JOURNAL OF CLINICAL MICROBIOLOGY, Nov. 2000, p. 4180–4185
0095-1137/00/$04.0010
Copyright © 2000, American Society for Microbiology. All Rights Reserved.
Vol. 38, No. 11
Evaluation of PCR-Based Methods for Discrimination of Francisella
Species and Subspecies and Development of a Specific PCR
That Distinguishes the Two Major Subspecies of
Francisella tularensis
ANDERS JOHANSSON,1,2,3 ASHRAF IBRAHIM,4 INGELA GÖRANSSON,2 ULLA ERIKSSON,2
D. GURYCOVA,5 JILL E. CLARRIDGE III,6 AND ANDERS SJÖSTEDT2,3*
Received 10 April 2000/Returned for modification 12 July 2000/Accepted 23 August 2000
Previous studies have demonstrated that the four subspecies of the human pathogen Francisella tularensis,
despite showing marked variations in their virulence for mammals and originating from different regions in the
Northern Hemisphere, display a very close phylogenetic relationship. This property has hampered the development of generally applicable typing methods. To overcome this problem, we evaluated the use of PCR for
discrimination of the subspecies using various forms of long arbitrary primers or primers specific for repetitive
extragenic palindromic sequences (REP) or enterobacterial repetitive intragenic consensus (ERIC) sequences.
Patterns generated by use of REP, ERIC, or long arbitrary primers allowed differentiation at the species level
and of the four subspecies of F. tularensis. With each of these three methods, similar or identical clustering of
strains was found, and groups of strains of different geographical origins or differing in virulence showed
distinct patterns. The discriminatory indices of the methods varied from 0.57 to 0.65; thus, the patterns were
not sufficiently discriminatory to distinguish individual strains. The sequence of a fragment generated by
amplification with an arbitrary primer was determined, and a region showing interstrain heterogeneity was
identified. Specific primers were designed, and a PCR was developed that distinguished strains of F. tularensis
subsp. holarctica from strains of other F. tularensis subspecies, including strains of the highly virulent F. tularensis subsp. tularensis. Notably, one European isolate showed the genetic pattern typical of the highly virulent
F. tularensis subsp. tularensis, generally believed to exist only in North America. It is proposed that a combination of the specific PCR together with one method generating subspecies-specific patterns is suitable as a
rapid and relatively simple strategy for discrimination of Francisella species and subspecies.
Francisella tularensis is one of two recognized species of the
genus Francisella, and almost all knowledge of the genus originates from work on this species. It is a virulent, facultative
intracellular bacterium and the etiological agent of tularemia,
a disease found in rodents, lagomorphs, and humans. The
bacterium is widely distributed in nature and has been isolated
from about 250 wildlife species (20), many of which can transmit disease to humans. Tularemia is acquired by direct contact
with infected animals, through contaminated water or food, or
from vectors such as biting insects or ticks. Airborne transmission also occurs, especially during processing of agricultural
products. The disease is often epidemic, both in humans and in
animals, and clinical manifestations depend on the type of
reservoir involved and the means of transmission. F. tularensis
is found throughout the Northern Hemisphere, and large outbreaks have been reported in parts of the continental United
States, the southern part of the former USSR, and northern
Scandinavia.
F. philomiragia, the other species of the genus, is a rarely
isolated, opportunistic pathogen closely linked to water (9).
The genus also comprises endosymbionts of ticks, although
their exact phylogenetic positions are uncertain (15, 16, 24).
All of the four recognized subspecies of F. tularensis (9, 18,
20) have been associated with human tularemia, although they
differ drastically in virulence for humans and rabbits. Until
recently, isolates of F. tularensis subsp. tularensis were isolated
only in North America, but a mite-derived isolate from Slovakia showed the phenotypic characteristics of the subspecies (8).
F. tularensis subsp. tularensis isolates in North America are
often associated with tick-borne tularemia in lagomorphs and
are highly virulent for many mammalian species, including
primates. Before the advent of effective antibiotics, mortality in
humans ranged from 5 to 30% (3, 4). F. tularensis subsp. holarctica, found in Europe, North America, and Japan, is often
associated with lagomorphs in Scandinavia, continental Europe, and Japan, ground voles in the former USSR, and beavers and muskrats in North America. The subspecies causes a
less severe form of human illness, often a localized ulceroglandular disease. F. tularensis subsp. mediaasiatica is moderately
virulent for rabbits and humans and has been isolated only in
the Central Asian republics of the former USSR (18). In 1950,
the type strain of F. tularensis subsp. novicida was isolated from
a water sample in Utah, and isolates of the subspecies known
as “novicida-like” isolates have been linked to human disease
on a few occasions (1, 9). Isolates of this subspecies have less
* Corresponding author. Mailing address: Department of Clinical
Microbiology, Clinical Bacteriology, Umeå University, SE-901 85
Umeå, Sweden. Phone: 46 90 7851120. Fax: 46 90 7852225. E-mail:
anders.sjostedt@climi.umu.se.
