Profile

Cystic fibrosis (CF) is a genetic condition, which causes difficult breathing, clearing mucus from the lungs and is for life. The lifespan of patients with CF has increased substantially but their lungs remain at risk from various microbes.

The leading cause of lung disease and death in cystic fibrosis patients is lung infection by the bacteria Pseudomonas aeruginosa; normally harmless, but in various people – such as those in hospital with burns, wounds or undergoing surgery – it can be harmful and even fatal.

There is a great amount of variation between separate isolates of Pseudomonas aeruginosa, for example those isolated from a CF lung in Spain or a lake in Australia will have different genes and variations of common genes.

To better understand this bacteria The International Pseudomonas aeruginosa Genomics Consortium based in Canada is sequencing 2,000 whole genomes of this bug; that is, all of its DNA.

It’s my job, working with the consortium and with a particular strain, The Liverpool Epidemic Strain, to better understand the genetic basis of how Pseudomonas aeruginosa causes disease, why some are more or less harmful, how it spreads and how it acquires antibiotic resistance genes.

Ultimately, this gene data will be incorporated with patient data of the past to fit statistical models and machine learning algorithms (artificial intelligence), to predict in the future which strains of Pseudomonas aeruginosa or even genetic variants of that strain will have a poorer outcome for the patient, upon infection.

This research is funded by the Cystic Fibrosis Trust.

When I’m at the computer I’ll be using other people’s software or writing my own to analyse DNA data from Pseudomonas aeruginosa and attempting to better understand its biology as a result. This might involve comparison of hundreds of these bacterial genomes, each with 6 million ‘bits’ of DNA.

When I’m in the lab I’ll be plating bacteria, allowing them to grow overnight and then extracting DNA from them, copying small chunks of their DNA I’m interested in or checking which antibiotics kill them and which don’t!