Single isolate pathogen sequencing

Project title
S. pneumonia resistance gene analysis

People involved
Principal investigator: Dr Clinton Moodley
Co-investigators: Kimona Rampersadh (PhD); Dr. Amanda Overmeyer (MMed)
Bioinformatics support team: Katie Lennard

Short description of project
The genetic characterization of pathogenic bacteria causing infection, and associated resistance and virulence factors which may contribute to these infections. Prokaryotic nucleic acid will be sequenced on the Illumina MiSeq platform using bacterial WGS from cultured isolates, to generate reads of bacterial genomes present.

Objectives
The data analysis will involve WGS de novo and remapping to reference sequences. The genomes generated will need to be annotated, resistance and virulence elements identified, and phylogenetic trees constructed.