Whole Genome Sequencing analysis of an outbreak of Mycobacterium caprae in alpine region affecting both domestic and wildlife animals: molecular epidemiological perspective By Ashok Varadharajan Msc Epidemiology LMU pervisor . Helmut Blum boratory for Functional Genome Analysis ne Center of the LMU odor-Lynen-Strasse 25 377 Munich
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Whole Genome Sequencing analysis of an outbreak of
Mycobacterium caprae in alpine region affecting both domestic and wildlife animals: molecular
epidemiological perspective
ByAshok VaradharajanMsc EpidemiologyLMU
SupervisorDr. Helmut BlumLaboratory for Functional Genome AnalysisGene Center of the LMUFeodor-Lynen-Strasse 2581377 Munich
BACKGROUND Tuberculosis An infectious bacterial disease characterized by the growth of nodules (tubercles) in the tissues, especially the lungs.
Mycobaterium Tuberculosis Complex (MTC) Genetically related group of Mycobacterium species causing tuberculosis in humans or other organisms Mycobacterium
tuberculosis
Mycobacterium africanum
Mycobacterium bovis
Mycobacterium microti
Mycobacterium canettii
Mycobacterium caprae
Mycobacterium pinnipedii
Mycobacterium suricattae
Mycobacterium mungi
tubercles
BACKGROUND
Mycobacterium caprae Formerly known as M. Tuberculosis subsp. caprae and M. Bovis subsp.
caprae
Designated as new species in the MTC in 2003
Predominantly found in Central and Western European countries
Pathogen can affect both animals and Humans
Differentiating Features in MTC Special combination of polymorphisms in the genes of oxyR , pncA,
katG, gyrA and gyrB Region of Differentiation 4 (RD4)
BACKGROUND
Phylogeny of MTC (Rodriguez-Campos et.al, 2014)
Differences between
M. caprae and M. bovis
PROBLEMS
Increased prevalance of tuberculosis by M. caprae around Alpine regions
Affected in various species such as Cattle, Red deer, Fox and Human
Lack of Knowledge about the transmission of infection between domestic and wildlife animals
Little knowledge about genomic features of M. Caprae concerning markers for genotyping
Lack of Complete genome sequence of M.caprae, complicating the differentiation of M. caprae and M. bovis
OBJECTIVES
Analysis of spatial spread of the disease by Whole Genome Sequencing analysis.
1. Identification of Variants 2. Clustering of isolates 3. Analysis of Infection chain4. Analysis of RD4 region
Development of Web Integrated Environment 1. Automation of Variant Calling pipeline 2. A tailored database to store the identified variants3. Real time generation of results such as phylogenetic tree, Minimum