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Journal of Clinical Microbiology, September 2003, p. 4292-4297, Vol. 41, No. 9
0095-1137/03/$08.00+0 DOI: 10.1128/JCM.41.9.4292-4297.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Discrimination of d-Tartrate-Fermenting and -Nonfermenting Salmonella enterica subsp. enterica Isolates by Genotypic and Phenotypic Methods
Burkhard Malorny, Cornelia Bunge, and Reiner Helmuth*
Federal Institute for Risk Assessment, National Salmonella Reference Laboratory, D-12277 Berlin, Germany
Received 22 April 2003/
Returned for modification 26 May 2003/
Accepted 5 July 2003

ABSTRACT
A multiplex PCR and an improved lead acetate test were developed
to discriminate
d-tartrate-fermenting and -nonfermenting
Salmonella enterica subsp.
enterica strains. Both methods showed an accuracy
of 100% when 125
Salmonella strains belonging to 15 serovars
were tested. Special emphasis was given to
S. enterica subsp.
enterica serovar Paratyphi B isolates because of the clinical
importance of its
d-tartrate-nonfermenting variant and the recently
increasing numbers of cases of human outbreaks caused by its
fermenting variant (formerly
Salmonella serovar Java). The lead
acetate test described previously (G. A. Alfredsson, R. M. Barker,
D. C. Old, and J. P. Duguid, J. Hyg. 70:651-666, 1972) was modified
in the inoculation and incubation procedure. The PCR assay was
based on the genotypic difference of the presence (
d-tartrate-fermenting
strains) or absence (
d-tartrate-nonfermenting strains) of the
ATG start codon for the gene STM 3356, which encodes a putative
cation transporter. Sequence data revealed a nucleotide exchange
from G to A within the ATG start codon of gene STM 3356 in the
d-tartrate-nonfermenting strains. In order to increase the reliability
of the PCR assay, a positive control based on a
Salmonella genus-specific
primer set for the detection of
Salmonella DNA was included.
The PCR-based discrimination needs only several hours compared
to 6 days needed by the improved lead acetate test to obtain
reliable results. Consequently, the PCR
d-tartrate assay should
be the method of choice for the discrimination of
d-tartrate-fermenting
and -nonfermenting
Salmonella strains in the future.

INTRODUCTION
Salmonella enterica subspecies
enterica serovar Paratyphi B
can be differentiated by the fermentation of dextrorotatory
[
L(+)]-tartrate (
d-tartrate). Kristensen and Kauffmann (
7) noted
a difference in clinical manifestation of both variants. Whereas
d-tartrate-nonfermenting (dT
-) strains exhibit an enhanced human
pathogenicity causing typhoid-like disease,
d-tartrate-fermenting
strains (dT
+) provoke the less severe gastroenteric disease.
Formerly, dT
+ strains of this serovar were designated
S. enterica subsp.
enterica serovar Java by Kauffmann (
6). Recently, the
Salmonella serovar Paratyphi B dT
+ variant has become increasingly
important. In The Netherlands, it is the predominating serovar
in poultry (
14) and has led to human outbreaks in Denmark, Scotland
(
4), and Canada (
13). Therefore, the rapid identification of
dT
+ and dT
- serovar Paratyphi B strains isolated from animals
and humans is important for
Salmonella risk assessment and adequate
surveillance interventions. The discrimination of dT
+ and dT
- isolates has also been used for the biotyping of other
Salmonella serovars (
2,
10).
