WORKINGGROUP 4
  • Participants:

    Participant
    Organization
    E-mail
    Phone number
    Fax
    Anders Sjostedt  Umea University  anders.sjostedt@climi.umu.se  +46 90 785 1120  +46 90 785 2225 
    Ariane Tatjana Pietzka  Austrian Agency for Health and Food Saftey  ariane.pietzka@ages.at  +43 505553 2210  +43 505553 2219 
    Frank Hufert  Institute of Virology  mweidma@gwdg.de  +49 551 3910556  +49 551 3910556 
    Ignacio Lopez-Goni  University of Navarra  ilgoni@unav.es  +34 948 425600  +34 948 425600 
    Ingmar Janse  RIVM  ingmarja@yahoo.com  +31 30 2743666  +31 30 2744434 
    Ivan Ivanov  National Center of Infectious and Parasitic Diseases  ivanoov@gmail.com  +359 2 9446999 ext.290  +359 2 9446999 
    Pierre WATTIAU  Veterinary & Agrochemical Research Center - Belgium  Pierre.Wattiau@var.fgov.be  +32 (0)2 379 04 41  +32 (0)2 379 06 70 
    Raquel Escudero  Centro Nacional de Microbiolog?a - Spain  rescude@isciii.es  91 8223953  91 5097966 
    Sally Cutler  University of East London  s.cutler@uel.ac.uk  +44(0)208 223 6386  +44(0)208 223 6386 
    Stefan Panaiotov  National Center of Infeciotus and Parasitic Diseases  spanaiotov@yahoo.com  +359 2 9446999 ext 290  +359 2 9446999 
    Victoria Levterova  NCIPD  vikis@abv.bg  +359 2 9446999 290  +359 2 943 3075 
    Werner Ruppitsch  Austrian Agency for Health and Food Saftey  werner.ruppitsch@ages.at  +43 (0) 50 555 32 204  +43 (0) 50 555 32 219 


  • Description:
    WG4 Genomics.
    • Objective:
      Preparation of DNA fragments representing whole genomes and specific parts of genomes from microorganisms for use in micro-arrays. Analysis DNA fragments by sequence analysis. Cloning ORFs of interest in expression vectors.
    • Description:
      First an inventory of actual data on differential DNA markers and genomic libraries will be constructed for the microorganisms that need further investigation.
      DNA will be sheared by sonication or partially digested by a restriction endonuclease, providing fragments of 1 to 2 kb. Fragments will be cloned into a conventional E. coli cloning vector and libraries will be propagated. Care will be taken to cover the complete genome of a microorganism. Libraries will be prepared from several strains of a species and from several strains of closely related species. Differences in virulence and antimicrobial resistance will be accounted for.
      The results of the array analysis will lead to the identification of certain clones having unique fragments. Participants will sequence and analyse these fragments for the presence of open reading frames. An annotation of the sequence function will be provided where possible. If ORFs of specific interest are incomplete, the full ORF will be looked for. A sequence databank will be made available. For certain microorganisms, we will aim to construct DNA libraries from strains of the bacterium, which are found in Europe, USA and the former Soviet Union. Shotgun sequencing of these libraries will allow comparisons to be made with the genome sequences of strains isolated these different geographical regions. This will allow a whole genome comparisons to be made, and regions which are conserved and unique to isolates from these different locations to be identified. In turn this will allow diagnostic PCR probes to be devised and tested for strains from these different geographical locations The selected fragments will be analysed for (sub) species specificity and relation with virulence using the reverse line blot technique hybridisation. To this end genomic DNA from a panel of closely related informative micro-organisms will be prepared and labelled by random priming. This DNA will be hybridised to the selected DNA probes obtained from the array information.
      Another task will be the search for potential diagnostic fragments in conserved areas of the genome using PCRs with universal primers. Generic PCRs based on allelic diversity of genes, having regions of universal conservation will be performed. Additionally generic PCRs will be exploited in the search for unique intergenic spacers present in microorganisms. Virulence associated genes are frequently found in these regions (as exemplified between the tRNA encoding genes).
      The gene sequences of the fragments obtained from the generic PCR approaches will be determined. Sequences will be annotated. Focus will be on (sub) species specificity virulence, specific target genes involved in antimicrobial resistance, and possible new antimicorbial targets.
