Evaluation of DNA extraction methods to detect bacterial targets in aerosol samples

Abstract DNA-based monitoring of pathogens in aerosol samples requires extraction methods that provide high recovery of DNA. To identify a suitable method, we evaluated six DNA extraction methods for recovery of target-specific DNA from samples with four bacterial agents at low abundance ( Bacillus anthracis, Yersinia pestis, Burkholderia pseudomallei, and Francisella tularensi s, each at about 10 5  CFU per sample. A custom method using paramagnetic Dynabeads for DNA capture greatly outperformed the other five methods. The cDynabead method provided about 80% recovery of target-specific DNA. The cDynabead method and a filtration method were further evaluated for DNA recovery from bacterial agents spiked on filters ( c.a. 10 5  CFU of each agent per filter quadrant) that were subsequently used to collect background outdoor air particulates for 24-h. The filtration method generally failed to recover detectable quantities of target DNA from the spiked filters, suggesting at least a 100-fold loss of target DNA during extraction, whereas the custom cDynabead method consistently yielded DNA sufficient for target detection.