Influenza coinfection inhibits control of mycobacterial infection in a human challenge model

Article https://doi.org/10.1038/s41467-026-72363-2 Influenza coinfection inhibits control of mycobacterial infection in a human challenge model Received: 22 May 2025 1 , Check for updates 1234567890():,; 1234567890():,; Accepted: 31 March 2026 Claire M. Broderick 1 , Oliver Powell1, Sam Nichols 1, Giselle D’Souza1, Dominic Habgood-Coote 1, Carlota Miranda-Sole 1, Emily M. Whettlock Zoe Gardener1, Emma Bergstrom1, Victoria J. Wright 1, Christopher W. Woods 2, Christopher Chiu 1, Sandra M. Newton 1,4, Elizabeth Whittaker1,3, Michael Levin 1,5 & Myrsini Kaforou 1,5 Mycobacterium tuberculosis infection is a dynamic continuum. Clinical outcomes reflect complex host-pathogen interactions. Epidemiological and animal studies have suggested influenza coinfection as a risk factor for progression from contained infection to active disease, but human studies have been lacking. Using a whole blood luminescent mycobacterial growth inhibition assay within a human influenza challenge study, we show that influenza infection reduces immunological control of mycobacterial growth. Transcriptome-wide RNA sequencing, cytokine and cellular analyses of subjects’ blood before and after influenza infection reveal that innate immune pathways, including type 1 interferon signalling, are activated by influenza but their subsequent responsiveness to mycobacteria is reduced, with multiple genes’ responses to BCG lux infection repressed by influenza coinfection. Our data suggest that influenza infection impairs immune mechanisms that contain mycobacterial growth and may be a risk factor for tuberculosis (TB) disease. Influenza vaccination might offer high risk, high prevalence populations protection against TB disease. Tuberculosis (TB) remains a major cause of global morbidity and mortality1. Millions of people are exposed to and infected with Mycobacterium tuberculosis (Mtb) each year, yet the majority do not develop disease. Understanding the factors that drive progression to TB disease is essential for improving TB prevention and control strategies. Mtb infection is now recognised as a dynamic continuum, from quiescent latent infection, through to destructive, potentially life-threatening disease2. Outcomes after exposure are thought to reflect the continuing balance between the host’s immunological defences and mycobacterial virulence mechanisms. In addition to the well-established effects of malnutrition, HIV infection and other immunosuppressive conditions2, coinfection with other pathogens has attracted increasing interest as a contributing factor to progression to active disease3. Humans are exposed to a range of pathogens throughout life, and there is growing evidence that the resulting immune responses may alter susceptibility to other infections. For example, influenza virus infection predisposes to secondary bacterial infections, including Streptococcus pneumoniae and Staphylococcus aureus, through a variety of mechanisms, including immunomodulation4. It has been postulated that concurrent influenza infection may also increase TB susceptibility and alter clinical outcomes after Mtb infection, through modulation of immunological pathways important in mycobacterial control3, with supporting evidence from epidemiological5–9 and animal 1 Department of Infectious Disease, Imperial College London, London, UK. 2Department of Medicine, Duke University Medical Center, Durham, NC, USA. Department of Paediatric Infectious Diseases, Imperial College Healthcare NHS Trust, London, UK. 4Deceased: Sandra M. Newton. 5These authors jointly e-mail: supervised this work: Michael Levin, Myrsini Kaforou. 3 Nature Communications | (2026)17:4884 1 Article model studies10–13. However, human studies have been limited, mostly observational and with mixed findings14–16. Given influenza is a widely circulating global pathogen (an estimated billion cases annually17), understanding its immunological interaction with Mtb may have implications for TB control, immunisation strategies and novel hostbased TB diagnostics. Mycobacterial growth inhibition assays (MGIAs) that measure the ability of whole blood or cells to inhibit mycobacterial growth in vitro allow a range of immunological components (cells, antibodies and cytokines) and their interactions to be considered in one model over time18,19. Human challenge studies provide a unique opportunity to observe pathogen-driven immune responses in a highly controlled environment. We employed a whole blood MGIA within the framework of a human influenza challenge study to investigate the effects of systemic influenza infection on host mycobacterial control. We utilised a recombinant reporter strain of mycobacteria, Mycobacterium bovis Bacille Calmette Guerin (BCG) lux, whose luminescence provides a quantitative read-out of live mycobacteria present20,21. Prior studies have demonstrated the BCG lux MGIA reflects differences in antimycobacterial immune responses from TB infection22, HIV infection23, BCG vaccination24, vitamin D25, neutrophil depletion26 and infliximab therapy27. Longitudinal RNA expression data from the model have provided insights into early immune responses to Mtb28,29. In this work, we test the hypothesis that influenza infection of healthy adults alters whole blood mycobacterial control through modulation of anti-mycobacterial immune responses. Volunteers were challenged with the Influenza A virus and subsequent infection virologically confirmed. Blood aliquots, taken from participants before and after influenza infection, were infected with BCG lux and incubated. Whole blood mycobacterial growth and transcriptomic, cytokine and cellular responses to mycobacterial infection were measured in parallel and compared in the same subjects, before versus after influenza infection. We show that systemic influenza infection reduces whole blood control of mycobacteria via its disruption of innate immunological pathways, including type 1 interferon signalling. Our data suggest that influenza infection may be a risk factor for developing TB disease, and interventions such as the seasonal influenza vaccine that protect against influenza could offer protection against TB disease. Results Thirty healthy adult participants were per nasally inoculated with Influenza A (subtype H3N2) virus, with 24 developing PCR-confirmed influenza infection (PCR-positive [+] group) and six remaining uninfected (PCR-negative [-]) group (Fig. 1). There were no significant differences in age, sex or ethnicity between the PCR + and PCR- groups (Supplementary Table 1). All participants had blood samples collected an hour prior to influenza inoculation (Day [D]0, pre-influenza) and 6 days after inoculation (D6, post-influenza), which were then incubated for 0 to 72 h, with and without BCG lux (Fig. 1). Influenza infection inhibits mycobacterial growth restriction Firstly, we investigated the effect of systemic influenza infection on mycobacterial growth restriction by whole blood. Mycobacterial growth was meas (...truncated)