). The second-most-common mutation was at residue 83 and involved a Ser-to-Asp change. This mutation was identified in six human and six animal strains. The third-most-common mutation was an Asp-87-to-Gly substitution, detected in five human and two animal isolates. Partial sequencing of the gyrA gene from the remaining six strains showed that two human strains and one animal strain had an Asp-87-to-Tyr substitution, two animal strains had a Ser-83-to-Tyr substitution, and one animal strain had no gyrA mutation. It is possible that in the single strain with no gyrA mutation there may be a novel mutation outside of the sequenced region, although the sequenced area included all residues previously identified as mutation hot spots. These results suggest that other mechanisms and/or mutations are responsible for decreased susceptibility to ciprofloxacin in this strain. These could include a mutation in either gyrB, which encodes the B subunit of DNA gyrase, or parC, which codes for the ParC subunit of topoisomerase IV. However this may be unlikely, as gyrB and parC mutations are not normally associated with resistance to nalidixic acid and reduced susceptibility to ciprofloxacin in Salmonella (15, 42). Other alternative mechanisms of resistance could be a decrease in permeability to quinolones through alterations of the outer membrane proteins (30), modifications of lipopolysaccharide or an active efflux mechanism (16). The mechanism(s) of quinolone resistance in this particular strain is under further investigation.
Five different gyrA mutations were identified in this study. This variation can be used as an additional subtyping tool for MR DT104 with decreased susceptibility to ciprofloxacin and indistinguishable by several phenotypic and genotypic tests. For example 63% (58 of 92) of the strains tested were identical by R type, PFGE, and plasmid profiling and possessed the same 13-kb antibiotic resistance gene cluster but could be further subdivided according to their gyrA mutations. These results also demonstrate that in respect to their gyrA mutations these isolates were not all clonal in origin and may have arisen independently, over time, against a background of clonal spread of MR DT104.
The two most common gyrA mutations in the animal isolates were also those most common in the human strains. These findings confirm the association between quinolone-resistant human and animal isolates of MR DT104. However, although different gyrA mutations were identified in the animal isolates, there was no obvious link between gyrA mutation and isolate source. Most GyrA substitutions were detected in both animal and human isolates; the exception to this was a Ser-83-to-Tyr mutation, which was only identified in two animal strains. The finding that the Ser-83-to-Tyr mutation is only present in animals suggests that some of these mutants originate in animals before being widely distributed to the human population.
Fluoroquinolones are an important group of antibiotics for the treatment of potentially life-threatening extraintestinal salmonella infections in humans. It is therefore vital to limit their administration both in food-producing animals and humans so as to preserve their value for the treatment of not only humans but also sick animals. It is encouraging that in the United Kingdom the 1998 Codes of Practice recommended by the House of Lords Select Committee on Science and Technology for the use of fluoroquinolones in animal husbandry have been introduced by some pharmaceutical companies in attempts to reduce the unnecessary prophylactic use of such antimicrobials (20). The Advisory Committee on the Microbiological Safety of Food has also recently published guidelines aimed at reducing the use of veterinary antibiotics in the United Kingdom (6). However, probably the most significant recent news is the proposal by the Food and Drug Administration's Center for Veterinary Medicine to withdraw approval of enrofloxacin for use in poultry. This step has been taken as a result of the sharp increase in resistance to fluoroquinolones in Campylobacter spp. in the United States following the licensing of enrofloxacin for poultry production in 1996 (34). It is now hoped that these concerted actions will result in a reduction in resistance to fluoroquinolones, not only among MR DT104 and other nontyphoidal salmonella serotypes but also among Campylobacter spp. and other zoonotic bacterial pathogens.
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ACKNOWLEDGMENTS |
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This work was funded by the Food Standards Agency, Code B10001 (formerly DH Code 240B), and the Ministry of Agriculture Fisheries and Food (MAFF Code FS3114).
We thank Mike Hampton for useful discussion.
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FOOTNOTES |
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* Corresponding author. Mailing address: Laboratory of Enteric Pathogens, Central Public Health Laboratory, 61 Colindale Ave., London NW9 5HT, United Kingdom. Phone: 44 (0)20 8200 4400. Fax: 44 (0)20 8905 9929. E-mail: rwalker{at}phls.org.uk.
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