      Specificity of the fragments at (sub) species level, possible relation with virulence or antimicrobial resistance/action will be determined by reverse line blot hybridisation, as described above. When a fragment has been proven to be associated with a single species, it can be included into the micro array for possible inclusion as a diagnostic probe.
  • Actions:

    Action
    Description
    download
    Booklet 'Genomics of BSL3 and BSL4 pathogens' Call for papers. Chapters to be sent to spanaiotov@yahoo.com


  • Publications:

    Name
    Year
    Title
    Periodical
    Volume
    Page
    Pubmed
    Victoria Levterova, Stefan Panaiotov, Nadia Brankova, Kristin Tankova. 2010 Typing of Genetic Markers Involved in Stress Response by Fluorescent cDNA-Amplified Fragment Length Polymorphism Technique. Molecular Biotechnology # # link to pubmed
    Padeshki PI, Ivanov IN, Popov B, Kantardjiev TV. 2010 The role of birds in dissemination of Francisella tularensis: first direct molecular evidence for bird-to-human transmission. Epidemiol Infect. 138(3) 376-9 link to pubmed
    Panaiotov S, Ciccozzi M, Brankova N, Levterova V, Mitova-Tiholova M, Amicosante M, Rezza G, Kantardjiev T. 2009 An outbreak of Q fever in Bulgaria. Ann Ist Super Sanita 45(1) 83-6 link to pubmed
    Boyanova L., Markovska R., Yordanov D., Marina M., Ivanova K., Panayotov S., Gergova G., Mitov I. 2009 High prevalence of virulent Helicobacter pylori strains in symptomatic Bulgarian patients. Diagn Microbiol Infect Dis. 64(4) 374-380 link to pubmed
    S. Panaiotov, Y. Evstatieva, S. Ilieva, V. Levterova, N. Brankova, D. Nikolova, A. Ivanova, V. Stefanova, K. Tankova and A. Atev. 2009 Quantitative assessment of the dominant genome in fusant cultures. Biotechnol. Biotechnol Eq. 1 892-895 link to pubmed
    S. Panaiotov 2009 Cristalline nitrate reductase reagent for drug susceptibility testing of Mycobacterium tuberculosis. Int. J. Antimirob. Agents. 34(2) 191-2 link to pubmed
    Russo G, Pasquali P, Nenova R, Alexandrov T, Ralchev S, Vullo V, Rezza G, Kantardjiev T. 2009 Reemergence of human and animal brucellosis, Bulgaria. Emerg Infect Dis. 15(2) 314-6 link to pubmed
    Marinov KT, Georgieva ED, Ivanov IN, Kantardjiev TV 2009 Characterization and genotyping of strains of Francisella tularensis isolated in Bulgaria. J Med Microbiol. 58(Pt 1) 82-5 link to pubmed
    Pichler J., Much P., Kasper S., Fretz R., Auer B., Kathan J., Mann M., Huhulescu S., Ruppitsch W., Pietzka A., Silberbauer K., Neumann C., Gschiel E., de Martin A., Schuetz A., Gindl J., Neugschwandtner E., Allerberger F. 2009 An outbreak of febrile gastroenteritis associated with jellied pork contaminated with Listeria monocytogenes. Wien Klin. Wochenschr. 121 149-156 link to pubmed
    Springer B., Orendi U., Much P., Höger G., Ruppitsch W., Krziwanek K., Metz-Gercek S., Mittermayer H. 2009 Methicillin-resistant Staphylococcus aureus: a new zoonotic agent? Wien Klin. Wochenschr. 121 86-90 link to pubmed
    Grisold AJ, Zarfel G, Stoeger A, Feierl G, Raggam RB, Marth E. 2009 Emergence of community-associated methicillin-resistant Staphylococcus aureus(CA-MRSA) in Southeast Austria. J Infect. 58 168-70 link to pubmed
    Schmid D, Fretz R, Winter P, Mann M, Höger G, Stöger A, Ruppitsch W, Ladstätter J, Mayer N, de Martin A, Allerberger F. 2009 Outbreak of staphylococcal food intoxication after consumption of pasteurized milk products Wien Klin. Wochenschr. 121 125-131 link to pubmed