Anaerobic fermentation of tartrate usually proceeds via stereospecific dehydratases to oxaloacetate, which is further converted via pyruvate to acetate, formate, and CO2, thus allowing the synthesis of ATP in the acetate kinase reaction (12). Previously it was shown that anaerobic growth of S. enterica subsp. enterica serovar Typhimurium in the presence of d-tartrate involves an oxaloacetate decarboxylase Na+ pump encoded by the oadGAB genes (15). Upstream of these genes, two open reading frames have been identified; these open reading frames show homology with the ttdB (67%) and ttdA (58%) genes of Escherichia coli (GenBank accession no. L14781), which encode the subunits of the oxygen-labile stereospecific L-tartrate dehydratase (11). These two genes were designated STM 3354 and STM 3355 in the complete genome sequence of Salmonella serovar Typhimurium strain LT2 (GenBank accession no. AE008854). Upstream of the ttdA and ttdB genes, an open reading frame encoding a putative cation transporter (STM 3356), two open reading frames encoding gntR family regulatory proteins (STM 3357 and STM 3358), and the mdh gene encoding the malate dehydrogenase were noted (Fig. 1).
Several biochemical tests, such as the anaerobic plate test,
the lead acetate test, and the turbidity test, have been developed
to discriminate dT
+ and dT
- Salmonella strains. A comparison
of these methods revealed poor correlation and reproducibility
(
3). Currently, the WHO Collaborating Centre for Reference and
Research on Salmonella located at the Institute Pasteur (Paris,
France) uses the lead acetate test as a "gold standard"-like
method as described by Alfredsson et al. (
2) but with a prolongation
of the incubation times to 3 and 6 days. The aim of this study
was to develop a rapid PCR-based method for the discrimination
of dT
+ and dT
- S. enterica subsp.
enterica isolates. The accuracy
of the PCR-based method was compared to that of the lead acetate
test as used by the WHO Collaborating Centre. We have found
that modifications of the inoculation and incubation conditions
of the lead acetate test resulted in 100% accuracy with the
PCR-based method.

MATERIALS AND METHODS
Salmonella strains.
Serovars, sources, and countries and years of isolation of the
strains used in this study are summarized in Table
1. Most of
the strains were isolated from various regions in Germany between
the years 1961 and 2002 and collected at the German National
Reference Laboratory for Salmonella (NRL-Salm, BfR, Berlin,
Germany). The strains originated from animals, foods, and environmental
and human sources. The molecular properties of many serovar
Paratyphi B dT
+ strains used in this study have been described
before (
9).
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TABLE 1. Results of the discrimination of dT+ and dT- S. enterica subsp. enterica strains by three lead acetate test protocols and a PCR-based method
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Molecular methods.
For sequencing of the intergenic region of the STM 3357 and
STM 3356 genes, two primers were designed based on the sequence
of the serovar Typhimurium LT2 strain (GenBank accession no.
AE008854), which amplified a 332-bp DNA fragment. Primer 165
(5'-TCC CAT ACA AAC ATG ACG AT-3') is located at the N-terminal
coding region of the STM 3356 gene, and primer 167 (5'-CAC ATT
ATT CGC TCA ATG GAG-3') is located at the C-terminal coding
region of the STM 3357 gene (Fig.
1). All PCRs were carried
out in a GeneAmp PCR system 9700 thermocycler (Applied Biosystems,
Weiterstadt, Germany). A 50-µl PCR mixture contained 0.4
µM concentrations of primers 167 and 165, a 200 µM
concentration of each deoxynucleoside triphosphate (Roche Applied
Science, Mannheim, Germany), 1
x PCR buffer (20 mM Tris-HCl [pH
8.4], 50 mM KCl), 1.5 mM MgCl
2, 1 U of Platinum
Taq polymerase
(Invitrogen, Karlsruhe, Germany), and a 5-µl aliquot of
the sample DNA (approximately 10
6 CFU). The incubation conditions
were 95°C for 1 min, followed by 30 cycles of 95°C for
30 s, 53°C for 30 s, and 72°C for 30 s. A final extension
of 72°C for 4 min was employed. The PCR products were sequenced
by automated cycle sequencing with an ABI Prism 310 genetic
analyzer (Applied Biosystems) according to the manufacturer's
instructions. PCR for sequencing the
ttdA and
ttdB genes of
serovar Paratyphi B strains NCTC 3176 and NCTC 5706 was carried
out with primers 141 (5'-GGT TAT TAT TAT CGT CAT AAC GTA-3')
and 142 (5'-TCA GCT TGA TCC TGC TGC CA-3'). The PCR conditions
used were those described above. The 1,652-bp PCR product was
sequenced with primers derived from the published serovar Typhimurium
LT2
ttdA (STM 3355) and
ttdB (STM 3354) sequences (GenBank accession
no.
