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Iron-Modified Blood Culture Media Allow for the Rapid Diagnosis and Isolation of the Slow-Growing Pathogen Francisella tularensis. Microbiol Spectr 2022; 10:e0241522. [PMID: 36190401 PMCID: PMC9603284 DOI: 10.1128/spectrum.02415-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The life-threatening disease tularemia is caused by Francisella tularensis, an intracellular Gram-negative bacterial pathogen. Due to the high mortality rates of the disease, as well as the low respiratory infectious dose, F. tularensis is categorized as a Tier 1 bioterror agent. The identification and isolation from clinical blood cultures of F. tularensis are complicated by its slow growth. Iron was shown to be one of the limiting nutrients required for F. tularensis metabolism and growth. Bacterial growth was shown to be restricted or enhanced in the absence or addition of iron. In this study, we tested the beneficial effect of enhanced iron concentrations on expediting F. tularensis blood culture diagnostics. Accordingly, bacterial growth rates in blood cultures with or without Fe2+ supplementation were evaluated. Growth quantification by direct CFU counts demonstrated significant improvement of growth rates of up to 6 orders of magnitude in Fe2+-supplemented media compared to the corresponding nonmodified cultures. Fe2+ supplementation significantly shortened incubation periods for successful diagnosis and isolation of F. tularensis by up to 92 h. This was achieved in a variety of blood culture types in spite of a low initial bacterial inoculum representative of low levels of bacteremia. These improvements were demonstrated with culture of either Francisella tularensis subsp. tularensis or subsp. holarctica in all examined commercial blood culture types routinely used in a clinical setup. Finally, essential downstream identification assays, such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), immunofluorescence, or antibiotic susceptibility tests, were not affected in the presence of Fe2+. To conclude, supplementing blood cultures with Fe2+ enables a significant shortening of incubation times for F. tularensis diagnosis, without affecting subsequent identification or isolation assays. IMPORTANCE In this study, we evaluated bacterial growth rates of Francisella tularensis strains in iron (Fe)-enriched blood cultures as a means of improving and accelerating bacterial growth. The shortening of the culturing time should facilitate rapid pathogen detection and isolation, positively impacting clinical diagnosis and enabling prompt onset of efficient therapy.
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Virulence of Francisella tularensis Subspecies holarctica Biovar japonica and Phenotypic Change during Serial Passages on Artificial Media. Microorganisms 2020; 8:microorganisms8121881. [PMID: 33261098 PMCID: PMC7760542 DOI: 10.3390/microorganisms8121881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023] Open
Abstract
Francisella tularensis (F. tularensis) is the etiological agent of the zoonotic disease tularemia. F. tularensis subspecies holarctica biovar japonica has rarely been isolated in Japan and is considered to have moderate virulence, although the biological properties of fresh isolates have not been analyzed in detail. Here, we analyzed the virulence of two strains of F. tularensis subspecies holarctica biovar japonica (NVF1 and KU-1) and their phenotypic stability during serial passages in Eugon chocolate agar (ECA) and Chamberlain's chemically defined medium (CDM) based agar (CDMA). C57BL/6 mice intradermally inoculated with 101 colony-forming units of NVF1 or KU-1 died within 9 days, with a median time to death of 7.5 and 7 days, respectively. Both NVF1 and KU-1 strains passaged on ECA 10 times had comparable virulence prior to passaging, whereas strains passaged on ECA 20 times and on CDMA 50 times were attenuated. Attenuated strains had decreased viability in 0.01% H2O2 and lower intracellular growth rates, suggesting both properties are important for F. tularensis virulence. Additionally, passage on ECA of the KU-1 strains altered lipopolysaccharide antigenicity and bacterial susceptibility to β-lactam antibiotics. Our data demonstrate F. tularensis strain virulence in Japan and contribute to understanding phenotypic differences between natural and laboratory environments.
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Busch A, Homeier-Bachmann T, Abdel-Glil MY, Hackbart A, Hotzel H, Tomaso H. Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis. PLoS Negl Trop Dis 2020; 14:e0008018. [PMID: 32991594 PMCID: PMC7523947 DOI: 10.1371/journal.pntd.0008018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/27/2019] [Indexed: 12/31/2022] Open
Abstract
By combining a reference-independent SNP analysis and average nucleotide identity (ANI) with affinity propagation clustering (APC), we developed a significantly improved methodology allowing resolving phylogenetic relationships, based on objective criteria. These bioinformatics tools can be used as a general ruler to determine phylogenetic relationships and clustering of bacteria, exemplary done with Francisella (F.) tularensis. Molecular epidemiology of F. tularensis is currently assessed mostly based on laboratory methods and molecular analysis. The high evolutionary stability and the clonal nature makes Francisella ideal for subtyping with single nucleotide polymorphisms (SNPs). Sequencing and real-time PCR can be used to validate the SNP analysis. We investigate whole-genome sequences of 155 F. tularensis subsp. holarctica isolates. Phylogenetic testing was based on SNPs and average nucleotide identity (ANI) as reference independent, alignment-free methods taking small-scale and large-scale differences within the genomes into account. Especially the whole genome SNP analysis with kSNP3.0 allowed deciphering quite subtle signals of systematic differences in molecular variation. Affinity propagation clustering (APC) resulted in three clusters showing the known clades B.4, B.6, and B.12. These data correlated with the results of real-time PCR assays targeting canSNPs loci. Additionally, we detected two subtle sub-clusters. SplitsTree was used with standard-setting using the aligned SNPs from Parsnps. Together APC, HierBAPS, and SplitsTree enabled us to generate hypotheses about epidemiologic relationships between bacterial clusters and describing the distribution of isolates. Our data indicate that the choice of the typing technique can increase our understanding of the pathogenesis and transmission of diseases with the eventual for prevention. This is opening perspectives to be applied to other bacterial species. The data provide evidence that Germany might be the collision zone where the clade B.12, also known as the East European clade, overlaps with the clade B.6, also known as the Iberian clade. Described methods allow generating a new, more detailed perspective for F. tularensis subsp. holarctica phylogeny. These results may encourage to determine phylogenetic relationships and clustering of other bacteria the same way.
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Affiliation(s)
- Anne Busch
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- * E-mail:
| | - Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Mostafa Y. Abdel-Glil
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Anja Hackbart
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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Pilo P. Phylogenetic Lineages of Francisella tularensis in Animals. Front Cell Infect Microbiol 2018; 8:258. [PMID: 30109216 PMCID: PMC6079424 DOI: 10.3389/fcimb.2018.00258] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/11/2018] [Indexed: 12/24/2022] Open
Abstract
Tularemia is a zoonotic disease caused by the facultative intracellular bacterium Francisella tularensis. This microorganism can infect a plethora of animal species and its ecology is particularly complex. Much research was performed to understand its biology but many questions are still open, especially concerning the life cycle of this bacterium in the environment related to physical and biological parameters. Numerous animals are major hosts of F. tularensis but precise reservoir species are not yet well defined. Moreover, the exact range of species susceptible to tularemia is not clear and is complicated by the differences in virulence and ecology observed among the subspecies of F. tularensis. Indeed, different life cycles in nature, including the animal species concerned, were previously described for F. tularensis subsp. tularensis and F. tularensis subsp. holarctica. Recently, molecular techniques showing adequate discrimination between strains were developed, leading to the possibility to investigate links between phylogenetic lineages and infection in animals. New perspectives in research are now possible thanks to the information available and the simplicity of the molecular procedures. Current studies are unfolding the evolution of F. tularensis and these developments will lead to the elucidation of geographical and ecological differences observed by veterinarians, microbiologists and conservation biologists. However, systematic, coordinated collection of data and extensive sampling are important to efficiently assemble the findings of future research.
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Affiliation(s)
- Paola Pilo
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
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Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+"). PLoS One 2015; 10:e0123298. [PMID: 25856198 PMCID: PMC4391923 DOI: 10.1371/journal.pone.0123298] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/17/2015] [Indexed: 11/19/2022] Open
Abstract
The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.
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Reif KE, Palmer GH, Crowder DW, Ueti MW, Noh SM. Restriction of Francisella novicida genetic diversity during infection of the vector midgut. PLoS Pathog 2014; 10:e1004499. [PMID: 25392914 PMCID: PMC4231110 DOI: 10.1371/journal.ppat.1004499] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/02/2014] [Indexed: 11/26/2022] Open
Abstract
The genetic diversity of pathogens, and interactions between genotypes, can strongly influence pathogen phenotypes such as transmissibility and virulence. For vector-borne pathogens, both mammalian hosts and arthropod vectors may limit pathogen genotypic diversity (number of unique genotypes circulating in an area) by preventing infection or transmission of particular genotypes. Mammalian hosts often act as “ecological filters” for pathogen diversity, where novel variants are frequently eliminated because of stochastic events or fitness costs. However, whether vectors can serve a similar role in limiting pathogen diversity is less clear. Here we show using Francisella novicida and a natural tick vector of Francisella spp. (Dermacentor andersoni), that the tick vector acted as a stronger ecological filter for pathogen diversity compared to the mammalian host. When both mice and ticks were exposed to mixtures of F. novicida genotypes, significantly fewer genotypes co-colonized ticks compared to mice. In both ticks and mice, increased genotypic diversity negatively affected the recovery of available genotypes. Competition among genotypes contributed to the reduction of diversity during infection of the tick midgut, as genotypes not recovered from tick midguts during mixed genotype infections were recovered from tick midguts during individual genotype infection. Mediated by stochastic and selective forces, pathogen genotype diversity was markedly reduced in the tick. We incorporated our experimental results into a model to demonstrate how vector population dynamics, especially vector-to-host ratio, strongly affected pathogen genotypic diversity in a population over time. Understanding pathogen genotypic population dynamics will aid in identification of the variables that most strongly affect pathogen transmission and disease ecology. Co-infection, the presence of multiple genotypes of the same pathogen species within an infected individual, is common. Genotype diversity, defined as the number of unique genotypes, and the interaction between genotypes, can strongly influence virulence and pathogen transmission. Understanding how genotypic diversity affects transmission of pathogens that naturally cycle among disparate hosts, such as vector-borne pathogens, is especially important as the capacity of the host and vector to sustain genotypic diversity may differ. To address this, we exposed Dermacentor andersoni ticks, via infected mice, to variably diverse populations of Francisella novicida genotypes. Interestingly, we found that ticks served as greater ecological filters for genotypic diversity compared to mice. This loss in genotypic diversity was due to both stochastic and selective forces. Based on these data and a model, we determined that high numbers of ticks in an environment support high genotypic diversity, while genotypic diversity will be lost rapidly in environments with low tick numbers. Together, these results provide evidence that vector population dynamics, vector-to-host ratios, and competition among pathogen genotypes play critical roles in the maintenance of pathogen genotypic diversity.
