Open master projects

1. Whole genome sequence based detection and typing of Avibacterium paragallinarum and related species. 

Avibacterium paragallinarum is responsible for infectious coryza, a serious poultry disease worldwide. Increasing free range conditions of poultry is providing an opportunity for the disease under free range conditions in N. Europe where risk for the disease normally is low related to high biosecurity. Control with vaccination and antibiotics require typing and identification of the agent involved, respectively. Classical serotyping is not performed routinely and the molecular tools have limitations in sensitivity and accuracy. The aim of the project is to develop alternative identification and typing systems for Avibacterium paragallinarum and related species based on whole genome sequence comparisons. The project will use the BIGSdb platform to compare and extract whole genome multilocus typing scemes of use for identification and typing of Avibacterium. The project will generate and compare different strains of Avibacterium mainly with origin in poultry production from Europe and S. Africa. The project will contribute to a review article of Avibacterium.

2. Investigation of host relationship of Mannheimia varigena for swine and cattle.

This species of Mannheimia varigena is very special of being pathogenic to both pig and cattle with typical lesions as septicaemia and pneumonia, respectiveiy. In the project a collection of 30 strains have to be investigated for molecular properties which can explain the host preference to pig and cattle, respectively. It needs to be considered if the populations associated pig and cattle, respectively can be named as new subspecies. The project will involve detailed molecular characterization of the strains and include whole genomic sequencing. The student will gain specialized knowledge about molecular characterization including identification of bacterial pathogens of veterinary importance. 

3. Investigation of members of Mannheimia group V for virulence and improved identification procedures.

Members of Mannheimia group V are not belonging to knows species. Their role in disease is unknown mainly related to limited procedures for identification. Twenty-two strains isolated from pneumonia and rumen of cattle will need to be characterized in the project. The aim is to improve classification hopefully followed by naming as new species and to characterize the virulence factor RTX (repeat in toxin) in the strains by whole genomic sequencing. The student will be specialized in advanced molecular characterization of bacterial pathogens of veterinary importance.   

4. Characterization of possible host association of Pasteurellaceae isolated from lions, tigers, leopards and cheetah.

The aim of the present investigation is characterize a strain collection of Pasteurellaceae isolated from large cats in confinement to extend our knowledge on the diversity and possible host adaptation of these taxa. Previous investigations have shown the majority of isolates from large cats to belong to Pasteurella multocida and taxon 45 of Bisgaard. We have performed preliminary investigation of a collection of 50 isolates of Pasteurellaceae form large cats. The partial rpoB sequence was determined for all strains and sequencing of the 16S rRNA gene was performed with 14 strains representing rpoB diversity. The phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the 50 isolates characterized formed five distinct groups. Two were related to known taxa (Frederiksenia canicola and taxon 46 of Bisgaard) whereas three were unrelated to know species or taxa. In the project you will work with whole genomic sequencing to further characterize the strains aiming of naming these taxa as new species. Indentification procedures will be developed for identification.