4180
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Infectious Diseases1 and Clinical Bacteriology,3 Department of Clinical Microbiology, Umeå University, and Department of
Microbiology, Defence Research Establishment,2 Umeå, Sweden; Department of Biotechnology, Technical University
of Denmark, Lyngby, Denmark4; Department of Epidemiology, Komensky University, Bratislava,
Slovak Republic5; and Microbiology, Serology and Molecular Biology Section,
PALMS, Veterans Affairs Medical Center, Houston, Texas6
VOL. 38, 2000
PCR FOR TYPING OF FRANCISELLA SPECIES AND SUBSPECIES
4181
TABLE 1. Strains included in the study
Species or subspecies
F. tularensis subsp. holarctica
F. tularensis subsp. mediaasiatica
F. tularensis subsp. novicida
F. philomiragia
a
Strain
Human lymph node, 1926, Japan
Japan
City water supply, Helena, Mont.
North America
Norway
Sweden
Sweden
Sweden
Human ulcer, 1981, Sweden
Human ulcer, 1981, Sweden
Norway rat, 1988, Russia
Russia
Human blood, 1994, Sweden
Water, 1995, Sweden
Human ulcer, 1995, Sweden
Human ulcer, 1995, Sweden
Ticks, 1995, Czech Republic
Human ulcer, 1996, Sweden
Mites, 1988, Slovakia
Squirrel, Georgia
Tick, 1935, British Columbia, Canada
Canada
Human ulcer, 1941, Ohio
Hare, 1954, Nevada
Human lymph node, 1920, Utah
Mites, 1988, Slovakia
Hare, 1965, Central Asia
Water, 1950, Utah
Human blood, 1991, Texas
Human blood, 1995, Texas
Water, 1960, Utah
Muskrat, 1959, Utah
Human abscess, 1982, Sweden
United States
Human blood, 1979, Switzerland
FSC017
FSC024
FSC044
FSC056
FSC091
FSC093
FSC094
FSC095
FSC108
FSC109
FSC150
FSC155
FSC157
FSC170
FSC171
FSC172
FSC180
FSC188
FSC196
FSC033
FSC041
FSC042
FSC043
FSC054
FSC138
FSC198
FSC149
FSC040
FSC156
FSC159
FSC038
FSC144
FSC145
FSC153
FSC154
Other strain
designation(s)
Jap S2
Yerma
Helena
Eigelsbach
NO 9/15/51
Sv 43
Sv 121
Sv 219
SBL R45/81
SBL R74/81
250
ATCC 29684, LVS
CCUG 33270
SMI R8/95
T-17
SE-210/37
SnMF
Vavenby
Utter
Schu
Nevada 14
ATCC 6223
SE-219/38
120
ATCC 15482
Fx1
Fx2
ATCC 25017
ATCC 25015
CCUG 12603
CCUG 13404
Pattern in:
REP
ERIC
RAPD
Specific PCR
A
A
B
B
B
B
B
B
B
B
B
B
B
B
B
B
B
B
B
C
C
C
C
C
D
C
E
F
G
H
I
J
K
L
M
a
a
b
b
b
b
b
b
b
b
b
b
b
b
b
b
b
b
b
c
c
c
c
c
d
c
e
f
g
h
i
j
k
l
m
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
3
2
4
5
6
7
8
9
10
11
12
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
II
II
II
II
II
II
II
II
II
II
IIa
None
None
None
None
None
The strain displayed a slightly smaller 0.4-kb amplicon due to a gene truncation.
stringent growth requirements than representatives of the
other F. tularensis subspecies and can therefore be misidentified as belonging to other genera (1).
Isolates of the genus Francisella are readily distinguishable
based on a unique set of phenotypic characteristics, including
coccoidal morphology, gram negativity, acid but no gas production from a limited number of carbohydrates, a growth
requirement for cysteine, and a unique fatty acid composition
(20). However, within the genus and particularly within the
species F. tularensis, discrimination of strains is not performed
conveniently. Due to the contagiousness of Francisella isolates,
only limited work has been performed to develop typing methods based on cultivation. Such work is further restricted by the
nonfermentative nature of F. tularensis, limiting the number of
biochemical tests available for biotyping. To this end, the development of techniques based on analyses of genomic variations is of special interest, since they can be done with killed
preparations of the bacterium.
Several molecular methods have been successfully used to
discriminate the Francisella species but not the subspecies (5,
11). Repetitive extragenic palindromic sequence (REP)-PCR
has been applied to specifically identifying strains of F. tularensis subsp. novicida, but patterns from F. tularensis subsp.
holarctica and F. tularensis subsp. tularensis strains were found
to be similar (1). A one-base variability in the 16S rRNA sequences of F. tularensis subsp. tularensis and F. tularensis subsp.
holarctica has been demonstrated, and on this basis, a PCR
that differentiated the two subspecies was developed (5). However, there is not sufficient sequence information available to
corroborate that there is a consistency at this position among
all isolates of each subspecies (5). A recent study investigated
PCR methods for the typing of F. tularensis subsp. holarctica
isolates, the majority of which originated from Spain (2). In the
present study, we evaluated if PCR-based methods are suitable
as generally applicable tools for discrimination of species and
subspecies within the genus Francisella.
