BACKGROUND:
Previous studies suggest that the nose/throat microbiome may play an important role in shaping host immunity and modifying the risk of respiratory infection. Our aim is to quantify the association between the nose/throat microbiome and susceptibility to influenza virus infection.
METHODS:
In this household transmission study, index cases with confirmed influenza virus infection and their household contacts were followed for 9-12 days to identify secondary influenza infections. Respiratory swabs were collected at enrollment to identify and quantify bacterial species via high- performance sequencing. Data were analyzed by an individual hazard-based transmission model that was adjusted for age, vaccination, and household size.
RESULTS:
We recruited 115 index cases with influenza A(H3N2) or B infection, and 436 household contacts. We estimated that a 10-fold increase in the abundance in Streptococcus spp. and Prevotella salivae was associated with 48% (95% CI: 9%, 69%) and 25% (95% CI: 0.5%, 42%) lower susceptibility to influenza A(H3N2) infection, respectively. By contrast, for influenza B infection, a 10-fold increase in the abundance in Streptococcus vestibularis and Prevotella spp. was associated with 63% (95% CI: 17%, 83%) lower and 83% (95% CI: 15%, 210%) higher susceptibility, respectively.
CONCLUSIONS:
Susceptibility to influenza infection is associated with the nose/throat microbiome at the time of exposure. The effects of oligotypes on susceptibility differ between influenza A(H3N2) and B viruses. Our results suggest that microbiome may be a useful predictor of susceptibility, with the implication that microbiome could be modulated to reduce influenza infection risk, should these associations be causal.