Previous Article | Next Article ![]()
Journal of Clinical Microbiology, October 2005, p. 5355-5358, Vol. 43, No. 10
0095-1137/05/$08.00+0 doi:10.1128/JCM.43.10.5355-5358.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Anna Magnusson,1,3,4
Jørgen Prag,2 and
Anders Johansson1,3*
Department of NBC-Analysis, Swedish Defence Research Agency, Umeå, Sweden,1 Department of Clinical Microbiology, Viborg Hospital, Viborg, Denmark,2 Department of Clinical Microbiology, Infectious Diseases, Umeå University, Umeå, Sweden,3 Department of Infectious Diseases, Sundsvall Hospital, Sundsvall, Sweden4
Received 14 March 2005/ Returned for modification 30 April 2005/ Accepted 10 July 2005
|
|
|---|
|
|
|---|
2% (4). Human or animal cases of type A tularemia have not been identified in Europe. Type B tularemia is endemic to countries of the Northern Hemisphere and is rarely life threatening but may lead to long-lasting complications (e.g., lymph node suppuration). Due to its virulence and potential for aerosol infection, F. tularensis has received attention as a feared biological threat agent (15). Because of a high risk of airborne laboratory-acquired infection, fastidious growth, and low biochemical reactivity, the bacterium poses a challenge to microbiological laboratories (1, 14). Using traditional bacteriological methods, identification of F. tularensis is difficult and time-consuming. The few biochemical reactions that are available for typing to the subspecies level may be inconclusive, and definite distinction of type A and type B organisms requires virulence tests in animals (14, 18). Therefore, there is a need for more rapid and accurate diagnostic methods as well as for assays capable of distinguishing type A and type B tularemia. Here, we demonstrate the utility of DNA-based methods for unambiguous identification and high-resolution characterization of F. tularensis and describe for the first time culture recovery of this pathogen in Denmark.
In July 2003, at the island Fur in Limfjorden, Denmark, a tick was observed on the left thigh of an 8-year-old boy and removed 1 day later. On day 3, the boy was brought to a general practitioner with high fever, generalized body aches, tenderness in his left groin, and an erythematic skin reaction at the bite wound. On suspicion of borreliosis, oral treatment with penicillin V at 500 mg x 3 for 6 days was instituted. On day 5, the patient was hospitalized due to persistent high fever and a painful left inguinal lymph node enlargement, and on day 9, progression of lymphadenopathy was noted and antibiotic treatment was changed to oral dicloxacillin at 250 mg x 3, assuming a staphylococcal infection. By day 13 the boy still had fever, lymph nodes continued to enlarge, and there was a surrounding erythema. The bite wound was 1 cm in diameter without signs of healing. On day 17, ulceroglandular tularemia was suspected and a lymph node was surgically removed. Tissue specimens were put in saline and sent for laboratory analysis. Treatment was changed to intravenous gentamicin at 150 mg daily for 10 days, and the patient recovered quickly.
A section of lymph node tissue was used for bacterial culture. On day 21, growth of small gram-negative rods was detected in the aerobic part of a medium denoted semisolid agar plus pepsin blood plus thioglycolate, product no. 1133, which is further detailed at the website of Statens Seruminstitut, Copenhagen, Denmark (http://www.ssi.dk/sw965.asp). On day 23, bacterial growth occurred on chocolate blood agar (Statens Serum Institute). The same day, F. tularensis DNA was detected in lymph node specimens by PCR amplification of rRNA and the gene lpnA encoding a 17-kDa lipoprotein (17). The bacterial strain was sent to a biosafety level 3 laboratory, and F. tularensis was identified by PCR and a specific agglutination reaction (18). Histological examination of excised lymph node tissue showed a necrotizing granulomatous reaction consistent with tularemia. A patient blood sample obtained on day 16 was subsequently found positive in an agglutination test for tularemia (Statens Serum Institut).
