Forschungsprojekt: Exploring the genomics tool box for tick-borne bacterial pathogens of the Borrelia burgdorferi sensu lato species complex
Kurzbeschreibung
In the proposed project we will evaluate the influence of different library preparation methods and sequencing technologies on the assembly and completion of bacterial genomes following next generation sequencing (NGS) using the widely distributed pathogen Borrelia burgdorferi as an example. Technologies to be compared include Illumina technology and PacBio sequencing. As the method of library preparation may critically impact the outcome of sequencing efforts, especially at genomic loci which are difficult to analyze, such as repeats, GC rich regions etc., we will explore and systematically evaluate the advantages of the different methods in this project.
We will use spirochetes of the Borrelia burgdorferi sensu lato complex for the proposed project. The complex genome structure of these tick-borne pathogens is ideally suited to compare the impact of different methods and sequencing platforms on successful prokaryotic genome and especially plasmid assembly. The genomes of Borrelia are highly fragmented, and possess a large number of linear and circular plasmids. These plasmids encode the majority of outer surface proteins located at the host-pathogen interface and may represent virulence determinants. Therefore, proper plasmid assembly is an absolute requirement to understand how plasmids differ between strains and what effect this has on human pathogenesis/ host associations. This is particularly important for genospecies such as B. bavariensis for which limited plasmid information is available but which is one of the main species causing neuroborreliosis. At the German National Reference Centre for Borrelia, the Slovak Academy of Sciences and the Medical University of Vienna, we have expertise in culturing and characterizing Borrelia species. In addition to experience in molecular epidemiology using multilocus sequence analysis, the LGL recently established NGS for isolate characterization. Our ultimate aim is to provide a set of completed reference genomes for different Borrelia species, which are currently not available but very important for understanding Borrelia human pathogenesis. Such information will ultimately aid the development of more precise diagnostic and therapeutic tools.
Laufzeit: 2015 bis 2016