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Affiliation(s)
- Kathryn E. Reif
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
- * E-mail:
| | - Guy H. Palmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
| | - David W. Crowder
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
| | - Massaro W. Ueti
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
| | - Susan M. Noh
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, and Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, United States of America
- Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
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Ahn YY, Lee DS, Burd H, Blank W, Kapatral V. Metabolic network analysis-based identification of antimicrobial drug targets in category A bioterrorism agents. PLoS One 2014; 9:e85195. [PMID: 24454817 PMCID: PMC3893172 DOI: 10.1371/journal.pone.0085195] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 11/29/2013] [Indexed: 11/29/2022] Open
Abstract
The 2001 anthrax mail attacks in the United States demonstrated the potential threat of bioterrorism, hence driving the need to develop sophisticated treatment and diagnostic protocols to counter biological warfare. Here, by performing flux balance analyses on the fully-annotated metabolic networks of multiple, whole genome-sequenced bacterial strains, we have identified a large number of metabolic enzymes as potential drug targets for each of the three Category A-designated bioterrorism agents including Bacillus anthracis, Francisella tularensis and Yersinia pestis. Nine metabolic enzymes- belonging to the coenzyme A, folate, phosphatidyl-ethanolamine and nucleic acid pathways common to all strains across the three distinct genera were identified as targets. Antimicrobial agents against some of these enzymes are available. Thus, a combination of cross species-specific antibiotics and common antimicrobials against shared targets may represent a useful combinatorial therapeutic approach against all Category A bioterrorism agents.
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Affiliation(s)
- Yong-Yeol Ahn
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Deok-Sun Lee
- Department of Natural Medical Sciences and Department of Physics, Inha University, Incheon, Korea
| | - Henry Burd
- Igenbio.Inc, Chicago, Illinois, United States of America
| | - William Blank
- Igenbio.Inc, Chicago, Illinois, United States of America
| | - Vinayak Kapatral
- Igenbio.Inc, Chicago, Illinois, United States of America
- * E-mail:
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Halkilahti J, Haukka K, Siitonen A. Genotyping of outbreak-associated and sporadic Yersinia pseudotuberculosis strains by novel multilocus variable-number tandem repeat analysis (MLVA). J Microbiol Methods 2013; 95:245-50. [DOI: 10.1016/j.mimet.2013.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/09/2013] [Accepted: 09/09/2013] [Indexed: 01/03/2023]
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Dieppedale J, Gesbert G, Ramond E, Chhuon C, Dubail I, Dupuis M, Guerrera IC, Charbit A. Possible links between stress defense and the tricarboxylic acid (TCA) cycle in Francisella pathogenesis. Mol Cell Proteomics 2013; 12:2278-92. [PMID: 23669032 PMCID: PMC3734585 DOI: 10.1074/mcp.m112.024794] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 05/01/2013] [Indexed: 12/16/2022] Open
Abstract
Francisella tularensis is a highly infectious bacterium causing the zoonotic disease tularemia. In vivo, this facultative intracellular bacterium survives and replicates mainly in the cytoplasm of infected cells. We have recently identified a genetic locus, designated moxR that is important for stress resistance and intramacrophage survival of F. tularensis. In the present work, we used tandem affinity purification coupled to mass spectrometry to identify in vivo interacting partners of three proteins encoded by this locus: the MoxR-like ATPase (FTL_0200), and two proteins containing motifs predicted to be involved in protein-protein interactions, bearing von Willebrand A (FTL_0201) and tetratricopeptide (FTL_0205) motifs. The three proteins were designated here for simplification, MoxR, VWA1, and TPR1, respectively. MoxR interacted with 31 proteins, including various enzymes. VWA1 interacted with fewer proteins, but these included the E2 component of 2-oxoglutarate dehydrogenase and TPR1. The protein TPR1 interacted with one hundred proteins, including the E1 and E2 subunits of both oxoglutarate and pyruvate dehydrogenase enzyme complexes, and their common E3 subunit. Remarkably, chromosomal deletion of either moxR or tpr1 impaired pyruvate dehydrogenase and oxoglutarate dehydrogenase activities, supporting the hypothesis of a functional role for the interaction of MoxR and TPR1 with these complexes. Altogether, this work highlights possible links between stress resistance and metabolism in F. tularensis virulence.
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Affiliation(s)
- Jennifer Dieppedale
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Gael Gesbert
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Elodie Ramond
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Cerina Chhuon
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- ¶Plateau Protéome Necker, PPN, IFR94, Université Paris-Descartes, Faculté de Médecine René Descartes, Paris 75015 France
| | - Iharilalao Dubail
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Marion Dupuis
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Ida Chiara Guerrera
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- ¶Plateau Protéome Necker, PPN, IFR94, Université Paris-Descartes, Faculté de Médecine René Descartes, Paris 75015 France
| | - Alain Charbit
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
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Müller W, Hotzel H, Otto P, Karger A, Bettin B, Bocklisch H, Braune S, Eskens U, Hörmansdorfer S, Konrad R, Nesseler A, Peters M, Runge M, Schmoock G, Schwarz BA, Sting R, Myrtennäs K, Karlsson E, Forsman M, Tomaso H. German Francisella tularensis isolates from European brown hares (Lepus europaeus) reveal genetic and phenotypic diversity. BMC Microbiol 2013; 13:61. [PMID: 23517149 PMCID: PMC3663675 DOI: 10.1186/1471-2180-13-61] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 03/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tularemia is a zoonotic disease caused by Francisella tularensis that has been found in many different vertebrates. In Germany most human infections are caused by contact with infected European brown hares (Lepus europaeus). The aim of this study was to elucidate the epidemiology of tularemia in hares using phenotypic and genotypic characteristics of F. tularensis. RESULTS Cultivation of F. tularensis subsp. holarctica bacteria from organ material was successful in 31 of 52 hares that had a positive PCR result targeting the Ft-M19 locus. 17 isolates were sensitive to erythromycin and 14 were resistant. Analysis of VNTR loci (Ft-M3, Ft-M6 and Ft-M24), INDELs (Ftind33, Ftind38, Ftind49, RD23) and SNPs (B.17, B.18, B.19, and B.20) was shown to be useful to investigate the genetic relatedness of Francisella strains in this set of strains. The 14 erythromycin resistant isolates were assigned to clade B.I, and 16 erythromycin sensitive isolates to clade B.IV and one isolate was found to belong to clade B.II. MALDI-TOF mass spectrometry (MS) was useful to discriminate strains to the subspecies level. CONCLUSIONS F. tularensis seems to be a re-emerging pathogen in Germany. The pathogen can easily be identified using PCR assays. Isolates can also be identified within one hour using MALDI-TOF MS in laboratories where specific PCR assays are not established. Further analysis of strains requires genotyping tools. The results from this study indicate a geographical segregation of the phylogenetic clade B.I and B.IV, where B.I strains localize primarily within eastern Germany and B.IV strains within western Germany. This phylogeographical pattern coincides with the distribution of biovar I (erythromycin sensitive) and biovar II (erythromycin resistance) strains. When time and costs are limiting parameters small numbers of isolates can be analysed using PCR assays combined with DNA sequencing with a focus on genetic loci that are most likely discriminatory among strains found in a specific area. In perspective, whole genome data will have to be investigated especially when terrorist attack strains need to be tracked to their genetic and geographical sources.
