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Investigating Enterohaemorrhagic Escherichia coli (EHEC) strain variability
Following bacterial evolution is essential to understand the development of pathogens and infectious disease. The Enterohaemorrhagic Escherichia coli (EHEC) outbreak during 2011 received quick response from the scientific community in order determine the genome of the new pathogen, and from that develop reliable assays for the hospitals. However, little is known of the variation of EHEC strains. We have developed a protocol for sequencing long stretches of DNA in heterogeneous samples with single molecule resolution. This is highly relevant for deep analysis of complex bacterial communities, such as of the human gut, since we will be able to determine the composition at the species or even strain level, and as well for typing infectious agents in e.g. blood samples. In this project, you will be working with DNA from EHEC isolates from patients to investigate whether the strains of the samples can be separated. We will compare our novel typing method to conventional methods previously applied to the same isolates, and determine how well our method can separate different strains. You will be working with both the basic, necessary tools of molecular biology including PCR, sample barcoding, enzymatic degradation, ligation and circularization to name a few. And you will also be using the state of the art sequencing facility of Science for Life Laboratory, including the latest high throughput sequencing instruments and library preparation techniques. Depending on the rate of success with the bacterial libraries, the protocol may also be adapted for fungal species, and could readily be applied for a huge range of questions in evolutionary and clinical microbiology.
Informationen om uppsatsförslag är hämtad från Nationella Exjobb-poolen.