MATERIALS AND METHODS
Bacteria, media, and growth conditions. The bacterial strains used in this study
are listed in Table 1. The strains belong to the Francisella Strain Collection,
which contains more than 200 Francisella strains (5). Each strain has been given
a strain collection number, indicated in Table 1. Strains were grown for 3 days at
37°C on modified Thayer-Martin agar plates (19) in 5% CO2 (GasPak; Becton
Dickinson, Paramus, N.J.). Cell suspensions of virulent Francisella strains in
saline, at a concentration of ;109 cells/ml, were heat killed at 65°C for 2 h.
Debris was removed by centrifugation at 12,000 3 g for 5 min. Supernatants were
collected and then stored at 220°C until used.
PCR template preparation. In an initial evaluation, DNA from bacteria was
extracted using a modification (12) of a technique based on the binding of DNA
to uniform glass beads (Bio 101, La Jolla, Calif.) in the presence of the chaotropic nuclease inhibitor guanidine isothiocyanate. This method has been previously shown to be superior to three other methods for the extraction of DNA
from F. tularensis (21). In an initial evaluation of the REP-PCR and enterobacterial repetitive intragenic consensus sequence (ERIC)-PCR protocols, the usefulness of these DNA preparations as DNA templates was compared to that of
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F. tularensis subsp. tularensis
Source
4182
JOHANSSON ET AL.
59-GCCTTAATAGTATGCATACGATT
T G T G
C TG
T
T
amplified a distinct PCR product from each F. tularensis strain. The PCR product, approximately 0.7 kb, showed one of two distinct sizes depending on the
strain used as the DNA template, with FSC043 exhibiting the larger fragment.
The fragment was isolated from a 1.5% SeaKem GTG agarose gel (FMC BioProducts, Rockland, Maine) and was purified by use of a GenElute agarose spin
column (Supelco, Bellafonte, Pa.). The fragment was ligated into vector
pGEM-T according to the instructions of the manufacturer (Promega Corp.,
Madison, Wis.) After transformation of Escherichia coli DH5a, recombinant
clones were identified by blue-white color screening; plasmid DNA was isolated
by the Wizard Plus miniprep procedure (Promega). Inserts were sequenced using
pUC/M13 forward and reverse primers and the Big Dye terminator cycle sequencing ready reaction kit (PE Applied Biosystems, Stockholm, Sweden). The
sequence was analyzed using an ABI 377 sequencer (PE Applied Biosystems).
Based on the sequence of the 0.7-kb amplicon derived from FSC043, specific
primers were designed. A 0.4-kb fragment was amplified from seven strains
representing the various Francisella species (FSC024, FSC033, FSC040, FSC056,
FSC144, FSC149, and FSC155), and the sequence was determined. Based on the
sequence, primers C1 (59TCCGGTTGGATAGGTGTTGGATT) and C4 (59G
CGCGGATAATTTAAATTTCTCATA) were designed. These primers, yielding an amplicon of approximately 0.3 kb that included the variable region, were
used in a multiplex PCR together with the F. tularensis-specific primers, TUL4435 and TUL4-863. The latter primers generate a 0.4-kb fragment of the gene
encoding a 17-kDa lipoprotein shown previously to be useful for the identification of F. tularensis (13, 21, 22).
The multiplex PCR was performed with a reaction mixture containing 1 ml of
bacterial supernatant, 0.8 mM each primer, 1 U of DyNAzyme polymerase (Finnzymes OY, Espoo, Finland), and 200 mM each dNTP (Finnzymes OY) in a final
volume of 25 ml. After denaturation at 94°C for 5 min, 30 cycles of amplification
were performed according to the following protocol: denaturation at 94°C for
30 s, primer annealing at 66°C for 30 s, and primer extension at 72°C for 30 s.
After a final extension at 72°C for 5 min, each reaction mixture was subjected to
electrophoresis with 3% NuSieve 3:1 agarose gel (FMC BioProducts). After
ethidium bromide staining, the DNA products were visualized with UV light.
Nucleotide sequence accession numbers. The 0.7-kb sequence from strain
FSC043 (Schu) has been assigned GenBank accession number AF240631. The
GenBank accession numbers of the 0.4-kb fragments are AF247690, (FSC024),
AF247689 (FSC033), AF247688 (FSC040), AF247687 (FSC056), AF247686
(FSC144), AF247685 (FSC149), and AF247642 (FSC155).
