Desktop DNA machine uncovers details about the deadly E. coli strain

Normally, it takes weeks to sequence pathogens of unknown origin. But scientists are using Ion Torrent's DNA machine to test E. coli in just two hours.

German authorities said contaminated bean sprouts are likely the cause of the outbreak of Escherichia coli in Europe. The death toll has risen to 35 and hundreds more suffer from severe kidney damage and bloody diarrhea.

Normally, it takes weeks to sequence pathogens of unknown origin. But scientists are using Ion Torrent's DNA machine to test E. coli in just two hours. The samples were tested by two groups - Beijing Genomics Institute in China and University Medical Centre Hamburg-Eppendorf in Germany - and the groups confirmed that this strain of E. coli is highly infectious and toxic.

While E. coli outbreaks have been occurring more often, the strain in Germany has been particularly dangerous.

E. coli is a bacterium that is found in the gut of humans and animals. While most strains are harmless, some can cause foodborne disease. It is transmitted when humans eat contaminated foods.

The current E. coli strain has it's roots in a strain of E. coli discovered in 2001. It had 10 years to acquire more genes for antibiotic resistance . The new genes may have been acquired through horizontal gene transfer.

The BGI researchers said "the analysis further showed that this deadly bacterium carries several antibiotic resistance genes, including resistance to aminoglycoside, macrolides and Beta-lactam antibiotics: all of which makes antibiotic treatment extremely difficult."

Ion Torrent's VP Maneesh Jain told me that the company's Personal Genome Machine rapidly identified the new hybrid E. coli. When Life Technologies, Ion Torrent's parent company, received fecal samples from patients, the sequencing only took a few hours. After all the sample prep work and the data analysis that followed, the whole process took about three days.

The PGM uses semiconductor technology to do rapid sequencing. By getting rid of light and sequencing right on a semiconductor chip, the machine decodes DNA quickly. Speed is very important, especially when you're in the middle of a healthcare crisis.

The machine is about the size of a desktop computer. Many labs can afford the PGM because it only costs $50,000.

I recently went to Ion Torrent to see how the PGM worked :

Researchers can get results quickly and publish faster, Jain said. Clinicians can get results to patients much faster. The results are delivered via an iTouch.

However, the machine can’t do a full genome sequence. But that’s not the point of it. It’s a research tool. It will enable researchers to sequence cancer samples or microbes. It will give researchers access to do more DNA-based research.

In this case, the researchers will continue to study the genes of this deadly strain of E. coli and put it in context with other types of strains. Knowing more about the DNA of this particular E. coli will help researchers develop diagnostic kits to help the outbreak from spreading.

DNA sequencers are playing a more important role in crises like this. As Matthew Herper pointed out in Forbes, a DNA sequencer from Pacific Biosciences was used to decode the DNA of the cholera bug that plagued Haiti.

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