    Brandes C., Joachimsthaler A., Stöger A., Ruppitsch W., Zimmermann H. 2009 Genetic characterization of the origin of offtype plants in maize inbred lines. Seed Sci. Technol. 37 423-435 link to pubmed
    Pietzka A.T., Stöger A., Zeinzinger J., Allerberger F., Ruppitsch W. 2009 Fast detection of multiresistant Mycobacterium tuberculosis isolates using high-resolution melting curve PCR analysis. Clin. Microb. Infect. 15(s4) 333 link to pubmed
    Pietzka A.T., Indra A., Stöger A., Zeinzinger J., Konrad M., Hasenberger P., Allerberger F., Ruppitsch W. 2009 Rapid identification of multidrug-resistant Mycobacterium tuberculosis isolates by rpoB gene scanning using high-resolution melting curve PCR analysis. J. Antimicrob. Chemother. 63 1121-1127 link to pubmed
    Bhowmick T.S., Das M., Ruppitsch W., Stoeger A., Pietzka A.T., Allerberger F., Rodrigues D.P., Sarkar B. 2009 Virulence associated and regulatory protein genes detection in association with phage typing of human V. cholerae population from several geographic regions of the world. J Med Microbiol. 58 1160-1167 link to pubmed
    Helena Lindgren, Marie Honn, Igor Golovlev, Konstantin Kadzhaev, Wayne 2009 The 58-kDa major virulence factor of Francisella tularensis is required for efficient utilization of iron. Infect. Immun. 77 4429-4436. link to pubmed
    Emelie Salomonsson, Kerstin Kuoppa, Anna-Lena Forslund, Carl Zingmark, Igor Golovliov, Anders Sjöstedt, Laila Noppa, and Åke Forsberg 2009 Reintroduction of two deleted virulence loci restores full virulence to the live vaccine strain (LVS) of Francisella tularensis. Infect. Immun. 77 3424-3431 link to pubmed
    Konstantin Kadzhaev, Carl Zingmark, Igor Golovliov, Mark Bolanowski, Hua Shen, Wayne Conlan, Anders Sjöstedt. 2009 Identification of genes contributing to the virulence of Francisella tularensis Schu S4 in a mouse intradermal infection model. PLoS ONE. 4(5): e5463. link to pubmed
    Mia D. Champion, Qiandong Zeng, Eli B. Nix, Francis E Nano, Paul Keim,Chinnappa D Kodira, Mark Borowsky, Sarah Young, Michael Koehrsen, Reinhard, Engels, Matthew Pearson, Clint Howarth, Lisa Larson, Jared White, Lucia Alvarado, Mats Forsman, Scott W. Bear 2009 Comparative Genomic Characterization of 20 Strains of Various Francisella tularensis Subspecies Exhibiting Distinct Differences in Human Host Virulence. PLoS Pathogens. 5(5) e1000459 link to pubmed
    Jeanette E Bröms, Moa Lavander, Anders Sjöstedt. 2009 A conserved alpha-helix essential for a type VI secretion-like system of Francisella tularensis. J Bacteriol. 119 3431-3446. link to pubmed
    Cutler, S.J., Scott, J.C. & Wright, D.J.M 2008 Phylogenic relationship between Borrelia recurrentis and Borrelia duttonii. International Journal of Medical Microbiology 298 (S1) 193-202 link to pubmed
    Marcus Thein, Ignas Bunikis, Katrin Denker, Christer Larsson, Sally Cutler, Michele Drancourt, Tom G. Schwan, Reinhard Mentele, Friedrich Lottspeich, Sven Bergström and Roland Benz. 2008 Oms38, a pore-forming protein in the outer membrane of relapsing fever spirochetes in press J. Bacteriology 190 7035-7042 link to pubmed
    Eliasson, H., Olcen, P., Sjöstedt, A., Jurstrand, M., Bäck, E., Andersson, S 2008 Kinetics of immune response in tularemia: comparison between ELISA, tube agglutination and a novel whole blood lymphocyte stimulation test Clin Vaccine Immunol 15 1238-1243 link to pubmed
