AAAR 33rd Annual Conference
October 20 - October 24, 2014
Rosen Shingle Creek
Orlando, Florida, USA
Abstract View
Improved Threat Characterization Using Next Generation Sequencing
ZAHRA CHAUDHRY, Peter Thielen, Verratti Kathleen, Christopher Bradburne, JHU APL
Abstract Number: 355 Working Group: Homeland Security
Abstract Most biosurveillance strategies and programs use PCR to detect threat agents. This technology is hampered by false positives and false negatives. Additionally, a positive hit provides no additional information such as whether or not the hit is actually a threat or within the noise of the background, if the threat is synthetic, or if it is a new or emerging pathogen. This study seeks to address these questions beyond the basic confirmation given by PCR, by collecting environmental aerosols and interrogating them using next generation sequencing, sensitive sample preparation techniques, and focused database development in order to fully characterize an aerosol sample.
Atmospheric aerosol samples were collected on the JHU/APL campus in Laurel, MD for 14 consecutive days to mimic a biosurvellance program. One sample day was spiked with a biosimulant to simulate a hypothetical threat event. The DNA was extracted from all the samples and purified using several methods: Powersoil, Boreal Aurora, LifeTech silica bead kit, and the Ampure bead kit. Two methods were used to aid in threat characterization: a hybridization-based background subtraction, and an informatics-based background subtraction. In the first method, the spiked sample is enriched with the background biome from a sample day with a similar back-trajectory and the combined sample is sequenced. In the second method, the spiked sample and background sample are sequenced separately, and the background data is informatically subtracted from the hypothetical data set. Results of the multiple purification methods and the characterization methods will be presented.
This study culminates in the creation of four databases: one for environmental background sequences, one for select agent reference strains, one for more focused threat sequences that are found in select agents, and one for synthetic sequences and commercial components that may indicate an engineered organism.