RESULTS
ERIC-PCR and REP-PCR. Amplification using REP-PCR
revealed similar but distinguishable patterns from strains of
each of the three subspecies, F. tularensis subsp. holarctica (19
representatives), F. tularensis subsp. mediaasiatica (1 represen-
FIG. 1. PCR amplification of DNA from various Francisella strains using the
REP1R-I and REP2-I primers. Samples represent F. tularensis subsp. tularensis
strains (FSC138, FSC043, FSC041, and FSC198) (lanes 1 to 4), F. tularensis
subsp. holarctica strains (FSC196, FSC155, FSC150, FSC108, and FSC157)
(lanes 5 to 9), an F. tularensis subsp. mediaasiatica strain (FSC149) (lane 10), an
F. tularensis subsp. holarctica strain from Japan (FSC024) (lane 11), F. tularensis
subsp. novicida strains (FSC040 and FSC156) (lanes 12 and 13), and an F.
philomiragia strain (FSC 144) (lane 14). Strain designations are indicated in
Table 1. Lane N, water used as a negative control. Lane M, molecular markers
(sizes in base pairs).
tative), and F. tularensis subsp. tularensis (7 representatives),
whereas patterns from strains of F. tularensis subsp. novicida
(3 representatives) and strains of the species F. philomiragia
(5 representatives) were unique for each strain. A sample of
strains representing each of the species and subspecies is
shown in Fig. 1. Clearly visible bands ranged from approximately 0.2 to 4.0 kb. Patterns from the seven isolates of F. tularensis subsp. tularensis were discernible from patterns of the
other subspecies and were characterized by prominent bands
of approximately 4.0 and 1.0 kb. Notably, FSC198, a Slovakian
isolate derived from a mite and reported to show the biochemical characteristics and virulence typical of F. tularensis subsp.
tularensis strains (8), also showed this pattern, thereby confirming the first isolation of this subspecies outside North America.
The attenuated type strain of the subspecies, ATCC 6223
(FSC138), also demonstrated the typical pattern but with a
minor variation in the sizes of the 0.9- and 3.0-kb bands. PCR
patterns from F. tularensis subsp. holarctica strains were distinguished by a prominent 1.6-kb band and the absence of a
1.2-kb band. Patterns from the F. tularensis subsp. holarctica
strains were identical, with the exception of those from the
Japanese strains. The pattern from the F. tularensis subsp.
mediaasiatica strain was distinct from those of the other strains
but was similar to patterns from F. tularensis subsp. tularensis
strains. A summary of the various REP patterns is given in
Table 1.
PCR amplification by use of ERIC primers corroborated the
clustering of strains observed with REP-PCR, although the
patterns were slightly less complex (data not shown). The visualized bands ranged in size from approximately 0.2 to 3.0 kb.
A summary of the various ERIC patterns is shown in Table 1.
A calculation of the discriminatory power (10) of REP-PCR or
ERIC-PCR for typing of the species F. tularensis revealed a
discriminatory index of 0.65.
Although the F. tularensis strains displayed very similar patterns after ERIC-PCR or REP-PCR, the patterns were distinct
from each of 15 patterns resulting from the amplification of
DNA of other clinically relevant species using the same primers (data not shown). Thus, the analyses indicated that patterns
generated by the F. tularensis isolates were unique and readily
distinguished from those of other clinically relevant species.
ERIC and REP sequences have been reported to be present
in a multitude of bacterial species (28), but there is no information confirming their presence in Francisella genomes. To
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heat-killed whole-cell preparations. No significant differences were noted. In
subsequent experiments, a supernatant of a heat-killed Francisella suspension
was therefore used as a template.
Primer sequences. The previously described primer pairs REP1R-I–REP2-I
and ERIC1R-ERIC2 were used (28). REP consensus primers contained inosine
at ambiguous positions. A number of 20-mer oligonucleotides were designed at
random, and their usefulness alone or in combination as PCR primers was
evaluated using a modified protocol for long-primer randomly amplified polymorphic DNA (RAPD) analysis (LP-RAPD) (6). The primer yielding the pattern with the highest resolution was selected: 59-GGTAATCGATGAATAAA
TGA (LP-RAPD2). Oligonucleotides were purchased from Pharmacia Biotech,
Uppsala, Sweden.
