Metagenomic identification of pathogenic bacteria for pneumonia from postmortem lung tissue

Abstract

Pathologists have been concerned about the validity of bacterial cultures from lung tissue for the postmortem identification of pneumonia-associated pathogens. Therefore, we studied whether pathogenic bacteria that cause pneumonia could be identified via the metagenomic analysis of lung tissue sampled at autopsy from 11 pneumonia cases and nine non-pneumonia cases. We demonstrated that metagenomic analysis of the postmortem lung microbiota could identify a bacterial genus as a pneumonia pathogen when the genus was predominant and an established pathogen. However, it is important to diagnose Enterobacteriaceae or anaerobic bacteria as pneumonia pathogens, because their abundance in the lung microbiota of non-pneumonia cases supports postmortem translocation and replacement. Moreover, we confirmed that postmortem bacterial culture from lung tissue could be misleading for the identification of the pneumonia pathogen based on postmortem anaerobic changes and artificial culture conditions. To our knowledge, this study is the first to demonstrate the conditions under which metagenomic analysis of postmortem lung tissue can identify bacterial genera that cause pneumonia.

Keywords

• Pneumonia
• Postmortem diagnosis
• 16S rRNA metagenomic analysis
• Postmortem microbiota
• Bacterial culture