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Affiliation(s)
- Wolfgang Müller
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96A, Jena D-07743, Germany
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11
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Turingan RS, Thomann HU, Zolotova A, Tan E, Selden RF. Rapid focused sequencing: a multiplexed assay for simultaneous detection and strain typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One 2013; 8:e56093. [PMID: 23418519 PMCID: PMC3572037 DOI: 10.1371/journal.pone.0056093] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 01/08/2013] [Indexed: 01/29/2023] Open
Abstract
Background The intentional release of Bacillus anthracis in the United States in 2001 has heightened concern about the use of pathogenic microorganisms in bioterrorism attacks. Many of the deadliest bacteria, including the Class A Select Agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis, are highly infectious via the pulmonary route when released in aerosolized form. Hence, rapid, sensitive, and reliable methods for detection of these biothreats and characterization of their potential impact on the exposed population are of critical importance to initiate and support rapid military, public health, and clinical responses. Methodology/Principal Findings We have developed microfluidic multiplexed PCR and sequencing assays based on the simultaneous interrogation of three pathogens per assay and ten loci per pathogen. Microfluidic separation of amplified fluorescently labeled fragments generated characteristic electrophoretic signatures for identification of each agent. The three sets of primers allowed significant strain typing and discrimination from non-pathogenic closely-related species and environmental background strains based on amplicon sizes alone. Furthermore, sequencing of the 10 amplicons per pathogen, termed “Rapid Focused Sequencing,” allowed an even greater degree of strain discrimination and, in some cases, can be used to determine virulence. Both amplification and sequencing assays were performed in microfluidic biochips developed for fast thermal cycling and requiring 7 µL per reaction. The 30-plex sequencing assay resulted in genotypic resolution of 84 representative strains belonging to each of the three biothreat species. Conclusions/Significance The microfluidic multiplexed assays allowed identification and strain differentiation of the biothreat agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis and clear discrimination from closely-related species and several environmental background strains. The assays may be extended to detect a large number of pathogens, are applicable to the evaluation of both environmental and clinical samples, and have the potential to be applied in military, public health, and clinical diagnostic settings.
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Affiliation(s)
| | | | - Anna Zolotova
- NetBio, Waltham, Massachusetts, United States of America
| | - Eugene Tan
- NetBio, Waltham, Massachusetts, United States of America
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Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia. J Bacteriol 2013; 194:6965-6. [PMID: 23209222 DOI: 10.1128/jb.01040-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of Francisella and is well-characterized.
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Duncan D, Vogler A, Wolcott M, Li F, Sarovich D, Birdsell D, Watson L, Hall T, Sampath R, Housley R, Blyn L, Hofstadler S, Ecker D, Keim P, Wagner D, Eshoo M. Identification and typing of Francisella tularensis
with a highly automated genotyping assay. Lett Appl Microbiol 2012; 56:128-34. [DOI: 10.1111/lam.12022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/24/2012] [Accepted: 10/29/2012] [Indexed: 01/21/2023]
Affiliation(s)
- D.D. Duncan
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - A.J. Vogler
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - M.J. Wolcott
- United States Army Medical Research Institute of Infectious Diseases; Fort Detrick MD USA
| | - F. Li
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - D.S. Sarovich
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - D.N. Birdsell
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - L.M. Watson
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - T.A. Hall
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - R. Sampath
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - R. Housley
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - L.B. Blyn
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | | | - D.J. Ecker
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - P. Keim
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - D.M. Wagner
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - M.W. Eshoo
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
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Whitehouse CA, Kesterson KE, Duncan DD, Eshoo MW, Wolcott M. Identification and characterization of Francisella species from natural warm springs in Utah, USA. Lett Appl Microbiol 2012; 54:313-24. [PMID: 22283482 DOI: 10.1111/j.1472-765x.2012.03214.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To characterize Francisella isolated from two natural warm springs in Utah and compare them to a strain isolated from a patient with probable exposure to one of the springs in 2001. METHODS AND RESULTS A total of 39 presumptive Francisella isolates were obtained from two springs, Wasatch Hot Spring and Hobo Warm Spring, just north of Salt Lake City, Utah. All isolates were characterized by a combination of biochemical and molecular analyses, including novel PCR/electrospray ionization-mass spectrometry (ESI-MS) typing assays. Thirty-one were identified as F. philomiragia, while the remaining eight were identified as F. tularensis ssp. novicida. Phylogenetic analysis of the 16S rRNA sequences revealed 27 isolates, which clustered with F. philomiragia, albeit into two distinct clades. The remaining isolates clustered along with other F. tularensis strains including the Utah clinical isolate. Testing with the PCR/ESI-MS assays confirmed the identities of the isolates, but both yielded DNA signatures distinct from that of the clinical isolate. CONCLUSION We were successful in isolating several Francisella strains from natural warm springs; however, none appeared to genetically match the original 2001 clinical isolate. SIGNIFICANCE AND IMPACT OF THE STUDY This work highlights the presence of viable, potentially pathogenic Franscisella species living in the unique environmental niche of natural warm springs.
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Affiliation(s)
- C A Whitehouse
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA.
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15
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Brevik ØJ, Ottem KF, Nylund A. Multiple-locus, variable number of tandem repeat analysis (MLVA) of the fish-pathogen Francisella noatunensis. BMC Vet Res 2011; 7:5. [PMID: 21261955 PMCID: PMC3037875 DOI: 10.1186/1746-6148-7-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 01/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since Francisella noatunensis was first isolated from cultured Atlantic cod in 2004, it has emerged as a global fish pathogen causing disease in both warm and cold water species. Outbreaks of francisellosis occur in several important cultured fish species making a correct management of this disease a matter of major importance. Currently there are no vaccines or treatments available. A strain typing system for use in studies of F. noatunensis epizootics would be an important tool for disease management. However, the high genetic similarity within the Francisella spp. makes strain typing difficult, but such typing of the related human pathogen Francisella tullarensis has been performed successfully by targeting loci with higher genetic variation than the traditional signature sequences. These loci are known as Variable Numbers of Tandem Repeat (VNTR). The aim of this study is to identify possible useful VNTRs in the genome of F. noatunensis. RESULTS Seven polymorphic VNTR loci were identified in the preliminary genome sequence of F. noatunensis ssp. noatunensis GM2212 isolate. These VNTR-loci were sequenced in F. noatunensis isolates collected from Atlantic cod (Gadus morhua) from Norway (n = 21), Three-line grunt (Parapristipoma trilineatum) from Japan (n = 1), Tilapia (Oreochromis spp.) from Indonesia (n = 3) and Atlantic salmon (Salmo salar) from Chile (n = 1). The Norwegian isolates presented in this study show both nine allelic profiles and clades, and that the majority of the farmed isolates belong in two clades only, while the allelic profiles from wild cod are unique. CONCLUSIONS VNTRs can be used to separate isolates belonging to both subspecies of F. noatunensis. Low allelic diversity in F. noatunensis isolates from outbreaks in cod culture compared to isolates wild cod, indicate that transmission of these isolates may be a result of human activity. The sequence based MLVA system presented in this study should provide a good starting point for further development of a genotyping system that can be used in studies of epizootics and disease management of francisellosis.
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Affiliation(s)
- Øyvind J Brevik
- Department of Biology, University of Bergen, Post box 7800, N-5020 Bergen, Norway
| | - Karl F Ottem
- Department of Biology, University of Bergen, Post box 7800, N-5020 Bergen, Norway
| | - Are Nylund
- Department of Biology, University of Bergen, Post box 7800, N-5020 Bergen, Norway
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16
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Petersen JM, Molins CR. Subpopulations of Francisella tularensis ssp. tularensis and holarctica: identification and associated epidemiology. Future Microbiol 2010; 5:649-61. [PMID: 20353304 DOI: 10.2217/fmb.10.17] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tularemia is primarily caused by two subspecies of Francisella tularensis worldwide, ssp. tularensis (type A) and ssp. holarctica (type B), which were originally delineated by phenotypic differences. Application of molecular typing methods to investigate population structure of F. tularensis has confirmed that categorizing the two subspecies via phenotypic characteristics corresponds with genotypic differentiation. In addition, genotyping methods have demonstrated that both subspecies, type A and type B, can be further distinguished into subpopulations and, in some cases, biological relevance has been ascribed to these identified subpopulations. Genetic variation among both type A and type B subpopulations has been shown to correlate with differences in geographic distribution and has also been coupled to distinct ecological niches, animal hosts and replication foci. Among type A subpopulations, strain variation is linked to differing clinical manifestations in humans and virulence in mice. This article will highlight our current understanding of F. tularensis subpopulations, including methods for their detection, their observed epidemiologic differences, implications for public health and basic research programs, as well as future challenges yet to be solved.
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Affiliation(s)
- Jeannine M Petersen
- Centers for Disease Control & Prevention, Division of Vector-Borne Diseases, Bacterial Diseases Branch, 3150 Rampart Road, Fort Collins, CO 80521, USA.
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17
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Rydén P, Sjöstedt A, Johansson A. Effects of climate change on tularaemia disease activity in Sweden. Glob Health Action 2009; 2. [PMID: 20052432 PMCID: PMC2799307 DOI: 10.3402/gha.v2i0.2063] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 09/17/2009] [Accepted: 09/17/2009] [Indexed: 11/14/2022] Open
Abstract
Tularaemia is a vector-borne infectious disease. A large majority of cases transmitted to humans by blood-feeding arthropods occur during the summer season and is linked to increased temperatures. Therefore, the effect of climate change is likely to have an effect on tularaemia transmission patterns in highly endemic areas of Sweden. In this report, we use simulated climate change scenario data and empirical data of temperatures critical to tularaemia transmission to forecast tularaemia outbreak activity. The five high-endemic counties: Dalarna, Gävleborg, Norrbotten, Värmland and Örebro represent only 14.6% of the total population of Sweden, but have recorded 40.1–81.1% of the number of annual human tularaemia in Sweden from 1997 until 2008. We project here earlier starts and a later termination of future tularaemia outbreaks for the time period 2010–2100. For five localised outbreak areas; Gagnef (Dalarna), Ljusdal (Gävleborg), Harads (Norrbotten), Karlstad (Värmland) and Örebro municipality (Örebro), the climate scenario suggests an approximately 2°C increase in monthly average summer temperatures leading to increases in outbreak durations ranging from 3.5 weeks (Harads) to 6.6 weeks (Karlstad) between 2010 and 2100. In contrast, an analysis of precipitation scenarios indicates fairly stable projected levels of precipitation during the summer months. Thus, there should not be an increased abundance of late summer mosquitoes that are believed to be main vectors for transmission to humans in these areas. In conclusion, the results indicate that the future climate changes will lead to an increased burden of tularaemia in high-endemic areas of Sweden during the coming decades.