AE008854).
A multiplex PCR for the discrimination of dT+ and dT- Salmonella strains contained 0.4 µM concentrations of primers 166 (5'-GTA AGG GTA ATG GGT TCC-3') and 167, 0.2 µM concentrations of primers ST11 and ST15 (1), a 200 µM concentration of each deoxynucleoside triphosphate (Roche Applied Science), 1x PCR buffer, 2.5 mM MgCl2, 1 U of Platinum Taq polymerase (Invitrogen), and a 5-µl aliquot of the sample DNA (approximately 106 CFU). The total volume was 25 µl. The incubation conditions were 95°C for 1 min, followed by three cycles of 95°C for 30 s, 61°C for 30 s, and 72°C for 30 s and 27 cycles of 95°C for 30 s, 58°C for 30 s, and 72°C for 30 s. A final extension of 72°C for 4 min was employed. Sample DNA for PCRs was prepared from an aerobically grown Salmonella culture (16 h in Luria-Bertani medium with shaking at 37°C) (approximately 2 x 109 CFU). A 1-ml aliquot of the culture was centrifuged in a tube for 5 min at 10,000 x g at 4°C. The supernatant was carefully discarded, and the cell pellet was suspended in 300 µl of Tris-EDTA buffer (10 mM Tris-HCl, 0.1 mM EDTA [pH 8.0]). The tube was incubated for 10 min at 100°C in a water bath and immediately chilled on ice. After centrifugation for 5 min at 14,000 x g at 4°C, the DNA-containing supernatant was carefully transferred to a new tube. A 5-µl aliquot was used as template DNA for the PCR. A 7-µl aliquot of a PCR product was loaded onto a 1.6% agarose gel, and electrophoresis was performed in 1 x Tris-borate-EDTA buffer at 6 V/cm for 90 min. After electrophoresis, the gel was stained for 10 min in 1 x Tris-borate-EDTA buffer containing 0.5 µg of ethidium bromide/ml. The gel results were documented with a video camera. The PCR was used for all 125 strains and performed in triplicate (see Table 2).
The detection limit of the multiplex PCR was determined with
DNA prepared from strains NCTC 5706 and NCTC 3176 with the Genomic-tip
100 columns (Qiagen, Hilden, Germany) according to the manufacturer's
manual. The DNA was serially diluted 10-fold in Tris-EDTA buffer
and cycled according to the incubation conditions described
above. The experiment was repeated three times.
Lead acetate test protocols.
Three different protocols of the test were used for all 125 strains and performed three times each (Table 2).
Protocol 1 was performed as described by Alfredsson et al. (2) with some minor modifications and is currently the gold standard-like method used by the WHO Collaborating Centre. Ten grams of Difco Bacto Peptone (Becton Dickinson, Heidelberg, Germany) per liter was autoclaved at 121°C for 15 min. Potassium sodium tartrate tetrahydrate (Merck Eurolab, Darmstadt, Germany; catalog no. 1.08087) was added to a final concentration of 1%. The pH was adjusted with NaOH to pH 7.4. A solution of bromothymol blue sodium salt was added as an indicator to a final concentration of 0.0023%. The broth was dispensed in 8-ml volumes in cotton-wool-stoppered test tubes and sterilized two times for 15 min at 100°C each time. The inoculate was prepared by suspension of several colonies in saline (0.85% NaCl) to a density of about 109 bacteria per ml. A 50-µl aliquot of this suspension was inoculated into the test tubes. The cultures were incubated at 37°C for 3 and 6 days aerobically without shaking. After incubation, the cultures were tested for d-tartrate utilization by the addition of a saturated aqueous lead acetate solution in the proportion of 0.1 ml per 1 ml of culture. The immediately produced precipitate was homogenized by brief mixing. dT+ strains were detected by the formation of a small precipitate after 1 to 2 h of lead acetate addition. The presence of a fluffy fine precipitate after the 1 to 2 h of lead acetate addition indicated a dT- strain (Fig. 2).
