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SPIE Professional July 2013

Bug detection gets quicker

A new technology with clever algorithms and a tiny microarray can identify thousands of pathogens in 24 hours.

By Arnie Heller

Photonics for a Better World logo

Speed and accuracy in identifying viruses, bacteria, fungi and other disease-causing pathogens are becoming increasingly important for public health, food safety, and biodefense. While several techniques exist for identifying pathogens via their genetic code, most methods are costly and/or slow.

The new technology, the Lawrence Livermore Microbial Detection Array (LLMDA), rapidly identifies any known microbe whose genetic code has been sequenced by combining innovative bioinformatics with a microarray.

Livermore scientists analyzed the genetic code of every microbe that has been sequenced (about 6,000 species and strains in all) and then selected the roughly 360,000 most important genetic markers. In one microarray configuration, 360,000 probes—short stretches of DNA or RNA that complement the isolated genetic markers—are arrayed in a microscopic square grid on a 2.5- by 7.5-centimeter glass slide.

LLNL biologist Crystal Jaing is shown loading a fluorescently labeled viral DNA sample onto the LLMDA as fellow biologist James Thissen watches.

When a fluorescently labeled fluid sample containing the genetic material of microbes contacts the microarray’s probes, only the squares with DNA or RNA unique to a particular organism are activated. The activated squares produce a fluorescent pattern, from which species present in the sample are identified. (See above.)

Laser and photodector help process pathogens

In this way, multiple pathogens are detected simultaneously, with typical processing times of less than 24 hours.

Analyzing the microarray results requires a workstation with 200 gigabytes of memory and 12 processors as well as the Livermore-developed analysis algorithm that makes sense of the voluminous data produced by the scan.

First, the slide containing x hybridized probes is placed in a scanner. A laser then scans across the slide’s surface, and a photodetector picks up the fluorescing squares. Within a few minutes, an enormous image file of 100 megabytes is built up.

Commercial software analyzes the image and produces a file quantifying the fluorescent intensity at each spot.

The LLMDA can identify 3111 viruses, 1967 bacteria, 94 protozoa, 136 fungi, and 126 archaea (primitive bacteria).

In trials for international researchers, government agencies, and health-product companies, it has accurately and rapidly identified bacterial and viral pathogens present in human and animal clinical samples, environmental samples, and product samples.

Government agencies and private research centers are collaborating with Livermore’s team to identify viruses and bacteria that are correlated with high cancer risk, vaccine safety, and defense against a bioterrorist attack.

If widely adopted, LLMDA could allow professionals in medicine, pharmaceuticals, law enforcement, product and food safety, public health, animal health, the military, and global disease surveillance to detect within one day any virus or bacteria included among the array’s probes.

The device also could realize significant cost savings in routine health care by readily identifying bugs causing the common cold, influenza, and other sicknesses.

  • Excerpted with permission from Science & Technology Review.
  • Read the full article.
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DOI: 10.1117/2.4201307.22

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