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Affiliation(s)
- Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
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18
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Escudero R, Elía M, Sáez-Nieto JA, Menéndez V, Toledo A, Royo G, Rodríguez-Vargas M, Whipp MJ, Gil H, Jado I, Anda P. A possible novel Francisella genomic species isolated from blood and urine of a patient with severe illness. Clin Microbiol Infect 2009; 16:1026-30. [PMID: 19709068 DOI: 10.1111/j.1469-0691.2009.03029.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two identical isolates were recovered in pure culture from the blood and urine of a patient suffering from severe septicaemia associated with obstructive pyelonephritis secondary to lithotripsy. Preliminary phenotypic and genotypic characterizations based on serological, biochemical and sequence analyses following PCR amplification of selected gene regions indicate that this organism represents a potential new Francisella genomic species.
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Affiliation(s)
- R Escudero
- Laboratorio de Espiroquetas y Patógenos Especiales, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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19
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Goethert HK, Saviet B, Telford SR. Metapopulation structure for perpetuation of Francisella tularensis tularensis. BMC Microbiol 2009; 9:147. [PMID: 19627585 PMCID: PMC2723117 DOI: 10.1186/1471-2180-9-147] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 07/23/2009] [Indexed: 11/12/2022] Open
Abstract
Background Outbreaks of Type A tularemia due to Francisella tularensis tularensis are typically sporadic and unstable, greatly hindering identification of the determinants of perpetuation and human risk. Martha's Vineyard, Massachusetts has experienced an outbreak of Type A tularemia which has persisted for 9 years. This unique situation has allowed us to conduct long-term eco-epidemiologic studies there. Our hypothesis is that the agent of Type A tularemia is perpetuated as a metapopulation, with many small isolated natural foci of transmission. During times of increased transmission, the foci would merge and a larger scale epizootic would occur, with greater likelihood that humans become exposed. Methods We sampled questing dog ticks from two natural foci on the island and tested them for tularemia DNA. We determined whether the force of transmission differed between the two foci. In addition, we examined the population structure of F. tularensis from ticks by variable number tandem repeat (VNTR) analysis, which allowed estimates of diversity, linkage disequilibrium, and eBURST analysis. Results The prevalence of tularemia DNA in ticks from our two field sites was markedly different: one site was stable over the course of the study yielding as many as 5.6% positive ticks. In contrast, infected ticks from the comparison site markedly increased in prevalence, from 0.4% in 2003 to 3.9% in 2006. Using 4 VNTR loci, we documented 75 different haplotypes (diversity = 0.91). eBURST analysis indicates that the stable site was essentially clonal, but the comparison site contained multiple unrelated lineages. The general bacterial population is evolving clonally (multilocus disequilibrium) and the bacteria in the two sites are reproductively isolated. Conclusion Even within an isolated island, tularemia natural foci that are no more than 15 km apart are uniquely segregated. One of our sites has stable transmission and the other is emergent. The population structure at the stable site is that of a clonal complex of circulating bacteria, whereas the emerging focus is likely to be derived from multiple founders. We conclude that the agent of tularemia may perpetuate in small stable natural foci and that new foci emerge as a result of spillover from such stable sites.
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Affiliation(s)
- Heidi K Goethert
- Division of Infectious Diseases, Tufts Cummings School of Veterinary Medicine, 200 Westboro Rd, North Grafton, MA 01536, USA.
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20
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Goethert HK, Telford SR. Nonrandom distribution of vector ticks (Dermacentor variabilis) infected by Francisella tularensis. PLoS Pathog 2009; 5:e1000319. [PMID: 19247435 PMCID: PMC2642597 DOI: 10.1371/journal.ppat.1000319] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 01/30/2009] [Indexed: 11/25/2022] Open
Abstract
The island of Martha's Vineyard, Massachusetts, is the site of a sustained outbreak of tularemia due to Francisella tularensis tularensis. Dog ticks, Dermacentor variabilis, appear to be critical in the perpetuation of the agent there. Tularemia has long been characterized as an agent of natural focality, stably persisting in characteristic sites of transmission, but this suggestion has never been rigorously tested. Accordingly, we sought to identify a natural focus of transmission of the agent of tularemia by mapping the distribution of PCR-positive ticks. From 2004 to 2007, questing D. variabilis were collected from 85 individual waypoints along a 1.5 km transect in a field site on Martha's Vineyard. The positions of PCR-positive ticks were then mapped using ArcGIS. Cluster analysis identified an area approximately 290 meters in diameter, 9 waypoints, that was significantly more likely to yield PCR-positive ticks (relative risk 3.3, P = 0.001) than the rest of the field site. Genotyping of F. tularensis using variable number tandem repeat (VNTR) analysis on PCR-positive ticks yielded 13 different haplotypes, the vast majority of which was one dominant haplotype. Positive ticks collected in the cluster were 3.4 times (relative risk = 3.4, P<0.0001) more likely to have an uncommon haplotype than those collected elsewhere from the transect. We conclude that we have identified a microfocus where the agent of tularemia stably perpetuates and that this area is where genetic diversity is generated.
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Affiliation(s)
- Heidi K. Goethert
- Division of Infectious Diseases, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Sam R. Telford
- Division of Infectious Diseases, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
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21
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Zhang F, Liu W, Wu XM, Xin ZT, Zhao QM, Yang H, Cao WC. Detection of Francisella tularensis in ticks and identification of their genotypes using multiple-locus variable-number tandem repeat analysis. BMC Microbiol 2008; 8:152. [PMID: 18798995 PMCID: PMC2567983 DOI: 10.1186/1471-2180-8-152] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 09/17/2008] [Indexed: 11/28/2022] Open
Abstract
Background Tularemia was reported in China over 50 years ago, however, many epidemical characteristics remain unclear. In the present study, the prevalence of Francisella tularensis in ticks was investigated during an epidemiological surveillance in China and then we measured their genetic diversity by conducting multiple-locus variable- number tandem repeat analysis (MLVA). Results 1670 ticks from 2 endemic areas (Inner Mongolia Autonomous Region and Heilongjiang Province) and 2 non-endemic areas (Jilin and Fujian Provinces) were collected and tested for evidence of tularemia by nested PCR. The prevalence of Francisella tularensis in ticks averaged 1.98%. The positive rates were significantly different among tick species, with Dermacentor silvarum and Ixodes persulatus responsible for all positive numbers. All F. tularensis that were detected in ticks belonged to F. tularensis subsp. holarctica and MLVA disclosed genetic diversity. One subtype was identified in 17 of 33 positive tick samples in three different study areas. Another subtype belonging to F. tularensis subsp. holarctica genotype was described for the first time in the current study. Conclusion The study showed two tick species, D. silvarum and I. persulatus harboring the pathogen of tularemia in natural environment, indicating these two tick species might have a role in tularemia existence in China. MLVA results disclosed the genetic diversity F. tularensis and identified one genotype as the most prevalent among the investigated ticks in China.
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Affiliation(s)
- Fang Zhang
- Beijing Institute of Microbiology and Epidemiology, State Key Lab of Pathogen and Biosecurity, 20 Dong-Da-Jie Street, Fengtai District, Beijing 100071, PR China.
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22
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Fujita O, Uda A, Hotta A, Okutani A, Inoue S, Tanabayashi K, Yamada A. Genetic diversity of Francisella tularensis subspecies holarctica strains isolated in Japan. Microbiol Immunol 2008; 52:270-6. [PMID: 18557897 DOI: 10.1111/j.1348-0421.2008.00036.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently developed MLVA has high discriminatory power for the typing of individual strains or isolates of Francisella tularensis. In the present study, MLVA was applied to 33 Japanese F. tularensis subspecies holarctica strains to examine the genetic diversity of F. tularensis isolated. Among the seven VNTR loci analyzed, Ft-M2, Ft-M10, and Ft-M20 loci showed high genetic polymorphism in Japanese strains, whereas Ft-M3 was most variable in non-Japanese strains. These results provide novel extended information about the genomic diversity among the strains of F. tularensis ssp. holarctica distributed in Japan and enable determination of whether a given isolate is indigenous to Japan by examining these loci using MLVA.
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Affiliation(s)
- Osamu Fujita
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan.
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23
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Abstract
Analysis of bacterial genomes revealed a high percentage of DNA consisting of repeats, in which DNA motifs existed in multiple copies. Study of these DNA motifs has resulted in the development of variable number tandem repeat (VNTR) or multilocus variant-repeat analysis (MLVA) assays, which have shown to be valuable bacterial typing methods, especially in relation to disease outbreaks. The VNTR-based assay is based on direct PCR amplification of a specific locus, which is well defined. The range and polymorphism index of each locus can be calculated. This chapter describes the VNTR analysis of Neisseria meningitides-based on separation in low resolution media agarose, and VNTR analysis of Salmonella enterica subsp. enterica serovars Typhimurium-based on high resolution capillary electrophoresis.
