Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens. clostridium difficile

We assessed the consistency between PCR from a diagnostic laboratory, qPCR from a research laboratory, and metagenomic 16S rRNA gene and whole genome shotgun sequencing in Clostridium difficile identification in diarrhea stool samples. Metagenomic sequencing is comparable to PCR and qPCR in known pathogen identification. It also allows identification of some unknown pathogens and co-infections. Integration of metagenomic sequencing into diagnostic testing might facilitate the diagnosis of infectious diseases