We applied a novel real-time PCR assay with melting point analysis of the obtained PCR amplicon to the Danish strain and control strains of F. tularensis. The assay detects strains of F. tularensis subsp. holarctica (type B) by identification of a 30-bp deletion unique to the subspecies at a genomic locus designated Ft-M19 (11). F. tularensis DNA was isolated as described previously (9, 17), and triplicate samples of each strain were amplified using 0.8 µM of each of the primers 5'-CCAGTACAAACTCAATTTGGTTATCATC-3' and 5'-GTTTCAGAATTCATTTTTGTCCGTAA-3' and the SYBR green PCR master mix (Applied Biosystems) in a total reaction volume of 25 µl. An initial denaturation at 50°C for 2 min and 95°C for 10 min was followed by 40 cycles of 95°C for 15 s and 60°C for 60 s on an iCycler (Bio-Rad Laboratories, Hercules, CA). Reference strains (F. tularensis subsp. tularensis strain SCHU S4 and F. tularensis subsp. holarctica, live vaccine strain) and negative controls (water) were included in all PCR runs. After the final cycle, melting point analysis was performed with 0.5°C temperature increments, using software version 3.0A (Bio-Rad Laboratories). The novel real-time PCR assay was confirmed to successfully amplify DNA from a test panel of F. tularensis strains with a worldwide geographical origin. Each strain was tested at least twice. Strains of F. tularensis subsp. holarctica (type B; n = 22) consistently showed melting points of 73.5 to 74.0°C, whereas strains of F. tularensis subsp. tularensis (type A; n = 10) and F. tularensis subsp. novicida (n = 2) showed melting points of 71.5 to 72.5°C, and strains of F. tularensis subsp. mediasiatica (n = 3), showed melting points of 72.0 to 73.0°C (Fig. 1). In each PCR analysis, melting peaks corresponding to different subspecies were easily distinguished, with the exception of F. tularensis subsp. tularensis and F. tularensis subsp. novicida, which often coincided. The Danish strain was identified as F. tularensis subsp. holarctica (type B) based on melting point analysis of the real-time PCR product (Fig. 1). Results were confirmed by GeneScan analysis of marker Ft-M19 performed as described previously (11) and using the primers 5'-AGGCGGAGATCTAGGAACCTTT-3' and 5'-AGCCCAAGCTGACTAAAATCTTT-3' to amplify DNA of the test panel strains. All strains of F. tularensis subsp. holarctica (type B), including the Danish strain, showed PCR amplicon sizes at Ft-M19 of 220 bp. Strains of F. tularensis subsp. tularensis (type A), F. tularensis subsp. mediasiatica, and F. tularensis subsp. novicida showed sizes of 250 bp. The results are in agreement with a deletion of 30 bp at the genomic locus Ft-M19 in all type B strains, as was recently verified in a broader analysis of 192 F. tularensis strains (11). Two direct nucleotide repeats in the F. tularensis genome flank the deletion site at Ft-M19, and it is possible that these repeats mediated the deletion by homologous recombination of the two repeats in an ancestor to all strains of F. tularensis subsp. holarctica (type B) (Fig. 1). We recently showed that several other similar subspecies-specific excisions of sequence located between two direct repeats have occurred during the evolution of F. tularensis subsp. holarctica (19). The PCR amplicon melting point of F. tularensis subsp. mediasiatica strains was intermediate to that of type A and type B strains and is likely explained by two point mutations (A
G) at the targeted genomic locus (Fig. 1). The difference in nucleotide composition causes a shift in melting point as compared to F. tularensis subsp. tularensis and F. tularensis subsp. novicida. Complete nucleotide sequences at Ft-M19 have previously been assigned accession no. AF247642, AF247685 to AF247690, and AF524865 in the GenBank database.