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24
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Larsson P, Svensson K, Karlsson L, Guala D, Granberg M, Forsman M, Johanssont A. Canonical insertion-deletion markers for rapid DNA typing of Francisella tularensis. Emerg Infect Dis 2008; 13:1725-32. [PMID: 18217558 PMCID: PMC2874433 DOI: 10.3201/eid1311.070603] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By combining analysis of indel markers with multiple-locus variable-number tandem repeat
analysis, individual strains were identified. To develop effective and accurate typing of strains of Francisella
tularensis, a potent human pathogen and a putative bioterrorist agent, we
combined analysis of insertion-deletion (indel) markers with multiple-locus
variable-number tandem repeat analysis (MLVA). From 5 representative F.
tularensis genome sequences, 38 indel markers with canonical properties, i.e.,
capable of sorting strains into major genetic groups, were selected. To avoid markers with
a propensity for homoplasy, we used only those indels with 2 allelic variants and devoid
of substantial sequence repeats. MLVA included sequences with much diversity in copy
number of tandem repeats. The combined procedure allowed subspecies division, delineation
of clades A.I and A.II of subspecies tularensis, differentiation of
Japanese strains from other strains of subspecies holarctica, and
high-resolution strain typing. The procedure uses limited amounts of killed bacterial
preparations and, because only 1 single analytic method is needed, is time- and
cost-effective.
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Affiliation(s)
- Pär Larsson
- Swedish Defence Research Agency, Umeå, Sweden
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25
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Lopes de Carvalho I, Escudero R, García-Amil C, Falcão H, Anda P, Núncio MS. Francisella tularensis, Portugal. Emerg Infect Dis 2007; 13:666-7. [PMID: 17561575 PMCID: PMC2725955 DOI: 10.3201/eid1304.060714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
| | | | | | - Helena Falcão
- Organização dos Produtores Pecuários do Mogadouro, Mogadouro, Portugal
| | - Pedro Anda
- Instituto de Salud Carlos III, Majadahonda, Spain
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26
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van Belkum A. Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA). ACTA ACUST UNITED AC 2007; 49:22-7. [PMID: 17266711 DOI: 10.1111/j.1574-695x.2006.00173.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All bacterial genomes contain multiple loci of repetitive DNA. Repeat unit sizes and repeat sequences may vary when multiple loci are considered for different isolates of an individual microbial species. Moreover, it has been documented on many occasions that the number of repeat units per locus is a strain-defining parameter. Consequently, there is isolate-specificity in the number of repeats per locus when different strains of a given bacterial species are compared. The experimental assessment of this variability for a number of different loci has been called 'multilocus variable number of tandem repeat analysis' (MLVA). The approach can be supported or extended by locus-specific DNA sequencing for establishing mutations in the individual repeat units, which usually enhances the resolution of the approach considerably. Essentially, MLVA with or without supportive sequencing has been developed for all of the medically relevant bacterial species and can be used effectively for tracing outbreaks or other forms of bacterial dissemination. MLVA is a modern, timely and versatile bacterial typing methodology.
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Affiliation(s)
- Alex van Belkum
- Department of Medical Microbiology and Infectious Diseases, Rotterdam, The Netherlands.
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27
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LoVullo ED, Sherrill LA, Perez LL, Pavelka MS. Genetic tools for highly pathogenic Francisella tularensis subsp. tularensis. MICROBIOLOGY-SGM 2007; 152:3425-3435. [PMID: 17074911 DOI: 10.1099/mic.0.29121-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This paper is the first detailed description of the development and use of new genetic tools specifically for the safe manipulation of highly pathogenic Francisella tularensis subsp. tularensis. Most of these tools are also demonstrated to work with other F. tularensis subspecies. Kanamycin and hygromycin resistance determinants that function as genetic markers in F. tularensis subsp. tularensis strain Schu and sets of episomal shuttle vectors that are either unstable or stably maintained in the absence of selection were developed. In addition, the hyg gene, expressed from the F. tularensis groESL promoter, was successfully used as a marker for transposon mutagenesis. This work also includes the development of sacB-based suicide plasmids expressing kanamycin resistance that can be used for electroporation-mediated allelic exchange of unmarked mutations in Schu and the F. tularensis live vaccine strain (LVS). Using these plasmids, the two predicted beta-lactamase genes, blaA and blaB, in Schu and LVS were deleted. Only the Delta blaB1 mutants had increased susceptibility to ampicillin, and this phenotype was complemented by a plasmid expressing blaB+. The results suggest that the beta-lactam antibiotic resistance phenotype of Schu and LVS is likely due to only one of the two beta-lactamase genes present and that ampicillin resistance can be used as an additional selectable marker in beta-lactamase deletion mutants. The collection of tools presented in this report will be helpful for the genetic analyses of F. tularensis subsp. tularensis pathogenesis.
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Affiliation(s)
- Eric D LoVullo
- University of Rochester Medical Center, 601 Elmwood Ave, Box 672, Rochester, NY 14642, USA
| | - Lani A Sherrill
- University of Rochester Medical Center, 601 Elmwood Ave, Box 672, Rochester, NY 14642, USA
| | - Lanyn L Perez
- University of Rochester Medical Center, 601 Elmwood Ave, Box 672, Rochester, NY 14642, USA
| | - Martin S Pavelka
- University of Rochester Medical Center, 601 Elmwood Ave, Box 672, Rochester, NY 14642, USA
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Fan J, Kraft AJ, Henrickson KJ. Current methods for the rapid diagnosis of bioterrorism-related infectious agents. Pediatr Clin North Am 2006; 53:817-42, vii-viii. [PMID: 17027612 DOI: 10.1016/j.pcl.2006.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioterrorism is the calculated use of violence against civilians to attain political, religious, or ideologic goals using weapons of biological warfare. Bioterrorism is of particular concern because these weapons can be manufactured with ease and do not require highly sophisticated technology. Moreover, biologic agents can be delivered and spread easily and can effect a large population and geographic area. The terrorist attacks occurring around the world necessitate society's continued investment in adequate defense against these unpredictable and irrational events.
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Affiliation(s)
- Jiang Fan
- Department of Pediatrics, Medical College of Wisconsin, and Pediatric Infectious Diseases, Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
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29
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Witonski D, Stefanova R, Ranganathan A, Schutze GE, Eisenach KD, Cave MD. Variable-number tandem repeats that are useful in genotyping isolates of Salmonella enterica subsp. enterica serovars Typhimurium and Newport. J Clin Microbiol 2006; 44:3849-54. [PMID: 16943354 PMCID: PMC1698354 DOI: 10.1128/jcm.00469-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 was analyzed for direct repeats, and 54 sequences containing variable-number tandem repeat loci were identified. Ten primer pairs that anneal upstream and downstream of each selected locus were designed and used to amplify PCR targets in isolates of S. enterica serovars Typhimurium and Newport. Four of the 10 loci did not show polymorphism in the length of products. Six loci were selected for analysis. Isolates of S. enterica serovars Typhimurium and Newport that were related to specific outbreaks and showed identical pulsed-field gel electrophoresis patterns were indistinguishable by the length of the six variable-number tandem repeats. Isolates that differed in their pulsed-field gel electrophoresis patterns showed polymorphism in variable-number tandem repeat profiles. Length of the products was confirmed by DNA sequence analysis. Only 2 of the 10 loci contained exact integers of the direct repeat. Eight loci contained partial copies. The partial copies were maintained at the ends of the variable-number tandem repeat loci in all isolates. In spite of having partial copies that were maintained in all isolates, the number of direct repeats at a locus was polymorphic. Six variable-number tandem repeat loci were useful in distinguishing isolates of S. enterica serovars Typhimurium and Newport that had different pulsed-field gel electrophoresis patterns and in identifying outbreak-associated cases that shared a common pulsed-field gel pattern.
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Affiliation(s)
- D Witonski
- Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock 72205, USA
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Nübel U, Reissbrodt R, Weller A, Grunow R, Porsch-Ozcürümez M, Tomaso H, Hofer E, Splettstoesser W, Finke EJ, Tschäpe H, Witte W. Population structure of Francisella tularensis. J Bacteriol 2006; 188:5319-24. [PMID: 16816208 PMCID: PMC1539956 DOI: 10.1128/jb.01662-05] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have sequenced fragments of five metabolic housekeeping genes and two genes encoding outer membrane proteins from 81 isolates of Francisella tularensis, representing all four subspecies. Phylogenetic clustering of gene sequences from F. tularensis subsp. tularensis and F. tularensis subsp. holarctica aligned well with subspecies affiliations. In contrast, F. tularensis subsp. novicida and F. tularensis subsp. mediasiatica were indicated to be phylogenetically incoherent taxa. Incongruent gene trees and mosaic structures of housekeeping genes provided evidence for genetic recombination in F. tularensis.
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Affiliation(s)
- Ulrich Nübel
- Robert Koch Institute, Burgstr. 37, 38855 Wernigerode, Germany.
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31
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Morse SA, Budowle B. Microbial forensics: application to bioterrorism preparedness and response. Infect Dis Clin North Am 2006; 20:455-73, xi. [PMID: 16762747 DOI: 10.1016/j.idc.2006.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Stephen A Morse
- Bioterrorism Preparedness and Response Program, Centers for Disease Control and Prevention, 1600 Clifton Road, MS C-12, Atlanta, GA 30333, USA.