    Fretin D, Whatmore AM, Al Dahouk S, Neubauer H, Garin-Bastuji B, Albert D, Van Hessche M, Ménart M, Godfroid J, Walravens K, Wattiau P 2008 Brucella suis identification and biovar typing by real-time PCR Vet Microbiol. 131(3-4): 376-85 link to pubmed
    Wattiau P, Klee SR, Fretin D, Van Hessche M, Ménart M, Franz T, Chasseur C, Butaye P, Imberechts H 2008 Occurrence and genetic diversity of Bacillus anthracis strains isolated in an active wool-cleaning factory. Appl Environ Microbiol 74(13) 4005-11 link to pubmed
    Wattiau P, Van Hessche M, Schlicker C, Vander Veken H, Imberechts H. 2008 Comparison of classical serotyping and PremiTest assay for routine identification of common Salmonella enterica serovars. J Clin Microbiol 46(12) 4037-40 link to pubmed
    P. Wattiau, Weijers T, Andreoli P, Schliker C, Vander Veken H, Maas HME, Verbruggen AJ, Heck MEOC, Wannet WJ, Imberechts H and Vos P. 2008 Evaluation of the Premi®Test Salmonella, a commercial low-density DNA microarray system intended for routine identification and typing of Salmonella enterica. Int J Food Microbiol 123(3) 293-298 link to pubmed
    P. Wattiau, Klee SR, Fretin D, Van Hessche M, Ménart M, Franz T, Chasseur C, Butaye P, Imberechts H. 2008 Occurrence and genetic diversity of Bacillus anthracis strains isolated in an active wool-cleaning factory Appl Environ Microbiol 74(13) 4005-11 link to pubmed
    P. Wattiau, M. Van Hessche, C. Schlicker, H. Vander Veken and H. Imberechts 2008 Comparison of classical sero-typing and Premi®Test assay for the routine identification of common Salmonella enterica serovars J Clin Microbiol. 46(12) 4037-40 link to pubmed
    Fretin D, Whatmore AM, Al Dahouk S, Neubauer H, Garin-Bastuji B, Albert D, Van Hessche M, Ménart M, Godfroid J, Walravens K, P. Wattiau. 2008 Brucella suis identification and biovar typing by real-time PCR Vet Microbiol 131 376-385 link to pubmed
    Schmid D, Fretz R, Kuo HW, Rumetshofer R, Meusburger S, Magnet E, Hürbe G, Indra A, Ruppitsch W, Pietzka AT, Allerberger F 2008 An outbreak of multidrug-resistant tuberculosis among refugees in Austria Int J Tuberc Lung Dis. 12(10) 1190-5 link to pubmed
    Pietzka A., Stöger A., Pietzka D., Hasenberger P., Indra A., Ruppitsch W., Allerberger F. 2008 Mycobacterial interspersed repetitive units (MIRU) typing reveals high genetic diversity of Mycobacterium tuberculosis isolates in Austria Clin. Microbiol. Infect 14(s7) 485 link to pubmed
    Lagler H., Stich K., Schmid D., Gattringer R., Ruppitsch W., Huhulescu S., Allerberger F., Graninger W., Knapp S. 2008 Outbreak of acute gastroenteritis caused by Staphylococcal enterotoxins affecting an Austrian school centre. Clin. Microbiol. Infect 14(s7) 540-541 link to pubmed
    Ruppitsch W., Calaway J., Van Ert M., Hadfield T., Stöger A., Grif K., Pietzka A., Allerberger F. 2008 High resolution melting curve analysis and strain-specific SNPs: a new method for differentiation of the Ames strain from other Bacillus anthracis strains Clin. Microbiol. Infect. 14(s7) 76-77 link to pubmed
    Stöger A., Barionovi D., Calzolari A., Gozzi R., Ruppitsch W. and Scortichini M. 2008 Genetic variability of Xanthomonas fragariae strains obtained from field outbreaks and culture collections as revealed by repetitive-sequence PCR and AFLP J. Plant Pathol 90 453-457 link to pubmed
    Martin A, Panaiotov S, Portaels F, Hoffner S, Palomino JC, Angeby K 2008 The nitrate reductase assay for the rapid detection of isoniazid and rifampicin resistance in Mycobacterium tuberculosis: a systematic review and meta-analysis. J Antimicrob Chemother. 62(1) 56-64 link to pubmed
