Respiratory Viruses in Mechanically Ventilated Patients

A Pilot Study

Raquel Nazareth; Maria-Jesus Chasqueira; Maria-Lúcia Rodrigues; Carolina Paulino; Catarina Conceição; Lia Lêdo; Úrsula Segura; Madalena Santos; António Messias; Pedro Póvoa; Paulo Paixão


BMC Pulm Med. 2020;20(39) 

In This Article


The human microbiome was firstly defined by Joshua Lederberg in 2001, as a community of microorganisms that live in our organism, establishing a relationship of commensalism, symbiosis or pathogenicity.[1]

Due to several factors, the study of the human virome has been neglected in comparison with the bacterial microbiome, namely the heterogeneity of the viral genome that leads to the absence of universal molecular markers, such as 16S ribosomal RNA for bacteria or fungal internal transcribed spacer region for fungi, the difficulty in working with small biomass samples, the interference of genetic material from the host, inadequate bioinformatic instruments for its analysis and the absence of robust databases.[2,3] In the particular case of lung virome, there is also the problem of the sample collection, unlike with other mucosal surfaces which are easily accessible.

Until recently, the lung was considered a sterile organ,[4] which was explained by the protective mechanisms of the upper airways and the barrier function of the mucosa of the lower airways. The presence of bacteria in the lower airways was interpreted as a pathological phenomenon, based on cultural microbiological information.[5] It was explained as transient migration by microaspiration, reflecting the composition of the upper respiratory tract, although the biomass would be lower. It was further conceded that the lower respiratory tract microbiome could be related to contamination of the upper tract during sampling.[6] According to Dickson and Huffnagle, the notion that the lungs are sterile is still frequently stated in textbooks, virtually always without citation.[7] Respiratory culture-based protocols sought only to identify clinically significant pathogens.[8]

At the beginning of the current decade, studies based on culture-independent methods have shown the presence of a small amount of bacterial communities in the lungs of healthy, non-smoker individuals, with some diversity in their elements. There are few studies available in the literature on the characterization of the respiratory tract virome, especially of the lower airways.[9–14] Essentialy, most of the studied population was in the pediatric age and the majority of them had respiratory infection. Most of the observations made on these studies were based on upper respiratory tract samples, like nasopharyngeal swabs and nasal mucosa exudates, because of its greater accessibility, assuming that the results obtained could translate what was happening in the lower airways.

The objective of this study was to evaluate the presence of respiratory viruses in the lower airways of individuals with and without acute lower respiratory infection undergoing invasive mechanical ventilation. In order to achieve this, we evaluated the presence of the most common respiratory viruses in the population,[15] in lower airway samples collected from individuals with and without respiratory infection, undergoing mechanical ventilation, using real-time Polymerase Chain Reaction and Reverse Transcription-Polymerase Chain Reaction (respectively PCR and RT-PCR) techniques.