REP, ERIC, and LP-RAPD amplification. A 15-ml mixture containing 1 ml of
bacterial supernatant, 3 mM MgCl2, and buffer 4 (Advanced Biotechnologies
Inc., London, United Kingdom) was heated to 94°C for 10 min. A 10-ml mixture
containing (all concentrations per final volume) 2 mM each REP primer, 0.8 mM
each ERIC primer, or 0.8 mM LP-RAPD2 primer, 200 mM each deoxynucleoside
triphosphate (dNTP) (Pharmacia Biotech), and 1 U of Taq DNA polymerase
(Advanced Biotechnologies) was added to the 15-ml mixture. After an additional
denaturation at 94°C (REP and ERIC, 10 min; LP-RAPD, 7 min), the reaction
mixtures were subjected to 40 cycles of amplification. Each cycle consisted of
denaturation at 94°C for 60 s, annealing (REP, 42°C, 120 s; ERIC, 52°C, 60 s;
LP-RAPD, 42°C, 60 s), and extension at 72°C for 5 min. The PCR amplification
was terminated after the samples were incubated at 72°C for 10 min (REP and
ERIC) or 7 min (LP-RAPD). Three microliters of each reaction mixture was
loaded onto a 1.5% agarose gel and subjected to electrophoresis, and the amplified products were visualized with UV light after ethidium bromide staining.
Pattern analysis. PCR patterns were analyzed by visual examination by two
individuals. Patterns were regarded as distinct if they repeatedly showed a oneband difference.
Specific PCR amplification. The degenerate primer
J. CLIN. MICROBIOL.
VOL. 38, 2000
PCR FOR TYPING OF FRANCISELLA SPECIES AND SUBSPECIES
this end, we searched for such sequences in the genome of
strain Schu S4 (unpublished data). More than 98% of the
genome has been sequenced. No sequences with similarities to
REP or ERIC sequences could be identified. Thus, it is likely
that the banding patterns obtained from PCR amplification
with primers complementary to consensus motifs of REP or
ERIC sequences were based on annealing to other types of
sequences present in the Francisella genome. It has been reported that ERIC primers can generate relatively complex
patterns from eukaryotic and prokaryotic genomes despite a
lack of the specific target sequences (7).
PCR amplification with random primers. Previously, it was
reported that the use of random primers containing 18 to 24
nucleotides results in patterns after PCR-based amplification
that are more reproducible than those seen after amplification
with shorter random primers (6, 7). PCR amplification based
on different combinations of six such random primers was
assessed. Only one of the primers gave an amplification pattern
of sufficient complexity. The numbers of amplicons observed
were similar to the numbers obtained by use of ERIC or REP
primers (Fig. 2). The sizes of the amplicons ranged from 0.4 to
5.0 kb. Strains of F. tularensis subsp. tularensis displayed two
distinct patterns, one for the avirulent type strain of the subspecies, ATCC 6223 (FSC138), and one for the other six
strains. Again, the recently isolated representative from Europe (FSC198) also showed the pattern typical of F. tularensis
subsp. tularensis. Patterns from F. tularensis subsp. holarctica
strains, including the Japanese ones, were all identical and
clearly discernible from those of other subspecies. A distinct
pattern was observed for the representative of F. tularensis
subsp. mediaasiatica. Patterns from strains of F. philomiragia
(five representatives) and F. tularensis subsp. novicida (three
representatives) were each unique (Fig. 2; not all strains are
shown). Clustering of the strains was thus very similar with
LP-RAPD–PCR, ERIC-PCR, and REP-PCR (Table 1). The
discriminatory index of LP-RAPD–PCR was 0.57. A summary
of the various LP-RAPD patterns is given in Table 1.
All the banding patterns produced by REP, ERIC, or LPRAPD from each of the studied strains were reproducible, but
variations in the relative intensities of the bands were observed
(data not shown). REP, ERIC, and LP-RAPD reactions were
performed at least four times on each strain using templates
prepared on three different occasions.
Amplification with F. tularensis-specific primers. Sequencing of a fragment obtained after amplification with a random
primer revealed that a 30-bp sequence was found only in some
F. tularensis genomes. By designing F. tularensis-specific primers specific for the region adjacent to this sequence, amplicons
of variable length were obtained after PCR. Amplification using these primers was combined with a previously described
PCR specific for a gene encoding a 17-kDa lipoprotein conserved in all investigated strains of F. tularensis (22).
The multiplex PCR was designed to generate bands of approximately 0.4 and 0.3 kb (Fig. 3). From all F. tularensis
strains, except for the F. tularensis subsp. novicida-like strain
FSC159, a fragment of the expected size, 0.4 kb, was amplified
from the 17-kDa lipoprotein gene. From strain FSC159, a
slightly smaller fragment resulted due to a gene truncation
(data not shown). No amplicons were amplified from F. philomiragia strains by use of the primers specific for the 17-kDa
lipoprotein gene. From all F. tularensis subsp. holarctica strains,
including the two strains from Japan, a 300-bp amplicon was
amplified, whereas amplification from all strains of F. tularensis
subsp. tularensis and F. tularensis subsp. mediaasiatica and the
reference strain of F. tularensis subsp. novicida (FSC 040;
ATCC 15482) generated a 330-bp band. The two F. tularensis
subsp. novicida-like strains (FSC156 and FSC159) both showed
very faint 330-bp bands. A summary of the two patterns for the
strains is shown in Table 1.
