genome sequencing and functional genomics national program in latvia and era-net “pathogenomics”...
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GENOME SEQUENCING AND FUNCTIONAL GENOMICS NATIONAL PROGRAM IN LATVIA AND ERA-NET “PATHOGENOMICS”
Viesturs Baumanis, Latvian Council of Science
Berlin, October 13 th, 2004
National Research Program in Latvia (2002-2005)Nr.02.0011 (2002-2005) “Molecular and epidemiological study of multiresistant and genetic variability of infections”
(Program covers bacterial and viral infections also, however bacterial ones will be described below)
Number of staff involved - 55 persons among them PhD 34
Institutions - 8
Papers published per year - 116 among them in SCI journals - 19 (including abstracts)
Besides this National Research Program about 10 separate “bacteriological” projects have been financed and are in progress
Incidence per 100.000 population for bacterial infectionsin Latvia and tendencies of their dynamics in 1999-2004 (population in Latvia ~ 2.5 miljons)
Incidence Average dynamics in 1999-2004 (%) Salmonellosis 12.11 - 43 Shigellosis 11.47 - 44 Other bacterial intestinal infections 7.03 -23 Unidentified enteritis 66.32 +5 Tuberculosis 35.06 -14 Leptospirosis 0.43 -23 Jersiniosis 0.65 -66 Diphtheria 0.13 -92 Wooping cough 1.16 -64 Scarlet fever 21.56 -1 Meningitis ~0.7 + 7 Syphilis 15.39 -34 Gonorrhoea 11.30 -28 Chlamidiosis 13.28 -9 Lyme borreliosis 10.22 +67 HIV 9.31 -27 Nosocomial infections 0.1-0.52 ~ -20
Riga Stradins University (Medical Academy of Latvia)
Rector - J.Vetra
Students ~ 1500 Professors 50 PhD 169
Departments - 40
Stradins Clinical HospitalBacteriological laboratoryChief- A.BalodeMolecular studies E.Miklashevics
Clinical infectologyU.Dumpis, I.Vingre, A.Zilevica, E.Daugulis, P.Oshs, A.Martinsons, R.Lācis, M.Cīrulis, M.Jansone, I.Logina , L.Sosāre, J.Pokrotnieks
Methicillin resistance in staphylococci - classical methods and PCR amplification of mecA geneNosocomial infections in surgical clinic - (Klebsiella, P. aeruginosa)Nosocomial infections in nephrology - (Klebsiella, P. aeruginosa)Nosocomial infections in cardiosurgeryInfections in obstetrics and gynecology - (Str. agalactiae)Cytokins in meningitisUlceral disease - (H.pylori)
Medical Faculty, University of Latvia
Department of Microbiology - Head A.Zilevica
Research - Multi drug resistant staphilococci Urogenital, veneral infections, dermatomycosis ( V.Miltins)
Prevalence of methicillin-resistant staphylococci in Hospital of Traumatology and Orthopedics, Latvia, 1998-2002 (by A.Zilevica).
Nosocomial infections - Staphylococcus spp.
Clinical hospital Nr.7 - “Gailezers”
The largest hospital in the Baltic countries
Director - E.Platkajs
Urological infections - P.Ivdre
Infectology Center of Latvia
Treatment of all contagious infectious diseasesexcept tuberculosis
Director - B.Rosentale
Bacteriological laboratory - R.Paberza
Department of infectious diseases of Riga Stradins UniversityHead - L. Viksna
Research: viral diseases, gram-negative infections
State Center of Tuberculosis and Lung Disease(SCTLD)
All M.tuberculosis isolates from Latvia arebeing collected and analysed by classical bacteriological methods here. Bactec cultivation.
Wide international collaboration CDC, WHO
Director of SCTLD - J.LeimansChief of Central Bacteriological Laboratory - G.Skenders
Tuberculosis in Latvia 2000 2001 2002 2003
New cases 1715 1729 1540 1481
MDR 648 587 539
HIV + TB 1 12 ~25 ~50
Multi-drug resistant (MDR) TB in Latvia, 1998-2002
24,0%28,0%
9.5% 9.3%9,0%10,9% 9,9%
27.9% 27.7% 27,3%
0,0%
5,0%
10,0%
15,0%
20,0%
25,0%
30,0%
1998 1999 2000 2001 2002
Primary MDR-TB
Acquired MDR-TB
Multi-drug resistant M.tuberculosis - resistant at least to rifampin and isoniazid
(State Tuberculosis and Lung Disease Center data)
Biomedical Research and Study Centre University of LatviaMolecular studies of pathogens, molecular genetics,recombinant biotechnology, protein engineering,human genome, sequencing, electron microscopy,mass spectroscopy
Department of Molecular Microbiology - Head V.Baumanis
1. Molecular epidemiology of tuberculosis analysis of molecular mechanisms of drug resistance in mycobacteria and staphylococci- I.Jansone, T.Tracevska 2. Molecular epidemiology and functional genomics of the tick born diseases: a) Lyme borreliosis b) Tick-born encephalytis c) Erlichiosis- R.Ranka, A.Bormane (6th Framework project EDEN-TBD)
Department of Protein Engineering - Head P.Pumpens
1. Virus-like particles as carriers of antigen determinants (mainly virological)2. Cloning of Treponema pallidum proteins
Spoligopattern of 109 MDR M. tuberculosis isolates
Beijing genotype - 58% Higher % of double mutations in the rpoB and K43R typical in the rpsL
Other genotypes (non-Beijing group)
Dendrogram
Training activities
Biological Faculty University of Latvia
04…Functional stability of microbial cultures I.Muiznieks, University of Latvia, Biological Faculty04…Studies no genotoxicity by microorganisms J.Raipulis, Institute of microbiology and biotechnology University of Latvia04…Bacterial safety of foodstuffs E.Liepins, Latvian University of Agriculture
Department of Microbiology - Head I.Muiznieks
Institute of Microbiology and biotechnology- Director - U.Viesturs