    Thirwall, R.E., Commander, N.J., Brew, S.D., Cutler, S.J., McGiven, J.A. & Stack, J.A 2008 Improving the specificity of immunodiagnosis for porcine brucellosis Veterinary Research Communications. 32 209-13 link to pubmed
    Cutler, S.J. 2008 Human brucellosis – where, when, what and how? Journal of Clinical Pathology e-letter 200705310. 0 jcp.2007.053108v1 link to pubmed
    . Henrik Andersson, Blanka Hartmanová, Rhonda KuoLee, Patrik Rydén, Wayne Conlan,Wangxue Chen, Anders Sjöstedt 2008 Transcriptional profiling of host responses in mouse lungs following aerosol infection with type A Francisella tularensis J. Med.Microbiol. 55 263-271 link to pubmed
    Cutler, S.J., Bouzid, M. & Cutler, R.R 2007 Q fever Journal of Infection 54 313-318 link to pubmed
    Cutler, S.J., & Cutler, R.R. 2007 Glanders and melioidosis – diseases caused by Burkholderia species. Biomedical Scientist 51 (5) 348-352 link to pubmed
    CUTLER, S.J., BROWNING, P. & SCOTT, J 2006 Ornithodoros moubata, a soft tick vector for Rickettsia in East Africa? Annals of the New York Academy of Sciences 1078 373-7 link to pubmed
    Kantardjiev T, Ivanov I, Velinov T, et al 2006 Tularemia outbreak, Bulgaria, 1997-2005. Emerg Infect Dis 12(4) 678-80 link to pubmed
    T. Kantardjiev, N. Brankova, E. Dobreva, S. Panaiotov, 2006 Advanced diagnosis of community acquired atypical pneumonia caused by Chlamydophila pneumoniae and Med. Rev 42.2 58-60 link to pubmed
    . N. Brankova, S. Panaiotov, V. Levterova, T. Kantardjiev 2006 Asimptomatic patients infected with C. trachomatis, Screening study Akush. Ginekol 2 25-28 link to pubmed
    T. Kantardjiev, V. Levterova, S. Panaiotov, I. Ivanov, E. Hristozova 2006 Molecular taxonomy of Cryptococcus neoformans varieties displaying phenotypic similarities Biotechnol. & Biotechnol. Eq vol.2 101-103 link to pubmed
    . Henrik Andersson, Blanka Hartmanová, Patrik Rydén, Laila Noppa, Linda Näslund,Anders Sjöstedt 2006 A microarray analysis of the murine macrophage response to infection with Francisella tularensis LVS J. Med. Microbiol 55 1023-1033 link to pubmed
    Patrik Rydén, Henrik Andersson, Mattias Landfors, Linda Näslund, Blanka Hartmanová, Laila Noppa and Anders Sjöstedt 2006 Evaluation of microarray data analysis methods using spike-in experiments BMC Bioinformatics 7 300-317 link to pubmed
    P. Wattiau and D. Fretin 2006 Real-time PCR typing of single nucleotide polymorphism in DNA containing inverted repeats BioTechniques 41 544-546 link to pubmed
    . T. Kantardjiev, V. Levterova, N. Brankova, I. Ivanov, P. Angelov, S. Panaiotov. 2006 Role of fluorescent amplified fragment length polymorphism analysis in taxonomy, identification and epidemiological examinations of yeast pathogens Biotechnol. & Biotechnol. Eq 1 103-106 link to pubmed
    Henrik Andersson, Blanka Hartmanová, Erik Bäck, Henrik Eliasson, Mattias Landfors,Linda Näslund, Patrik Rydén, Anders Sjöstedt 2006 Transcriptional profiling of the peripheral blood response during tularemia Genes Immun 7 503-513 link to pubmed
    Magali Lescot, Stéphane Audic, Catherine Robert, Thitien Nguyen, Guillaume Blanc, Sally J. Cutler, Jean-Michel Claverie, Didier Raoult & Michel Drancourt 0 The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii. PLoS Genetics 4(9): e1000185. doi:10.1371 journal.pgen.1000185 link to pubmed