Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation

Abstract

Background: The lung microbiome is composed of bacteria, viruses and fungi that interplay with each other and participate in mucosal defense protecting the lungs from colonization and infection by pathogenic microorganisms. In intensive care, a change in the composition of the lung microbiome, called dysbiosis, could be associated to the occurrence of ventilator-associated pneumonia. The objective of the study was to test a method to assess the lung virome. Methods: We applied a protocol including the same nucleic acid extraction methods as used for bacterial lung microbiome and a metagenomic next-generation sequencing (mNGS) to detect eukaryotic RNA, DNA viruses and bacteriophages. Results: Our method was able to detect all viruses identified with multiplex polymerase chain reaction (PCR), other eukaryotic viruses not included in the multiplex PCR panel, and bacteriophages. Notably persistent viruses, mainly Herpesviridae, associated with opportunistic infections and those showing immunodepression such as Anellovirus have been identified. Conclusions: A better description of the global composition and evolution of the lung microbiome, including viruses, could help to better understand ventilator-associated pneumonia occurrence and outcomes.