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32
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Hyytiä-Trees E, Smole SC, Fields PA, Swaminathan B, Ribot EM. Second Generation Subtyping: A Proposed PulseNet Protocol for Multiple-Locus Variable-Number Tandem Repeat Analysis of Shiga Toxin–ProducingEscherichia coliO157 (STEC O157). Foodborne Pathog Dis 2006; 3:118-31. [PMID: 16602987 DOI: 10.1089/fpd.2006.3.118] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most bacterial genomes contain tandem duplications of short DNA sequences, termed "variable-number tandem repeats" (VNTR). A subtyping method targeting these repeats, multiple-locus VNTR analysis (MLVA), has emerged as a powerful tool for characterization of clonal organisms such as Shiga toxin-producing Escherichia coli O157 (STEC O157). We modified and optimized a recently published MLVA scheme targeting 29 polymorphic VNTR regions of STEC O157 to render it suitable for routine use by public health laboratories that participate in PulseNet, the national and international molecular subtyping network for foodborne disease surveillance. Nine VNTR loci were included in the final protocol. They were amplified in three PCR reactions, after which the PCR products were sized using capillary electrophoresis. Two hundred geographically diverse, sporadic and outbreak- related STEC O157 isolates were characterized by MLVA and the results were compared with data obtained by pulsed-field gel electrophoresis (PFGE) using XbaI macrorestriction of genomic DNA. A total of 139 unique XbaI PFGE patterns and 162 MLVA types were identified. A subset of 100 isolates characterized by both XbaI and BlnI macrorestriction had 62 unique PFGE and MLVA types. Although the clustering of isolates by the two subtyping systems was generally in agreement, some discrepancies were observed. Importantly, MLVA was able to discriminate among some epidemiologically unrelated isolates which were indistinguishable by PFGE. However, among strains from three of the eight outbreaks included in the study, two single locus MLVA variants and one double locus variant were detected among epidemiologically implicated isolates that were indistinguishable by PFGE. Conversely, in three other outbreaks, isolates that were indistinguishable by MLVA displayed multiple PFGE types. An additional more extensive multi-laboratory validation of the MLVA protocol is in progress in order to address critical issues such as establishing epidemiologically relevant interpretation guidelines for the MLVA data.
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Affiliation(s)
- Eija Hyytiä-Trees
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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33
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Splettstoesser WD, Tomaso H, Al Dahouk S, Neubauer H, Schuff-Werner P. Diagnostic procedures in tularaemia with special focus on molecular and immunological techniques. ACTA ACUST UNITED AC 2005; 52:249-61. [PMID: 16219088 DOI: 10.1111/j.1439-0450.2005.00863.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tularaemia is a severe bacterial zoonosis caused by the highly infectious agent Francisella tularensis. It is endemic in countries of the northern hemisphere ranging from North America to Europe, Asia and Japan. Very recently, Francisella-like strains causing disease in humans were described from tropical northern Australia. In the last decade, efforts have been made to develop sensitive and specific immunological and molecular techniques for the laboratory diagnosis of tularaemia and also for the definite identification of members of the species F. tularensis and its four subspecies. Screening for the keyword 'Francisella' a Medline search over the last decade was performed and articles describing diagnostic methods for tularaemia and its causative agent were selected. Besides classical microbiological techniques (cultivation, biochemical profiling, susceptibility testing) several new immunological and molecular approaches to identify F. tularensis have been introduced employing highly specific antibodies and various polymerase chain reaction (PCR)-based methods. Whereas direct antigen detection by enzyme-linked immunosorbent assay (ELISA) or immunofluorescence might allow early presumptive diagnosis of tularaemia, these methods--like all PCR techniques--still await further evaluation. Therefore, diagnosis of tularaemia still relies mainly on the demonstration of specific antibodies in the host. ELISA and immunoblot methods started to replace the standard tube or micro-agglutination assays. However, the diagnostic value of antibody detection in the very early clinical phase of tularaemia is limited. Francisella tularensis is regarded as a 'highest priority' biological agent (category 'A' according to the CDC, Atlanta, GA, USA), thus rapid and reliable diagnosis of tularaemia is required not only for a timely onset of therapy, the handling of outbreak investigations but also for the surveillance of endemic foci. Only very recently, evaluated test kits for serological diagnosis of human tularaemia became available, while the introduction of standardized molecular techniques for detection and typing is still missing.
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Affiliation(s)
- W D Splettstoesser
- Department of Medical Microbiology and Hospital Hygiene, Institute of Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Schillingallee 70, 18057 Rostock, Germany.
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Lindstedt BA. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005; 26:2567-82. [PMID: 15937984 DOI: 10.1002/elps.200500096] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Division for Infectious Diseases Control, Oslo, Norway.
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35
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Bricker BJ, Ewalt DR. Evaluation of the HOOF-Print assay for typing Brucella abortus strains isolated from cattle in the United States: results with four performance criteria. BMC Microbiol 2005; 5:37. [PMID: 15975142 PMCID: PMC1183211 DOI: 10.1186/1471-2180-5-37] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Accepted: 06/23/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A fundamental question that arises during epidemiological investigations of bacterial disease outbreaks is whether the outbreak strain is genetically related to a proposed index strain. Highly discriminating genetic markers for characterizing bacterial strains can help in clarifying the genetic relationships among strains. Under the auspices of the European Society of Clinical Microbiology and Infectious Diseases, the European Study Group for Epidemiological Markers (ESGEM) established guidelines for evaluating the performance of typing systems based of a number of criteria. Recently, HOOF-Print genotype analysis, a new method for typing Brucella abortus strains based on hypervariability at eight tandem repeat loci, was described. This paper evaluates the HOOF-Print assay by four of the criteria set out by the ESGEM: typeability, reproducibility, power of discrimination, and concordance with other typing methods. RESULTS The HOOF-Print Assay was evaluated with a test population composed of 97 unrelated field isolates and 6 common laboratory strains of B. abortus. Both typeability and reproducibility of the assay were excellent. Allele diversity and frequency varied widely among the eight loci, ranging from 1 to 13 alleles. The power of discrimination, measured by the Hunter-Gaston discrimination index (HGDI), varied by locus ranging from 0 to 0.89, where a maximal value of 1.0 indicates discrimination of all strains. The HGDI values calculated for subgroups sorted by biovar were similar to the values determined for the whole population. None of the individual loci achieved the recommended HGDI threshold of 0.95, but the HGDI of the composite profiles was 0.99 (93 unique genotypes from 97 field strains evaluated), well above the recommended threshold. By comparison, the HGDI value for biovar typing was 0.61 in a test population biased with disproportionate numbers of the less common biovars. Cluster analysis based on HOOF-Print genotypes assembled the strains into hierarchical groups with no apparent association with the time or location of strain isolation. Likewise, these hierarchical groups were not homogeneous with regard to biotype. In one extreme case, two field isolates with identical fingerprints were identified as different biovars by conventional methods. CONCLUSION The main purpose of this study was to assess the ability of HOOF-Print genotyping to discriminate unrelated field strains of B. abortus, and whether the assay met established requirements for bacterial strain typing methods. The discriminatory power of the assay was remarkable, considering the genetic homogeneity found among species within the genus. The assay met or exceeded all of the recommended levels for the performance criteria of typeability, reproducibility, and power of discrimination, however some inconsistencies with conventional biovar typing were observed. Nevertheless, the results indicate that with cautious interpretation, multilocus genotyping of polymorphic tandem repeats by HOOF-Print analysis could be a valuable complement to routine epidemiological investigations into localized B. abortus outbreaks.
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Affiliation(s)
- Betsy J Bricker
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, 2300 Dayton Rd, Ames, IA, 50010, USA
| | - Darla R Ewalt
- Diagnostic Bacteriology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, 1800 Dayton Rd, Ames, IA, 50010, USA
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36
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Yazdankhah SP, Lindstedt BA, Caugant DA. Use of variable-number tandem repeats to examine genetic diversity of Neisseria meningitidis. J Clin Microbiol 2005; 43:1699-705. [PMID: 15814988 PMCID: PMC1081323 DOI: 10.1128/jcm.43.4.1699-1705.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repetitive DNA motifs with potential variable-number tandem repeats (VNTR) were identified in the genome of Neisseria meningitidis and used to develop a typing method. A total of 146 meningococcal isolates recovered from carriers and patients were studied. These included 82 of the 107 N. meningitidis isolates previously used in the development of multilocus sequence typing (MLST), 45 isolates recovered from different counties in Norway in connection with local outbreaks, and 19 serogroup W135 isolates of sequence type 11 (ST-11), which were recovered in several parts of the world. The latter group comprised isolates related to the Hajj outbreak of 2000 and isolates recovered from outbreaks in Burkina Faso in 2001 and 2002. All isolates had been characterized previously by MLST or multilocus enzyme electrophoresis (MLEE). VNTR analysis showed that meningococcal isolates with similar MLST or MLEE types recovered from epidemiologically linked cases in a defined geographical area often presented similar VNTR patterns while isolates of the same MLST or MLEE types without an obvious epidemiological link showed variable VNTR patterns. Thus, VNTR analysis may be used for fine typing of meningococcal isolates after MLST or MLEE typing. The method might be especially valuable for differentiating among ST-11 strains, as shown by the VNTR analyses of serogroup W135 ST-11 meningococcal isolates recovered since the mid-1990s.
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Affiliation(s)
- Siamak P Yazdankhah
- Division of Infectious Disease Control, Norwegian Institute of Public Health, P.O. Box 4404, Nydalen, N-0403 Oslo, Norway.
