Alejandra Hernández-Terán
◽
Angel E. Vega-Sánchez
◽
Fidencio Mejía-Nepomuceno
◽
Ricardo Serna-Muñoz
◽
Sebastián Rodríguez-Llamazares
◽
...
AbstractSeveral factors are associated with the severity of the respiratory disease caused by the influenza virus. Although viral factors are one of the most studied, in recent years the role of the microbiota and co-infections in severe and fatal outcomes has been recognized. However, most of the work has focused on the microbiota of the upper respiratory tract (URT), hindering potential insights from the lower respiratory tract (LRT) that may help to understand the role of the microbiota in Influenza disease. In this work, we characterized the microbiota of the LRT of patients with Influenza A using 16S rRNA sequencing. We tested if patients with different outcomes (deceased/recovered), use of antibiotics, and different days of symptoms onset differ in their microbial community composition. We found striking differences in the diversity and composition of the microbiota depending on the days of symptoms onset and with mortality of the studied patients. We detected a high abundance of opportunistic pathogens such as Enterococcus, Granulicatella, and Staphylococcus in patients either deceased or with antibiotic treatment. Also, we found that antibiotic treatment deeply perturbs the microbial communities in the LRT and affect the probability of survival in Influenza A patients. Altogether, the loss of microbial diversity could, in turn, generate a disequilibrium in the community, potentially compromising the immune response increasing viral infectivity, promoting the growth of potentially pathogenic bacteria that, together with altered biochemical parameters, can be leading to severe forms of the disease. Overall, the present study gives one of the first characterizations of the diversity and composition of microbial communities in the LRT of Influenza patients and its relationship with clinical variables and disease severity.