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 ( ) Nr ( ) “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 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 population for bacterial infections in Latvia and tendencies of their dynamics in (population in Latvia ~ 2.5 miljons) Incidence Average dynamics in (%) Salmonellosis Shigellosis Other bacterial intestinal infections Unidentified enteritis Tuberculosis Leptospirosis Jersiniosis Diphtheria Wooping cough Scarlet fever Meningitis ~ Syphilis Gonorrhoea Chlamidiosis Lyme borreliosis HIV Nosocomial infections ~ -20

Riga Stradins University (Medical Academy of Latvia) Rector - J.Vetra Students ~ 1500 Professors 50 PhD 169 Departments - 40

Stradins Clinical Hospital Bacteriological laboratory Chief- A.Balode Molecular studies E.Miklashevics Clinical infectology U.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 gene Nosocomial infections in surgical clinic - (Klebsiella, P. aeruginosa) Nosocomial infections in nephrology - (Klebsiella, P. aeruginosa) Nosocomial infections in cardiosurgery Infections in obstetrics and gynecology - (Str. agalactiae) Cytokins in meningitis Ulceral 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, (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 diseases except tuberculosis Director - B.Rosentale Bacteriological laboratory - R.Paberza Department of infectious diseases of Riga Stradins University Head - L. Viksna Research: viral diseases, gram-negative infections

State Center of Tuberculosis and Lung Disease(SCTLD) All M.tuberculosis isolates from Latvia are being collected and analysed by classical bacteriological methods here. Bactec cultivation. Wide international collaboration CDC, WHO Director of SCTLD - J.Leimans Chief of Central Bacteriological Laboratory - G.Skenders Tuberculosis in Latvia New cases MDR HIV + TB 1 12 ~25 ~50

Multi-drug resistant (MDR) TB in Latvia, 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 Latvia Molecular 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 Faculty 04…Studies no genotoxicity by microorganisms J.Raipulis, Institute of microbiology and biotechnology University of Latvia 04…Bacterial safety of foodstuffs E.Liepins, Latvian University of Agriculture Department of Microbiology - Head I.Muiznieks Institute of Microbiology and biotechnology- Director - U.Viesturs