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37
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Johansson A, Forsman M, Sjöstedt A. The development of tools for diagnosis of tularemia and typing of Francisella tularensis. APMIS 2005; 112:898-907. [PMID: 15638842 DOI: 10.1111/j.1600-0463.2004.apm11211-1212.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid development of molecular techniques for the diagnosis of infections and typing of microbes has been seen during the last 10 years. The present review exemplifies this development by presenting the work of the authors and others regarding techniques for the diagnosis of tularemia and typing of Francisella tularensis. The lack of rapid and safe methods for the laboratory diagnosis of tularemia was the rationale behind the development of methods for the direct detection of F. tularensis in clinical specimens. Today, detection by polymerase chain reaction has become an important adjunct to clinical decisions for the early diagnosis of tularemia. The elucidation of the epidemiology and epizootology of the disease has been hampered by the lack of suitable methods. During recent years several DNA-based methods that allow rapid identification of the four F. tularensis subspecies, including differentiation of strains of the two clinically important subspecies, the highly virulent type A strains and less virulent type B strains, have been developed. Since F. tularensis strains of any origin exhibit highly conserved genomic sequences, the availability of extensive genome sequence data was a prerequisite for the development of a typing system that allows discrimination of individual isolates. The most discriminatory method is based on multiple-locus variable-number tandem repeat analysis (MLVA) and uses highly variable parts of the F. tularensis genome. The method will be an important tool in future studies of the molecular epidemiology of tularemia.
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38
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Kawula TH, Hall JD, Fuller JR, Craven RR. Use of transposon-transposase complexes to create stable insertion mutant strains of Francisella tularensis LVS. Appl Environ Microbiol 2005; 70:6901-4. [PMID: 15528561 PMCID: PMC525197 DOI: 10.1128/aem.70.11.6901-6904.2004] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a highly virulent zoonotic bacterial pathogen capable of infecting numerous different mammalian species, including humans. Elucidation of the pathogenic mechanisms of F. tularensis has been hampered by a lack of tools to genetically manipulate this organism. Herein we describe the use of transposome complexes to create insertion mutations in the chromosome of the F. tularensis live vaccine strain (LVS). A Tn5-derived transposon encoding kanamycin resistance and lacking a transposase gene was complexed with transposase enzyme and transformed directly into F. tularensis LVS by electroporation. An insertion frequency of 2.6 x 10(-8) +/- 0.87 x 10(-8) per cell was consistently achieved using this method. There are 178 described Tn5 consensus target sites distributed throughout the F. tularensis genome. Twenty-two of 26 transposon insertions analyzed were within known or predicted open reading frames, but none of these insertions was associated with the Tn5 target site. Analysis of the insertions of sequentially passed strains indicated that the transposons were maintained stably at the initial insertion site after more than 270 generations. Therefore, transformation by electroporation of Tn5-based transposon-transposase complexes provided an efficient mechanism for generating random, stable chromosomal insertion mutations in F. tularensis.
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Affiliation(s)
- Thomas H Kawula
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, North Carolina 27599-7290, USA.
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Lundquist M, Caspersen MB, Wikström P, Forsman M. Discrimination ofFrancisella tularensissubspecies using surface enhanced laser desorption ionization mass spectrometry and multivariate data analysis. FEMS Microbiol Lett 2005; 243:303-10. [PMID: 15668033 DOI: 10.1016/j.femsle.2004.12.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Revised: 12/13/2004] [Accepted: 12/16/2004] [Indexed: 11/24/2022] Open
Abstract
Francisella tularensis causes the zoonotic disease tularemia, and is considered a potential bioterrorist agent due to its extremely low infection dose and potential for airborne transmission. Presently, F. tularensis is divided into four subspecies; tularensis, holarctica, mediasiatica and novicida. Phenotypic discrimination of the closely related subspecies with traditional methods is difficult and tedious. Furthermore, the results may be vague and they often need to be complemented with virulence tests in animals. Here, we have used surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) to discriminate between the four subspecies of F. tularensis. The method is based on the differential binding of protein subsets to chemically modified surfaces. Bacterial thermolysates were added to anionic, cationic, and copper ion-loaded immobilized metal affinity SELDI chip surfaces. After binding, washing, and SELDI-TOF-MS different protein profiles were obtained. The spectra generated from the different surfaces were then used to characterize each bacterial strain. The results showed that the method was reproducible, with an average intensity variation of 21%, and that the mass precision was good (300-450 ppm). Moreover, in subsequent cluster analysis and principal component analysis (PCA) data for the analyzed Francisella strains grouped according to the recognized subspecies. Partial least squares-discriminant analysis (PLS-DA) of the protein profiles also identified proteins that differed between the strains. Thus, the protein profiling approach based on SELDI-TOF-MS holds great promise for rapid high-resolution phenotypic identification of bacteria.
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Affiliation(s)
- Margaretha Lundquist
- Swedish Defence Research Agency, Department of NBC-analysis, 901 82, Umeå, Sweden
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40
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Goethert HK, Shani I, Telford SR. Genotypic diversity of Francisella tularensis infecting Dermacentor variabilis ticks on Martha's Vineyard, Massachusetts. J Clin Microbiol 2005; 42:4968-73. [PMID: 15528681 PMCID: PMC525218 DOI: 10.1128/jcm.42.11.4968-4973.2004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Martha's Vineyard, Mass., has been the site of two outbreaks of tularemia (1978 and 2000). Although most patients from both outbreaks presented with pneumonic disease and although aerosol transmission has been suggested, the bite of a dog tick and exposure to rabbits remain the only proven modes of transmission. The factors that precipitated the tularemia outbreaks or the proximal determinants of human risk remain undescribed. We sought to test the hypothesis that the ongoing outbreak is due to a recent introduction event as opposed to amplification of a cryptic enzootic cycle. From 2001-2003, we collected 4,246 dog ticks and tested them in pools for evidence of tularemia by PCR. We then measured the genetic diversity of Francisella tularensis by using multiple-locus variable-number tandem repeat analysis. The prevalence of F. tularensis in dog ticks averaged 0.7%. From 29 positive pools, we identified 10 unique genotypes, which was an unexpectedly large degree of diversity (Simpson's index = 0.86). This degree of genetic diversity is inconsistent with a recent introduction event. We conclude that there has been long-standing enzootic transmission of tularemia on the island.
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Affiliation(s)
- Heidi K Goethert
- Tufts University School of Veterinary Medicine, Division of Infectious Diseases, 200 Westboro Rd., North Grafton, MA 01536, USA
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41
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Nano FE, Zhang N, Cowley SC, Klose KE, Cheung KKM, Roberts MJ, Ludu JS, Letendre GW, Meierovics AI, Stephens G, Elkins KL. A Francisella tularensis pathogenicity island required for intramacrophage growth. J Bacteriol 2004; 186:6430-6. [PMID: 15375123 PMCID: PMC516616 DOI: 10.1128/jb.186.19.6430-6436.2004] [Citation(s) in RCA: 290] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Francisella tularensis is a gram-negative, facultative intracellular pathogen that causes the highly infectious zoonotic disease tularemia. We have discovered a ca. 30-kb pathogenicity island of F. tularensis (FPI) that includes four large open reading frames (ORFs) of 2.5 to 3.9 kb and 13 ORFs of 1.5 kb or smaller. Previously, two small genes located near the center of the FPI were shown to be needed for intramacrophage growth. In this work we show that two of the large ORFs, located toward the ends of the FPI, are needed for virulence. Although most genes in the FPI encode proteins with amino acid sequences that are highly conserved between high- and low-virulence strains, one of the FPI genes is present in highly virulent type A F. tularensis, absent in moderately virulent type B F. tularensis, and altered in F. tularensis subsp. novicida, which is highly virulent for mice but avirulent for humans. The G+C content of a 17.7-kb stretch of the FPI is 26.6%, which is 6.6% below the average G+C content of the F. tularensis genome. This extremely low G+C content suggests that the DNA was imported from a microbe with a very low G+C-containing chromosome.
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Affiliation(s)
- Francis E Nano
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
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42
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Johansson A, Farlow J, Larsson P, Dukerich M, Chambers E, Byström M, Fox J, Chu M, Forsman M, Sjöstedt A, Keim P. Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J Bacteriol 2004; 186:5808-18. [PMID: 15317786 PMCID: PMC516809 DOI: 10.1128/jb.186.17.5808-5818.2004] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Accepted: 06/06/2004] [Indexed: 11/20/2022] Open
Abstract
The intracellular bacterium Francisella tularensis is the causative agent of tularemia and poses a serious threat as an agent of bioterrorism. We have developed a highly effective molecular subtyping system from 25 variable-number tandem repeat (VNTR) loci. In our study, multiple-locus VNTR analysis (MLVA) was used to analyze genetic relationships and potential population structure within a global collection of 192 F. tularensis isolates, including representatives from each of the four subspecies. The VNTR loci displayed between 2 and 31 alleles with Nei's diversity values between 0.05 and 0.95. Neighbor-joining cluster analysis of VNTR data revealed 120 genotypes among the 192 F. tularensis isolates, including accurate subspecies identification. F. tularensis subsp. tularensis (type A) isolates showed great diversity at VNTR loci, while F. tularensis subsp. holarctica (type B) isolates showed much lower levels despite a much broader geographical prevalence. The resolution of two distinct clades within F. tularensis subsp. tularensis (designated A.I and A.II) revealed a previously unrecognized genetic division within this highly virulent subspecies. F. tularensis subsp. holarctica appears to have recently spread globally across continents from a single origin, while F. tularensis subsp. tularensis has a long and complex evolutionary history almost exclusively in North America. The sole non-North American type A isolates (Slovakian) were closely related to the SCHU S4 strain. Significant linkage disequilibrium was detected among VNTR loci of F. tularensis consistent with a clonal population structure. Overall, this work greatly augments the study of tularemia ecology and epidemiology, while providing a framework for future forensic analysis of F. tularensis isolates.
