Pathogen outbreak study - Pseudomonas single isolate WGS

Project title
Pathogen outbreak study - Pseudomonas single isolate WGS

People involved
Principal investigator : Prof Mark Nicol
Bioinformatics support team: Katie Lennard

Short description of project
This study was prompted by an unusual outbreak of wild type Pseudomonas that coincided with the Cape Town drought. Preliminary molecular analysis suggests clonality, the interest is therefore to try an establish how this outbreak came about and whether the drought is in some way responsible. Pseudomonas are waterborne opportunistic pathogens that can form biofilms in plumbing pipes. One hypothesis is therefore that the drought, with decreased water pressure allowed increased biofilm formation and subsequently increased concentrations in drinking water. The data will include WGS of blood culture isolates and water samples from before, during, and after the outbreak (96 samples).

Objectives
Perform whole-genome assembly of single isolates. Trace clonality, SNV and look into drug resistance and virulence elements.