DISCUSSION
The family Francisellaceae, a member of the g-subclass of
Proteobacteria, comprises closely related organisms within the
single genus Francisella (20). Previous studies have revealed
that the two recognized species, F. tularensis and F. philomiragia, show a 16S rRNA sequence similarity of $98% (5). The
close relationship has hampered the development of generally
applicable methods for discrimination of F. tularensis subspecies that differ in virulence or geographical origins. PCR amplification of REP and ERIC sequences often enables discrimination of bacterial isolates (17, 26), and it has even been
proposed that PCR fingerprinting can be used to elucidate the
genetic basis of phenotypic variability for certain species (26).
FIG. 3. Multiplex PCR amplification using F. tularensis-specific primers. Samples represent F. tularensis subsp. tularensis strains (FSC138, FSC043, FSC041,
and FSC198) (lanes 1 to 4), F. tularensis subsp. holarctica strains (FSC196,
FSC155, FSC150, FSC108, and FSC157) (lanes 5 to 9), an F. tularensis subsp.
mediaasiatica strain (FSC149) (lane 10), an F. tularensis subsp. holarctica strain
from Japan (FSC024) (lane 11), F. tularensis subsp. novicida strains (FSC040 and
FSC156) (lanes 12 and 13), and an F. philomiragia strain (FSC144) (lane 14).
Strain designations are indicated in Table 1. Lane N, water used as a negative
control. Lane M, molecular markers (sizes in base pairs).
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FIG. 2. PCR amplification of DNA from various Francisella strains using the
LP-RAPD2 primer. Samples represent F. tularensis subsp. tularensis strains
(FSC138, FSC043, FSC041, and FSC198) (lanes 1 to 4), F. tularensis subsp.
holarctica strains (FSC196, FSC155, FSC150, FSC108, and FSC157) (lanes 5 to
9), an F. tularensis subsp. mediaasiatica strain (FSC149) (lane 10), an F. tularensis
subsp. holarctica strain from Japan (FSC024) (lane 11), F. tularensis subsp.
novicida strains (FSC040 and FSC156) (lanes 12 and 13), and an F. philomiragia
strain (FSC144) (lane 14). Strain designations are indicated in Table 1. Lane N,
water used as a negative control. Lane M, molecular markers (sizes in base
pairs).
4183
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JOHANSSON ET AL.
F. tularensis subsp. tularensis are readily distinguished from
those of the other subspecies.
A recently published study (2) aimed to identify methods
that allowed discrimination of isolates of F. tularensis subsp.
holarctica, the majority of which originated from Spain. The
study evaluated PCR methods based on REP, ERIC, M13, or
T3-T7 primers. It was reported that the discriminatory indices
(10) of the methods ranged from 0.14 (REP) to 0.65 (T3-T7),
below the recommended value of .0.95 for a method considered suitable for routine typing of individual isolates (23). Our
finding of discriminatory indices of #0.65 correlates well with
those of the Spanish study and shows that the investigated
methods do not meet the required minimum criterion for typing of individual isolates. The test population is also an important factor to consider when assessing discriminatory power;
the population should reflect the diversity of the particular
species as much as possible (23). We believe that our collection
of strains, which included strains from the various regions of
the Northern Hemisphere where tularemia is endemic and all
four subspecies of F. tularensis, is more representative than the
Spanish collection for an analysis of the discriminatory indices
of the PCR-based methods. It should be noted that even when
the results of the four methods analyzed by de la PuenteRedondo et al. (2) were combined, the discriminatory index
was 0.90, still below the recommended value of .0.95 (23).
Moreover, considering that REP and ERIC sequences do not
exist in the Francisella genome, probably all of the methods
used are variants of RAPD-PCR, a technique with moderate
or low reproducibility (14, 25–27). Although we consider that
the investigated methods have discriminatory powers too low
to be useful for typing of strains, this conclusion does not
exclude, however, the use of one or several of the methods by
reference laboratories because a positive finding, i.e., strains
showing distinct patterns, may still be of epidemiological interest.
In summary, the relative simplicity and discriminatory power
of several of the investigated methods make them useful for
clinical laboratories as tools for rapidly identifying and discriminating Francisella species and subspecies but not for discriminating individual strains.
ACKNOWLEDGMENTS
Grant support was obtained from the Swedish Medical Research
Council (no. 9485); Samverkansnämnden Norra Sjukvårdsregionen,
Umeå, Sweden; and the Medical Faculty, Umeå University, Umeå,
Sweden.
REFERENCES
1. Clarridge, J. E., III, T. J. Raich, A. Sjöstedt, G. Sandström, R. O. Darouiche,
R. M. Shawar, P. R. Georghiou, C. Osting, and L. Vo. 1996. Characterization
of two unusual clinically significant Francisella strains. J. Clin. Microbiol. 34:
1995–2000.
2. de La Puente-Redondo, V. A., N. G. del Blanco, C. B. Gutierrez-Martin, F. J.