Protocol 2 was identical to protocol 1 except that incubation
was in the presence of a 10% CO
2 atmosphere instead of air.
Identical inoculates were used.
Protocol 3 differed from protocol 1 in the incubation conditions (protocol 3 was in the presence of a 10% CO2 atmosphere) and the type of inoculate. Inoculation was performed with a loopful of bacteria grown aerobically overnight on Luria-Bertani plates (Merck Eurolab). Before use, the test tubes were preincubated at 37°C in a 10% CO2 atmosphere for 30 min.
Statistics.
The accuracy of the assay was determined as described by Gardner and Greiner (5). It describes the closeness of agreement between a test result and the accepted reference value.
Nucleotide sequence accession numbers.
The sequences of strains NCTC 5706 (dT+) and NCTC 3176 (dT-) have been deposited in GenBank (accession no. AY211490 and AY211491).

RESULTS AND DISCUSSION
Development of a PCR assay for the discrimination of dT+ and dT- Salmonella strains.
PCR amplification and sequencing showed the presence of the
ttdA and
ttdB genes in the serovar Paratyphi B dT
+ reference
strain NCTC 5706 and the dT
- reference strain NCTC 3176 (GenBank
accession no.
AY211492 and
AY211493). The translated protein
sequences of TtdA and TtdB in both strains were identical to
those in the serovar Typhimurium strain LT2. To identify possible
sequence differences of both strains in potential regulatory
binding sites next to the
ttdA and
ttdB genes, the intergenic
region of the STM 3357 and STM 3356 genes was amplified and
sequenced (Fig.
1). The sequences showed that only a single
nucleotide located in the ATG start codon of gene STM 3356 was
different. The serovar Paratyphi B dT
+ strain possessed a regular
ATG start codon, whereas the serovar Paratyphi B dT
- strain
possessed an A nucleotide instead of a G within the start codon.
Consequently, a gene transcript cannot be translated into the
essential putative cation transporter protein. This affects
the anaerobic growth of
Salmonella in the presence of
d-tartrate.
The role of the protein encoded by the STM 3356 gene in the
fermentation pathway for
d-tartrate remains unknown and has
yet to be elucidated.
A primer set (primers 167 and 166) was designed to give a positive PCR signal (290-bp PCR product) when the ATG start codon is present in the STM 3356 gene and no PCR amplicon when the start codon is absent (Fig. 3). The forward primer, 167, is located at the C-terminal coding region of the STM 3357 gene and anneals to both variants. The backward primer, 166, is located at the N-terminal coding region of the STM 3356 gene. The 3' primer end fits exactly with the G located in the ATG codon in dT+ strains (Fig. 1). This primer set is combined with a second primer set (ST11-ST15) generating a 429-bp PCR fragment when Salmonella DNA is present (1). This primer set serves as an internal positive control and detects the presence of amplifiable Salmonella DNA in the PCR. Using purified chromosomal DNA of strains NCTC 5706 (dT+) and NCTC 3176 (dT-) as a template, the detection limit was determined to be 10 to 1 pg of DNA (approximately 104 to 103 Salmonella genome equivalents (8) for both strains.
Comparison of the PCR assay with three lead acetate test protocols.
One hundred two
Salmonella serovar Paratyphi B strains isolated
between 1961 and 2002 in various countries worldwide, 6 serovar
Typhimurium strains, 5 serovar Enteritidis strains, and 12
Salmonella strains belonging to various other serovars were selected to
determine the accuracy between the genotypic PCR-based method
and three phenotypic lead acetate test protocols (Table
1).
