Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in humans and ferrets

Drishti Kaul, Raveen Rathnasinghe, Marcela Ferres, Gene S. Tan, Aldo Barrera, Brett E. Pickett, Barbara A. Methe, Suman Das, Isolda Budnik, Rebecca A. Halpin, David Wentworth, Mirco Schmolke, Ignacio Mena, Randy A. Albrecht, Indresh Singh, Karen E. Nelson, Adolfo García-Sastre, Chris L. Dupont, Rafael A. Medina

May 20, 2019

Received Date: 3rd May 19

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation because of host responses and cellular damage. The native upper respiratory tract (URT) microbiome likely plays a role, yet the effects of influenza infection on the URT microbiome are largely unknown. We performed a longitudinal study to assess the temporal dynamics  of  the  URT  microbiomes  of  uninfected  and  influenza  virus-infected  humans and ferrets. Uninfected human patients and ferret URT microbiomes had stable “heathy ecostate” communities  both  within  and  between  individuals.  In  contrast,  infected  patients  and ferrets exhibited large changes in bacterial community composition over time and between individuals. The “unhealthy” ecostates of infected individuals progressed towards the “healthy ecostate” over time, coinciding with viral clearance and recovery. Blooms of Pseudomonas were a statistically associated  constant  in  the  disturbed  microbiomes  of  infected  individuals.  The  dynamic and resilient nature of the microbiome during influenza virus infection in multiple hosts provides a compelling   rationale   for  the  maintenance  of   the  microbiome   homeostasis  as  a   potential therapeutic target to prevent IAV associated bacterial co-infections.

Read in full at bioRxiv.

This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

Nature Communications

Nature Research, Springer Nature