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Dalhousie scientist leading project to develop new software, database tools to combat antibiotic resistance

Posted by Fram Dinshaw, The Chronicle Herald on September 16, 2016 in Research, Bioinformatics & Algorithms, Faculty, News, Innovation, Research

A Dalhousie scientist is leading the way in pinpointing and analyzing antibiotic resistance in bacteria by profiling the DNA of entire communities of microbes.

But the clock is ticking for project leader Dr. Robert Beiko, as antibiotics are losing ground to new ‘superbug’ bacteria that have evolved resistance to conventional antibiotics, which threatens to undo nearly a century of medical progress.

“The problem of antimicrobial resistance is global and is affecting the order of millions of people right now,” Beiko told the Chronicle Herald.

Enter metagenomics, which allows the genetic profiling of microbes as a community.

There remains just one problem: Bacterial DNA datasets mapped out in this way are massive and contain huge amounts of irrelevant data.

Indeed, the increase of data production in recent years has been particularly dramatic in the ‘omics’ technologies — dealing with genomics and related fields of study — especially in the area of genome sequencing. Some estimates suggest that by 2020, data will be generated at up to one million times the current rate.

That’s why Beiko and his colleagues Andrew G. McArthur of McMaster University and Simon Fraser University’s Fiona Brinkman are leading a project to develop new software and database tools that will provide a near-instantaneous profile of bacterial samples.

“The real challenge in all of this is that these metagenomic methods generate huge amounts of DNA sequential data. Even a small metagenomic run can generate nearly the same amount of DNA equal to a human genome,” said Beiko. “We’re talking tens of millions of genes at a minimum.”

The federal government announced Tuesday that it is kicking in $250,000 in funding to Genome Atlantic and project co-lead Ontario Genomics, under whose auspices Beiko and his team are conducting their research.

Read the full story on The Chronicle Herald.