Catching a Pathogen

When a particularly deadly pathogen appears, any delay in identifying it can slow the development of treatments and diagnostic tests. But until recently, identifying a pathogen usually required some advance knowledge of its genetic makeup. Now a team led by W. Ian ­Lipkin, director of the Center for Infection and Immunity at ­Columbia University’s Mailman School of Public Health, has shown how to use advanced gene-sequencing tech­nology to identify even the most mysterious pathogen. Lipkin starts by partly isolating a pathogen’s genetic material from that of its human host. Then he sequences the ­sample using technology developed by 454 Life Sciences of Branford, CT; unlike other systems, 454’s doesn’t require prior information about the sequence you are looking for. Finally, ­Lipkin searches a database to see if any known sequences match the ones he’s identified.

The team’s first feat: identifying the virus that killed three Australian transplant patients who had received organs from a single donor. Lipkin has since used the technique to identify more than 20 viruses.

1. To identify an unknown pathogen, researchers begin by extracting a tissue sample from an infected patient.

2. An enzyme is used to remove all traces of human and microbial DNA, leaving a mix of human and microbial RNA sequences. This step can increase the technique’s sensitivity to viruses.

3. DNA sequences that correspond to these RNA sequences are copied millions of times. Then they’re read using technology from 454 Life Sciences.

4. The sequencing done, computational techniques developed at Columbia University weed out human sequences and assemble the remaining microbial sequences to create the “fingerprint” of the mystery microbe.

5. Bioinformatics software compares the microbial fingerprint against databases of known microbial sequences, searching for close matches. Once the variant is fully characterized, diagnostic tools can be developed to detect the microbe in future patients.

Credit: Tami Tolpa