Master Thesis in Human Medicine
Creation of a phylogenetic tree of 160 Corynebacterium sp strains
The genus Corynebacterium includes more than 150 species and belongs to the family Corynebacteriaceae. Members of this genus are only rarely associated with disease among humans and animals. Common pathogenic members include C. diphtheriae, the causative agent of the disease diphtheria, and C. pseudotuberculosis and C. ulcerans, which are frequent causes of zoonotic infections. Historically, species of the genus Corynebacterium have been differentiated based on their host, ecological niche and biochemical characteristics. Newer methods are MALDI-TOF MS or sequencing of specific genetic loci. As a result of decreasing sequencing costs and improved tools for genomic analysis, whole-genome sequencing is increasingly being performed for taxonomic classification of Corynebacterium strains.
For this project 160 strains were collected during routine diagnostics at the clinical microbiology laboratory of the University hospital Basel, Switzerland and were submitted to whole genome sequencing.
The work of this thesis consists of the analysis of the sequenced strains and the construction of a phylogenetic tree of the different sequenced Corynebacteria to illustrate their shared evolutionary history based on physical or genetic similarities and differences. The similarity in their genetic makeup will be measured based on pairwise distance between their gene sequences using sequence alignment methods. The set of sequenced strains may also contain the sequences of yet unidentified Corynebacterium sp.. In case new species are detected they will be re-cultivated and isolates will be submitted to the strain collection at the Louis Pasteur Institute, Paris, France as well as the DSZM-German Collection of Microorgansims, and Cell Cultures, Braunschweig, Germany.
Your position
- literature research
- evaluation of quality of sequencing results
- creation of a phylogenetic tree
- identification of potentially new strains/species
- comparison of phenotypic marker (resistance, biochemistry)
Your profile
- Interest in biology and biostatistics
- Prior knowledge in biostatistics
- Programming skills (e.g. R++)
Application / Contact
Contact
Dr. med Peter Keller, Fachleiter, FAMH Medizinische Mikrobiologie, Labormedizin, Klinische Bakteriologie/Mycologie, Universitätsspital Basel, petermichael.keller@usb.ch, Tel. +41 61 556 57 49.
Please submit your application (CV, motivation letter, relevant certificates and diploma) by email to: petermichael.keller@usb.ch
