HPC Aids Fight Against Toxic Bacteria

By Tiffany Trader

May 13, 2014

A group of researchers at the University of South Wales’ Genomics and Computational Biology lab are using supercomputing to help solve a critical public health issue. With antibiotic resistance a growing concern and drug resistant infections, such as MRSA and tuberculosis, on the rise, scientists are keen to understand how bacteria evolve into deadly strains.

The University of South Wales project, led by PhD student Farzana Rahman, is focused on predicting drug resistance so that patients receive the drug that is most likely to be effective. The effort is part of the new frontier of personalized medicine, which holds enormous promise for treating and curing many kinds of diseases, including bacterial infections.

Supercomputer modeling illustrates how fairly benign bacterial strains can evolve into toxic ones, such as E Coli 0157. The work is supported by High Performance Computing (HPC) Wales, which provides the advanced technology that facilitates science that is both compute- and data-intensive.

In the video case study below, Rahman describes her experience growing up in Bangladesh, where diseases like typhoid, cholera, and gangrene plagued the population. Rahman was deeply troubled by the suffering and was moved to make a difference to bring positive change to society and human life.

Click to open video

“While scientists are accessing many avenues to solve this issue, my research takes a different approach,” says Rahman. “I’m developing an open method to predict the risk of a bacterial strain becoming toxic. This project involves data mining and biostatistical modeling using high-performance computing.”

Fujitsu is funding the transformational research, which the company believes will have a huge impact both socially and commercially. Rahman’s vision for her work is to create a mechanism for more affordable, relevant treatments that can be used by public health organizations, disaster relief efforts and emergency services. Currently, identifying the best antibiotic for a given strain can take days to weeks, but with this new approach, the matching process can be done in a matter of hours. When you’re fighting an infectious disease, getting an effective treatment days sooner can literally be the difference between life and death.

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