Researchers identify illnesses far more quickly


When a deadly E. coli outbreak hit Germany this summer, scientists struggled to pinpoint its source. But the hunt quickly expanded, from mapping the outbreak, to mapping the bug itself.

"Not only sequence the entire genome of that E. coli strain, but sequencing 11 other strains that were in the same type, or closely related, to understand where does this thing fit in the evolutionary tree and how could it have evolved to become so pathogenic?" said Eric Schadt, Ph.D. from Pacific Biosciences in Menlo Park.

Schadt said researchers used the company's high-speed DNA sequencing technology to identify the genes that made the strain both highly toxic and resistant to antibiotics, giving doctors a roadmap to predict the strain's effects and how to treat it.

"For example with this strain in Germany, we predicted that in response to treatments with Cipro, one of the common antibiotic treatments for E.coli, that not only would it be resistant, but also increase toxin production, so actually make you feel worse," said Schadt.

Charles Chiu, M.D., tracks major outbreaks from the Viral Diagnostics and Discovery Center at UCSF. He believes a wave of new DNA technology could ultimately allow health officials plan for mutated pathogens, before they even show-up.

"If we can really understand the patterns of how these bacteria evolve, we'll better be able to understand and prepare for these outbreaks and potential problems in the future," said Chiu.

Chiu says his researchers are currently studying the genomes of bugs ranging from antibiotic resistant staph known as MRSA to influenza.

"Having the whole genome sequence will yield some important information in terms of what strains exist out there, and potentially what strains of influenza that you wish to target with the design of a vaccine," said Chiu.

Newer high-end machines can identify most pathogens, and parse their genomes in a matter of hours. Some researchers even envision a kind of early warning system, using widespread sampling within the community.

"Predict sort of the evolution, evolutionary directions of these bugs and how much we expect them to arise in the population in the future," said Schadt.

And one update: Chiu's lab is currently working on a high-speed micro-array designed to identify every currently known virus, including the avian flu.

Written and produced by Tim Didion

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