Lead acetate test protocol 1 is currently used as the gold standard-like
method for the discrimination of dT
+ and dT
- Salmonella strains
at the WHO Collaborating Centre for Reference and Research on
Salmonella (M. Popoff, personal communication). The accuracy
of this protocol compared to that of the PCR-based method was
47% after 3 days of incubation and 90% after 6 days of incubation.
When the incubation was performed under a 10% CO
2 atmosphere
(protocol 2), the accuracy increased to 58% (3 days of incubation)
and 91% (6 days of incubation). A change in inoculation method
from use of a sodium chloride suspension to a loopful of bacteria
from a plate (protocol 3) led to an accuracy of 78% after 3
days of incubation and 100% after 6 days of incubation.
These data indicate that obviously poorly aerated conditions and the inoculation of approximately 5 x 107 bacterial cells per culture suspended in 0.85% NaCl are not sufficient to activate the oxygen-labile stereospecific L-tartrate dehydratase in all strains. A loopful of bacteria contains approximately 10- to 50-fold more cells.
An improved performance of the lead acetate assay was also shown when a 10% CO2 atmosphere was used during incubation. Fifty percent of the results were false negative when reference strain NCTC 5706 (dT+) was subcultured 20 times under the conditions of protocol 1 (2) for 2 days of incubation. In the presence of a 10% CO2 atmosphere, 17 of 20 (85%) subcultures reacted positively.
It is interesting that various strains showed a delay in fermenting d-tartrate, which can lead to a false-negative result depending on the test conditions. Barker (3) described eight strains which were d-tartrate negative after 24 h of incubation but positive after 48 h. It was speculated that the delay in fermenting d-tartrate was due to a deficient permease system responsible for the passage of d-tartrate into the cell or for the export of d-tartrate dehydrase. However, the reasons for such a delay remain to be elucidated. To our knowledge, nothing is known about the frequency with which dT+ strains become dT- and if the DNA region of the genome is located within a mutational hot spot. Our data indicate a stable phenotype because triplicate determinations of nonfermenting strains showed no phenotypic or genotypic exceptions.
The PCR and lead acetate test results presented here indicate quite clearly that the incubation times and conditions used by Alfredsson et al. (2) and Barker (3) should give a high degree of false-negative results and were insufficient to generate correct and reliable results.
In conclusion, despite the improved lead acetate test (protocol 3), the PCR assay described here should be the method of choice to discriminate between dT+ and dT- Salmonella strains in the future. The assay is rapid and reliable. An interlaboratory validation study is in progress to evaluate the reproducibility of the PCR method.

ACKNOWLEDGMENTS
B.M. was supported by the Bundesministerium für Verbraucherschutz,
Ernährung und Landwirtschaft (BMVEL).
We thank C. Kornschober (BBSUA, Graz, Austria), H. Imberechts (CODA, Brussels, Belgium), Philippe Bouvet (Institut Pasteur, Paris, France), W. Rabsch (RKI, Wernigerode, Germany), D. Lightfoot (University of Melbourne, Australia), S. Chappell (Veterinary Laboratory Agency, Weybridge, United Kingdom), W. Wannett (RIVM, Bilthoven, The Netherlands) for kindly providing Salmonella serovar Paratyphi B strains.

FOOTNOTES
* Corresponding author. Mailing address: Bundesinstitut für Risikobewertung, National Salmonella Reference Laboratory, Diedersdorfer Weg 1, D-12277 Berlin. Phone: (49 30) 8412 2233. Fax: (49 30) 8412 2953. E-mail:
r.helmuth{at}bfr.bund.de.


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Journal of Clinical Microbiology, September 2003, p. 4292-4297, Vol. 41, No. 9
0095-1137/03/$08.00+0 DOI: 10.1128/JCM.41.9.4292-4297.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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