Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens

This study compared six automated nucleic acid extraction systems and one manual kit for their ability to recover nucleic acids from human nasal wash specimens spiked with five respiratory pathogens, representing Gram-positive bacteria (Streptococcus pyogenes), Gram-negative bacteria (Legionella pneumophila), DNA viruses (adenovirus), segmented RNA viruses (human influenza virus A), and non-segmented RNA viruses (respiratory syncytial virus). The robots and kit evaluated represent major commercially available methods that are capable of simultaneous extraction of DNA and RNA from respiratory specimens, and included platforms based on magnetic-bead technology (KingFisher mL, Biorobot EZ1, easyMAG, KingFisher Flex, and MagNA Pure Compact) or glass fiber filter technology (Biorobot MDX and the manual kit Allprep). All methods yielded extracts free of cross-contamination and RT-PCR inhibition. All automated systems recovered L. pneumophila and adenovirus DNA equivalently. However, the MagNA Pure protocol demonstrated more than 4-fold higher DNA recovery from the S. pyogenes than other methods. The KingFisher mL and easyMAG protocols provided 1- to 3-log wider linearity and extracted 3- to 4-fold more RNA from the human influenza virus and respiratory syncytial virus. These findings suggest that systems differed in nucleic acid recovery, reproducibility, and linearity in a pathogen specific manner.

Research highlights▶ Comparison of six automated nucleic acid extraction systems and one manual kit for extraction of nucleic acids from DNA/RNA Respiratory Pathogens. ▶ All methods yielded extracts free of cross-contamination and RT-PCR inhibition. ▶ All automated systems recovered Legionella pneumophila and adenovirus DNA equivalently. ▶ The MagNA Pure protocol demonstrated the best DNA recovery from the Streptococus pyogenes than other methods. ▶ The KingFisher mL and easyMAG protocols are most suitable for RNA extraction from the human influenza virus and respiratory syncytial virus.