Use of peptide nucleic acid probes for pathogen-targeted metagenomics

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Metagenomics is becoming an important tool for comprehensive pathogen detection from clinical specimens. So far, using this methodology, we have detected pathogenic bacteria, influenza viruses and noroviruses from clinical samples. In this study, to increase the sensitivity and efficiency of our method, we developed a basic protocol for influenza-targeted-metagenomics using a peptide nucleic acid (PNA) probe. A PNA probe that recognizes a conserved sequence among influenza A viruses was designed and synthesized. The efficiency of the probe for target capturing was assessed using a mouse model for influenza infection. We show that treatment of the probe results in a 27-fold increase in the ratio of mouse genome to target DNA, compared to a 7-fold increase without the use of the probe. The protocol established here will serve as a basis for pathogen-targeted metagenomics.