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Affiliation(s)
- Anders Johansson
- Divisions of Infectious Diseases, Department of Clinical Microbiology, Umeå University, Sweden
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Abstract
Tularaemia exists endemically in most European countries. In some areas, such as Finland and Sweden, outbreaks comprising hundreds of cases are recorded at least once a decade. In other areas, outbreaks of such a magnitude occur only occasionally, except in times of war. Between outbreaks, the natural reservoir of the causative agent, Francisella tularensis, is unknown. The organism replicates intracellularly in protozoans. An association of tularaemia to natural water may be of significance in locating the reservoir. Epidemiological work has to date been slow, but is now facilitated by the development of new molecular methods. Due to a variation in numbers of short sequence-tandem repeats in the bacterial genome, individual strains of F. tularensis can today be distinguished.
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Affiliation(s)
- Arne Tärnvik
- Department of Clinical Microbiology, Infectious Diseases, Umeå University, Sweden.
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Samrakandi M, Zhang C, Zhang M, Nietfeldt J, Kim J, Iwen P, Olson M, Fey P, Duhamel G, Hinrichs S, Cirillo J, Benson A. Genome diversity among regional populations ofFrancisella tularensissubspeciestularensisandFrancisella tularensissubspeciesholarcticaisolated from the US. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09672.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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45
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Lindstedt BA, Heir E, Gjernes E, Vardund T, Kapperud G. DNA fingerprinting of Shiga-toxin producing Escherichia coli O157 based on Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA). Ann Clin Microbiol Antimicrob 2003; 2:12. [PMID: 14664722 PMCID: PMC317353 DOI: 10.1186/1476-0711-2-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2003] [Accepted: 12/10/2003] [Indexed: 12/03/2022] Open
Abstract
Background The ability to react early to possible outbreaks of Escherichia coli O157:H7 and to trace possible sources relies on the availability of highly discriminatory and reliable techniques. The development of methods that are fast and has the potential for complete automation is needed for this important pathogen. Methods In all 73 isolates of shiga-toxin producing E. coli O157 (STEC) were used in this study. The two available fully sequenced STEC genomes were scanned for tandem repeated stretches of DNA, which were evaluated as polymorphic markers for isolate identification. Results The 73 E. coli isolates displayed 47 distinct patterns and the MLVA assay was capable of high discrimination between the E. coli O157 strains. The assay was fast and all the steps can be automated. Conclusion The findings demonstrate a novel high discriminatory molecular typing method for the important pathogen E. coli O157 that is fast, robust and offers many advantages compared to current methods.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Even Heir
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Elisabet Gjernes
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Traute Vardund
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
| | - Georg Kapperud
- Norwegian Institute of Public Health, Department of Infectious Disease Control, Oslo, Norway
- Department of Pharmacology, Microbiology and Food Hygiene, Norwegian School of Veterinary Sciences, Oslo, Norway
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Broekhuijsen M, Larsson P, Johansson A, Byström M, Eriksson U, Larsson E, Prior RG, Sjöstedt A, Titball RW, Forsman M. Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis. J Clin Microbiol 2003; 41:2924-31. [PMID: 12843022 PMCID: PMC165330 DOI: 10.1128/jcm.41.7.2924-2931.2003] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Francisella tularensis is a potent pathogen and a possible bioterrorism agent. Little is known, however, to explain the molecular basis for its virulence and the distinct differences in virulence found between the four recognized subspecies, F. tularensis subsp. tularensis, F. tularensis subsp. mediasiatica, F. tularensis subsp. holarctica, and F. tularensis subsp. novicida. We developed a DNA microarray based on 1,832 clones from a shotgun library used for sequencing of the highly virulent strain F. tularensis subsp. tularensis Schu S4. This allowed a genome-wide analysis of 27 strains representing all four subspecies. Overall, the microarray analysis confirmed a limited genetic variation within the species F. tularensis, and when the strains were compared, at most 3.7% of the probes showed differential hybridization. Cluster analysis of the hybridization data revealed that the causative agents of type A and type B tularemia, i.e., F. tularensis subsp. tularensis and F. tularensis subsp. holarctica, respectively, formed distinct clusters. Despite marked differences in their virulence and geographical origin, a high degree of genomic similarity between strains of F. tularensis subsp. tularensis and F. tularensis subsp. mediasiatica was apparent. Strains from Japan clustered separately, as did strains of F. tularensis subsp. novicida. Eight regions of difference (RD) 0.6 to 11.5 kb in size, altogether comprising 21 open reading frames, were identified that distinguished strains of the moderately virulent subspecies F. tularensis subsp. holarctica and the highly virulent subspecies F. tularensis subsp. tularensis. One of these regions, RD1, allowed for the first time the development of an F. tularensis-specific PCR assay that discriminates each of the four subspecies.
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Haristoy X, Lozniewski A, Tram C, Simeon D, Bevanger L, Lion C. Francisella tularensis bacteremia. J Clin Microbiol 2003; 41:2774-6. [PMID: 12791928 PMCID: PMC156490 DOI: 10.1128/jcm.41.6.2774-2776.2003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteremia caused by Francisella tularensis is rare and has been reported mainly in the United States and infrequently in Europe. We report herein the first case of bacteremic F. tularensis pneumonia in an immunocompetent individual in southern Europe.
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Affiliation(s)
- X Haristoy
- Laboratoire de Bactériologie, Centre Hospitalier et Universitaire, Nancy, France
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48
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Lindstedt BA, Heir E, Gjernes E, Kapperud G. DNA fingerprinting of Salmonella enterica subsp. enterica serovar typhimurium with emphasis on phage type DT104 based on variable number of tandem repeat loci. J Clin Microbiol 2003; 41:1469-79. [PMID: 12682132 PMCID: PMC153889 DOI: 10.1128/jcm.41.4.1469-1479.2003] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seventy-eight human and environmental strains of Salmonella enterica subsp. enterica serovar Typhimurium, as well as 18 isolates of other Salmonella serovars and 6 isolates of Escherichia coli, were subjected to a novel variable number of tandem repeats (VNTR)-based fingerprinting method that showed high discrimination and reproducibility for typing serovar Typhimurium isolates. The method is based on capillary separation of PCR products from fluorescence-labeled VNTR in the serovar Typhimurium genome. The serovar Typhimurium isolates displayed 54 VNTR patterns, and the VNTR assay correctly identified strains from a well-characterized outbreak. Among 37 serovar Typhimurium phage type DT104 isolates, 28 distinct VNTR patterns were found. This VNTR-based method is fast and suitable for complete automation. Our VNTR-based method was capable of high discrimination within the homogeneous serovar Typhimurium DT104 phage type and can be used to trace outbreaks and to monitor DT104 as well as other phage types. The VNTR assay was compared to XbaI pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, integron-cassette profiles and gene PCR of intI1, qacEDelta1, sulI1, and floR. The VNTR assay showed greatly improved resolution compared to all other tested methods in this study.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Division for Infectious Diseases Control, Norwegian Institute of Public Health, N-0403 Oslo, Norway.
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Thomas R, Johansson A, Neeson B, Isherwood K, Sjöstedt A, Ellis J, Titball RW. Discrimination of human pathogenic subspecies of Francisella tularensis by using restriction fragment length polymorphism. J Clin Microbiol 2003; 41:50-7. [PMID: 12517824 PMCID: PMC149632 DOI: 10.1128/jcm.41.1.50-57.2003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Revised: 09/14/2002] [Accepted: 10/24/2002] [Indexed: 11/20/2022] Open
Abstract
We describe the use of two insertion sequence elements (ISFtu1 and ISFtu2) in Francisella tularensis to type strains by restriction fragment length polymorphism (RFLP). The RFLP profiles of 17 epidemiologically unrelated isolates were determined and compared. Our results showed that RFLP profiles can be used to assign F. tularensis strains into five main groups corresponding to strains of F. tularensis subsp. tularensis, F. tularensis strain ATCC 6223, strains of F. tularensis subsp. holarctica, strains of F. tularensis subsp. holarctica from Japan, and F. tularensis subsp. mediaasiatica. The results confirm the genetic identities of these subspecies and also support the suggestion that strains of F. tularensis subsp. holarctica from Japan should be considered members of a separate biovar. These findings should support future studies to determine the genetic differences between strains of F. tularensis at the whole-genome level.
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Affiliation(s)
- Rebecca Thomas
- Defence Science and Technology Laboratory, CBS Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom.
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50
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Abstract
Francisella tularensis is the etiological agent of tularemia, a serious and occasionally fatal disease of humans and animals. In humans, ulceroglandular tularemia is the most common form of the disease and is usually a consequence of a bite from an arthropod vector which has previously fed on an infected animal. The pneumonic form of the disease occurs rarely but is the likely form of the disease should this bacterium be used as a bioterrorism agent. The diagnosis of disease is not straightforward. F. tularensis is difficult to culture, and the handling of this bacterium poses a significant risk of infection to laboratory personnel. Enzyme-linked immunosorbent assay- and PCR-based methods have been used to detect bacteria in clinical samples, but these methods have not been adequately evaluated for the diagnosis of pneumonic tularemia. Little is known about the virulence mechanisms of F. tularensis, though there is a large body of evidence indicating that it is an intracellular pathogen, surviving mainly in macrophages. An unlicensed live attenuated vaccine is available, which does appear to offer protection against ulceroglandular and pneumonic tularemia. Although an improved vaccine against tularemia is highly desirable, attempts to devise such a vaccine have been limited by the inability to construct defined allelic replacement mutants and by the lack of information on the mechanisms of virulence of F. tularensis. In the absence of a licensed vaccine, aminoglycoside antibiotics play a key role in the prevention and treatment of tularemia.
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Affiliation(s)
- Jill Ellis
- Defence Science and Technology Laboratory, CBS Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
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