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