Garcia-Pena, and E. F. Ferri. 2000. Comparison of different PCR approaches for typing of Francisella tularensis strains. J. Clin. Microbiol. 38:
1016–1022.
3. Dienst, J., F. T. 1963. Tularemia—a perusal of three hundred thirty-nine
cases. J. La. State Med. Soc. 115:114–127.
4. Evans, M. E., D. W. Gregory, W. Schaffner, and Z. A. McGee. 1985. Tularemia: a 30-year experience with 88 cases. Medicine (Baltimore) 64:251–269.
5. Forsman, M., G. Sandström, and A. Sjöstedt. 1994. Analysis of 16S ribosomal DNA sequences of Francisella strains and utilization for determination of the phylogeny of the genus and for identification of strains by PCR.
Int. J. Syst. Bacteriol. 44:38–46.
6. Gillings, M., and M. Holley. 1997. Amplification of anonymous DNA fragments using pairs of long primers generates reproducible DNA fingerprints
that are sensitive to genetic variation. Electrophoresis 18:1512–1518.
7. Gillings, M., and M. Holley. 1997. Repetitive element PCR fingerprinting
(rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC)
primers is not necessarily directed at ERIC elements. Lett. Appl. Microbiol.
25:17–21.
Downloaded from http://jcm.asm.org/ on January 24, 2016 by guest
In addition, amplification of bacterial genomes using arbitrary
primers has been successfully used for the same purpose.
In the present study, all the protocols based on PCR amplification using specific or arbitrary primers allowed differentiation of strains at the species level. Moreover, the PCR analyses based on the use of ERIC, REP, or long arbitrary primers
yielded reproducible banding patterns of similar complexity
and allowed the differentiation of strains at the subspecies
level. We believe that the significance of this clustering was
strengthened by the facts that the fingerprints were reproduced
for a rather large number of strains, that each of the three
methods supported the same clustering of strains, and that the
clusters correlated with the geographical origins of the strains.
It was not totally unexpected that the patterns of the subspecies were rather similar, considering that previous analyses of
16S rRNA sequences (5) and recent analyses of three complete
23S rRNA gene sequences, representing three out of the four
subspecies of F. tularensis, and seven partial sequences of gyrase B genes (unpublished data) showed them to be very similar and not suitable as a basis for the development of molecular typing methods discriminatory at the subspecies level.
Within all of the four subspecies, with the exception of
F. tularensis subsp. novicida, very similar or identical patterns
were generated. One notable exception was that F. tularensis
subsp. holarctica isolates from Japan were distinguished from
other isolates of the subspecies after amplification with REP or
ERIC primers. Japanese isolates are also distinguished by lower virulence in experimental animals than F. tularensis subsp.
tularensis and F. tularensis subsp. holarctica isolates from Europe and North America, and they cause a relatively mild form
of human disease. On this basis, a more detailed analysis of the
phenotypic and genotypic properties of Japanese isolates may
be warranted to determine whether they should comprise a
separate subspecies. Isolates of F. tularensis subsp. mediaasiatica are found only in some areas of the Central Asian republics of the former USSR, and only limited information is available regarding their characteristics. The isolates have been
considered to belong to a separate subspecies on the bases of
their ability to produce acid from glycerol and degrade ornithine and their low virulence in experimental models of tularemia. This subspecies differentiation was supported by the
observation that the isolates showed distinct patterns in each of
the three PCR-based methods.
In contrast to isolates of the other subspecies of F. tularensis,
F. tularensis subsp. tularensis isolates cause a life-threatening
disease, and this high virulence necessitates the availability of
methods for their rapid identification. It has long been accepted that isolates of the subspecies exist only in North America (8, 20). Notably, we found that the pattern obtained from a
Slovakian strain derived from a mite was identical to those
obtained from North American F. tularensis subsp. tularensis
strains, thus supporting the recently reported finding that,
based on biochemical characteristics and virulence for rabbits,
this strain should be classified as a member of F. tularensis
subsp. tularensis. This situation is of concern for European
reference laboratories, since the highly contagious F. tularensis
strains always pose a risk that laboratory staff may acquire
tularemia. Although the presented specific PCR does not distinguish among F. tularensis subsp. tularensis, F. tularensis subsp.
novicida, and F. tularensis subsp. mediaasiatica strains, it nevertheless could provide useful clinical information by rapidly
identifying the highly virulent strains of F. tularensis subsp.
tularensis, especially in North America, where these strains, in
contrast to strains of the other two subspecies, are relatively
common. Moreover, when the specific PCR is combined with
one of the described arbitrary-primer PCR methods, isolates of
J. CLIN. MICROBIOL.
VOL. 38, 2000
PCR FOR TYPING OF FRANCISELLA SPECIES AND SUBSPECIES
Francisella tularensis. Int. J. Syst. Bacteriol. 33:872–874.
