A new study from the Institute of Food Research could help us trace sources of microbial infections more quickly.
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.
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.
We were really pleased to see that the analysis methods stood up to the challenge. This suggests that we can do these types of analyses with many other bacteria of interest, and look forward to the field further developing. Dr Arnoud van Vliet
van Vliet AHM, Kusters JG Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility, Journal of Clinical Microbiology 53, 2877-88 doi: 10.1128/JCM.01357-15.