Wiki¶

Study background¶

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).

Pipeline tool options considered¶

Data location¶

Raw reads¶

• E. coli test reads: Med Micro server( http://athena.medmicro.uct.ac.za:5000/ )in the File Station /MedMicro/Clinton/E. coli/original_data

Processed data¶

Final results for publishing¶