19. Sandström, G., A. Tärnvik, H. Wolf-Watz, and S. Löfgren. 1984. Antigen
from Francisella tularensis: nonidentity between determinants participating
in cell-mediated and humoral reactions. Infect. Immun. 45:101–106.
20. Sjöstedt, A. Family XVII. Francisellaceae, genus I. Francisella. In D. J. Brenner (ed.), Bergey’s manual of systematic bacteriology, in press. SpringerVerlag, New York, N.Y.
21. Sjöstedt, A., U. Eriksson, L. Berglund, and A. Tärnvik. 1997. Detection of
Francisella tularensis in ulcers of patients with tularemia by PCR. J. Clin.
Microbiol. 35:1045–1048.
22. Sjöstedt, A., K. Kuoppa, T. Johansson, and G. Sandström. 1992. The 17 kDa
lipoprotein and encoding gene of Francisella tularensis LVS are conserved in
strains of F. tularensis. Microb. Pathog. 13:243–249.
23. Struelens, M. J., and the Members of the European Study Group on Epidemiological Markers (ESGEM) of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). 1996. Consensus guidelines
for appropriate use and evaluation of microbial epidemiologic typing systems. Clin. Microbiol. Infect. 2:2–11.
24. Suitor, E. C., Jr., and E. Weiss. 1961. Isolation of a rickettsialike microorganism (Wohlbachia persica n. sp.) from Argas persicus (Oken). J. Infect. Dis.
108:95–106.
25. Tyler, K. D., G. Wang, S. D. Tyler, and W. M. Johnson. 1997. Factors
affecting reliability and reproducibility of amplification-based DNA fingerprinting of representative bacterial pathogens. J. Clin. Microbiol. 35:339–
346.
26. van Belkum, A. 1994. DNA fingerprinting of medically important microorganisms by use of PCR. Clin. Microbiol. Rev. 7:174–184.
27. van Belkum, A., J. Kluytmans, W. van Leeuwen, R. Bax, W. Quint, E. Peters,
A. Fluit, C. Vandenbroucke-Grauls, A. van den Brule, H. Koeleman, et al.
1995. Multicenter evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains. J. Clin. Microbiol. 33:1537–1547.
28. Versalovic, J., T. Koeuth, and J. R. Lupski. 1991. Distribution of repetitive
DNA sequences in eubacteria and application to fingerprinting of bacterial
genomes. Nucleic Acids Res. 19:6823–6831.
Downloaded from http://jcm.asm.org/ on January 24, 2016 by guest
8. Gurycova, D. 1998. First isolation of Francisella tularensis subsp. tularensis in
Europe. Eur. J. Epidemiol. 14:797–802.
9. Hollis, D. G., R. E. Weaver, A. G. Steigerwalt, J. D. Wenger, C. W. Moss, and
D. J. Brenner. 1989. Francisella philomiragia comb. nov. (formerly Yersinia
philomiragia) and Francisella tularensis biogroup novicida (formerly Francisella novicida) associated with human disease. J. Clin. Microbiol. 27:1601–
1608.
10. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity.
J. Clin. Microbiol. 26:2465–2466.
11. Ibrahim, A., P. Gerner-Smidt, and A. Sjöstedt. 1996. Amplification and
restriction endonuclease digestion of a large fragment of genes coding for
rRNA as a rapid method for discrimination of closely related pathogenic
bacteria. J. Clin. Microbiol. 34:2894–2896.
12. Ibrahim, A., L. Norlander, A. Macellaro, and A. Sjöstedt. 1997. Specific
detection of Coxiella burnetii through partial amplification of 23S rDNA.
Eur. J. Epidemiol. 13:329–334.
13. Johansson, A., L. Berglund, U. Eriksson, I. Göransson, R. Wollin, M. Forsman, A. Tärnvik, and A. Sjöstedt. 2000. Comparative analysis of PCR versus
culture for diagnosis of ulceroglandular tularemia. J. Clin. Microbiol. 38:
22–26.
14. Meunier, J. R., and P. A. Grimont. 1993. Factors affecting reproducibility of
random amplified polymorphic DNA fingerprinting. Res. Microbiol. 144:
373–379.
15. Niebylski, M. L., M. G. Peacock, E. R. Fischer, S. F. Porcella, and T. G.
Schwan. 1997. Characterization of an endosymbiont infecting wood ticks,
Dermacentor andersoni, as a member of the genus Francisella. Appl. Environ.
Microbiol. 63:3933–3940.
16. Noda, H., U. G. Munderloh, and T. J. Kurtti. 1997. Endosymbionts of ticks
and their relationship to Wolbachia spp. and tick-borne pathogens of humans
and animals. Appl. Environ. Microbiol. 63:3926–3932.
17. Olive, D. M., and P. Bean. 1999. Principles and applications of methods for
DNA-based typing of microbial organisms. J. Clin. Microbiol. 37:1661–1669.
18. Olsufjev, N. G., and I. S. Meshcheryakova. 1983. Subspecific taxonomy of
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