![]() View larger version (28K): [in a new window] |
FIG. 1. Real-time PCR assay diagnostic of F. tularensis subsp. holarctica (type B). (A) The peaks show the melting point (Tm) of amplified DNA from the Danish strain and reference strains of F. tularensis subsp. holarctica (live vaccine strain, type B; Tm, 73.5°C), F. tularensis subsp. tularensis (strain SCHU S4, type A; Tm, 72.0°C), F. tularensis subsp. novicida (strain Utah 112; Tm, 72.0°C), and F. tularensis subsp. mediasiatica (strain FSC149; Tm, 72.5°C). The rate of change of the relative fluorescence units with time, d(RFU)/dT, is indicated on the y axis, and the temperature is indicated on the x axis. (B) Alignment of the nucleotide sequences that were amplified by real-time PCR. Arrows indicate forward and reverse primers. The difference in melting point between strains is explained by a 30-bp deletion at the amplified genomic locus in the F. tularensis subsp. holarctica strains and by the nucleotide substitutions in the F. tularensis subsp. mediasiatica strain. The deletion is flanked by two direct repeats.
|
Multiple-locus variable-number tandem repeat analysis (MLVA), a highly discriminatory typing system based on detection of variable numbers of tandem repeats in the F. tularensis genome (11), was applied to investigate the genetic relationship of the Danish strain to other Eurasian strains. Six genomic loci (Ft-M3, Ft-M6, Ft-M20, Ft-M21, Ft-M22, and Ft-M24), previously found polymorphic among type B strains, were assayed in 16 of the 22 F. tularensis subsp. holarctica strains that were analyzed by the real-time PCR assay. Briefly, primers flanking each locus amplified DNA from each strain, and PCR fragments were size determined as described previously (11), using a 377XL DNA sequencer (PE Applied Biosystems). Primers were fluorescence labeled with 6-carboxyfluorescein or 6-carboxytetramethylrhodamine, and filter set A was applied. Typing data were analyzed using Bionumerics v. 3.5 (Applied-Maths, Saint-Martens-Latem, Belgium), the categorical coefficient, and the unweighted pair-group with arithmetic means algorithm.
Using MLVA, the most variable marker (Ft-M3) showed nine different PCR fragment sizes among 16 strains (Fig. 2). The observed size variation represents a difference in repeat copy numbers at the marker. Other markers showed less variability, with only two or three PCR fragment sizes being observed among the strains. Cluster analysis assigned the 16 strains into 15 genotypes (Fig. 2). The tree topology obtained indicated a correlation of geographical origin of a strain and its genotype. Clustering of the Danish strain with strains from Norway was consistent using the unweighted pair-group with arithmetic means (Fig. 2) or the neighbor-joining algorithm, and the obtained overall tree topologies were highly similar (not shown). Although this clustering is intriguing, analysis of larger numbers of strains will be required to make more firm conclusions regarding a geographic relationship. The Danish strain was genetically similar to several F. tularensis strains of European origin, which all share a relatively low variability at genomic loci exhibiting variable numbers of tandem repeats. Thereby, the present analysis supports a previous suggestion that F. tularensis subsp. holarctica is an evolutionarily young F. tularensis lineage with limited genetic diversity even at highly mutable sequences assayed by MLVA (11).
![]() View larger version (28K): [in a new window] |
FIG. 2. Cluster analysis of 16 strains of F. tularensis subsp. holarctica using the unweighted pair-group with arithmetic means algorithm and based upon differences in repeat copy numbers at six genomic loci exhibiting variable numbers of tandem repeats. An F. tularensis strain originating in Japan was used as the outgroup. Similarity using the categorical coefficient is indicated on the scale bar.
|
DNA detection in human specimens has proven a valuable tool for tularemia diagnosis in an acute setting (using wound swabs) as well as in retrospective analysis of archived samples (formalin-fixed tissues) (10, 13, 17). In this study, we showed a fresh lymph node specimen to be useful for detection of F. tularensis. This is in concordance with previous case reports on lymph node aspirates, even after the initiation of relevant antibiotic treatment (2, 5). In conclusion, our study demonstrates that new DNA-based methods for laboratory diagnosis and high-resolution characterization of F. tularensis make diagnostic work more rapid, more safe for laboratory personal, and more precise.
This work was supported by funding from the Swedish Medical Research Council project no. 9485; the Medical Faculty, Umeå University; the County Council of Västernorrland; and the Swedish MoD, project no. A4854.
Present address: National Center for Antimicrobials and Infection Control, Statens Serum Institut, Copenhagen, Denmark. ![]()
|
|
|---|
This article has been cited by other articles:
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»