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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)

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slide1

GENOME SEQUENCING AND FUNCTIONAL GENOMICS NATIONAL PROGRAM IN LATVIA

AND ERA-NET “PATHOGENOMICS”

Viesturs Baumanis, Latvian Council of Science

Berlin, October 13 th, 2004

slide2

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

slide3

Incidence per 100.000 population for bacterial infections

in 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

slide4

Riga Stradins University

(Medical Academy of Latvia)

Rector - J.Vetra

Students ~ 1500

Professors 50

PhD 169

Departments - 40

slide5

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)

slide6

Medical Faculty, University of Latvia

Department of Microbiology - Head A.Zilevica

Research - Multi drug resistant staphilococci

Urogenital, veneral infections, dermatomycosis ( V.Miltins)

slide7

Nosocomial infections - Staphylococcus spp.

Prevalence of methicillin-resistant staphylococci in Hospital of

Traumatology and Orthopedics, Latvia, 1998-2002 (by A.Zilevica).

slide8

Clinical hospital Nr.7 - “Gailezers”

The largest hospital in the Baltic countries

Director - E.Platkajs

Urological infections - P.Ivdre

slide9

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

slide10

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

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
Multi-drug resistant (MDR) TB in Latvia, 1998-2002

Multi-drug resistant M.tuberculosis - resistant at least to rifampin and isoniazid

(State Tuberculosis and Lung Disease Center data)

slide12

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 o f 109 mdr m tuberculosis isolates
Spoligopattern of 109 MDR M. tuberculosis isolates

Dendrogram

Other genotypes (non-Beijing group)

Beijing genotype - 58% Higher % of double mutations in the rpoB and K43R typical in the rpsL

slide15

Biological Faculty University of Latvia

Department of Microbiology - Head I.Muiznieks

Institute of Microbiology and biotechnology-

Director - U.Viesturs

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