Comparative meta-transcriptomic analysis of nasal and anal microbiota in respiratory syncytial virus mono and co-infected children.

BACKGROUND: Respiratory syncytial virus is among the most common viruses causing respiratory infections in children. It has been suggested that imbalance of the respiratory microbiota could be involved in the prognosis of RSV illness. The aim of this work is to explore dysbiosis of nasal/anal microbiota in children upon RSV infection, compared to controls. RESULTS: Fifty-nine subjects were enrolled in this study and included: 23 controls, 17 infected only with RSV, and 19 RSV infected together with other respiratory viruses. Multi-infected subjects had non-statistically significant, higher rates of ICU admission (8 versus 3), oxygen supplementation (13 versus 9), and longer hospital stay (20 versus 15 mean days), compared to those single infected with RSV (P > 0.05). Meta-transcriptomic analysis revealed that the nasal microbiota of multi-infected RSV patients had significantly lower alpha richness compared to RSV mono-infected and control group. Principal component analysis revealed the distinct clustering of the nasal microbiome based on the infectious category (P < 0.05). Following the control of confounders i.e. age, gender, comorbidities and antimicrobial intake, Pseudomonas were significantly increased in RSV patients compared to controls. Lactobacillus, Bacteroides, and Staphylococcus were significantly decreased in multi-infected compared to the control subjects. For the anal microbiota, multi-RSV-infected patients had significantly lower alpha richness according to the observed indices, when compared only to the control group. RSV patients had both significantly lower abundance of Spirochaetes and Actinobacteria compared to the control group (P < 0.05). However, following the control of confounders, no significant difference was observed (P > 0.05). CONCLUSION: Our study revealed that multi-infected RSV subjects revealed the highest difference in microbial composition of the nasal microbiota compared to single infected and control subjects. Whether the observed microbiome difference is related to increased disease severity is yet to be explored in future studies. Moreover, the potential use of Lactobacillus and Bacteroides as probiotics for the treatment and prevention of RSV infection should be explored in future research.