Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Existing detection technologies are based on nucleic acid amplification of sequences from one or a small set of organisms. While they are able to rapidly identify selected pathogens at the species or strain level, they cannot be multiplexed to the degree required to detect hundreds to thousands of different organisms.
Lawrence Livermore National Laboratory’s scientists have developed the Lawrence Livermore Microbial Detection Array (LLMDA), a technology enabling detection of bacteria, viruses and other organisms. This technology has shown value for applications in detection for product safety, diagnostics and bioterrorism events.
LLMDA contains probes fitted onto a one-inch by three-inch glass slide. Each probe tests for a particular sequence of DNA and small groups of probes can be used to check for specific bacteria or viruses up to the species level. The LLMDA can test for over 2,000 viruses and 900 bacteria. The newer version of the LLMDA will expand that capability to nearly 6,000 viruses and 15,000 bacteria as well as fungi and protozoa organisms. After DNA and/or RNA is extracted from a sample, it is applied to the LLMDA. Any probe that detects its specific sequence will fluoresce, and be read by a scanner. The raw data from the scanner is then analyzed using algorithms developed by LLNL run on high performance computing (HPC) machines.
Bioinformatics is used in identifying the large numbers of nucleic acid sequences, or probes, which are the signatures of microbes. LLNL has developed software to design probes from genomic data. High performance computers at LLNL play a crucial role in meeting the extensive requirements of designing these probe sequences and updating them regularly.
Publications:
- The Microbial Detection Array Combined with Random Phi29-Amplification Used as a Diagnostic Tool for Virus Detection in Clinical Samples. Erlandsson L, Rosenstierne MW, McLoughlin K, Jaing C, Fomsgaard A., PLoS ONE 6(8):e22631, 2011.
- Collaboration with the Marine Mammal Center to identify potential causes of death of sea lions and seals was featured on Channel 2 KTVU News, June 2010. (The transcript can be read here.)
- Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus. Victoria JG, Wang C, Jones MS, Jaing C, McLoughlin K, Gardner S and Delwart EL. J. Virol. 84: 6033-40, 2010.
- This work was featured on KGO-TV San Francisco, CA, ABC Channel 7 News, April 2010. (Watch the report here.)
- A Microbial Detection Array (MDA) for Viral and Bacterial Detection. Gardner SN, Jaing CJ, McLoughlin KS, Slezak TR, BMC Genomics 11:668, 2010.
- A functional gene array for detection of bacterial virulence elements. Jaing C, Gardner S, McLoughlin K, Mulakken N, Alegria-Hartman M, Banda P, Williams P, Gu P, Wagner M, Manohar C, and Slezak T. PLoS ONE, 2008.
- Gardner, S.N., et. al., U.S. Patent Publication 2011/0152109.
- Gardner, S.N., et. al., U.S. Patent Application 2013/0267429
- Rapid and comprehensive detection of viruses, bacteria and fungi.
- The designed probes can be used on various microarray platforms that support long probes, such as from Roche NimbleGen and Agilent Technologies.
- Custom probe sets can be designed (and further developed).
- High performance computing enables the bioinformatics and data processing required for designing probes and analyzing data from the comprehensive arrays.
LLMDA has a wide variety of potential applications:
- Public Health
- Animal and Crop Health
- Homeland Security
- Food/Product Safety
- Force Protection
- Forensics
- Molecular Diagnostics