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Rapid genome analysis enhancing analysis of epidemiology and antimicrobial resistance in microbial pathogens

A new study from the Institute of Food Research could help us trace sources of microbial infections more quickly.

27 October 2015

It uses a computer program to analyse large amounts of genome sequence data, without the need for large, powerful computer equipment, making this sort of analysis more accessible to a greater number of scientists.

It could also be used in other applications such as screening bacteria for antibiotic resistance, according to Dr Arnoud van Vliet from the IFR, which is strategically supported by the Biotechnology and Biological Sciences Research Council.

campylobacter_genome_

campylobacter_genome_

 

The study, published in The Journal of Clinical Microbiology shows that a previously described software program, called Feature Frequency Profiling (FFP), can be utilised for rapid analysis of large genome datasets on a standard desktop PC.

Dr van Vliet from IFR’s Gut Health and Food Safety programme, working with a colleague from University Medical Center Utrecht, compared the FPP software with the output from currently used software analyses, running on much more powerful computers. They used 377 Helicobacter pylori genomes, deliberately selecting bacteria that are known to be challenging to work with.

Read more about this work on the Gut Health and Food Safety blog

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