Heterogeneity across mammalian- and avian-origin A(H1N1) influenza viruses influences viral infectivity following incubation with host bacteria from the human respiratory tract

Influenza A viruses (IAVs) are primarily transmitted between mammals by the respiratory route and encounter bacteria in the respiratory tract before infecting susceptible epithelial cells. Previous studies have shown that mammalian-origin IAV can bind to the surface of different bacterial species and purified bacterial lipopolysaccharides (LPS), but despite the broad host range of IAV, few studies have included avian-origin IAV in these assessments. Since IAVs that circulate in humans and birds are well adapted to replication in the human respiratory and avian gastrointestinal tracts, respectively, we investigated the ability of multiple human and avian A(H1N1) IAVs to associate with bacteria and their surface components isolated from both host niches. Binding interactions were assessed with microbial glycan microarrays, revealing that seasonal and avian IAV strains exhibited binding diversity to multiple bacterial glycans at the level of the virus and the bacterium, independent of sialic acid binding preference of the virus. Coincubation of diverse IAV with LPS derived from <i>Pseudomonas aeruginosa</i>, a respiratory tract bacterium, led to reduced retention of viral infectivity in a temperature-dependent manner, which was not observed when co-incubated with LPS from <i>Escherichia coli</i>, a gut bacterial isolate. Reduction of viral infectivity was supported by disruption of IAV virions following incubation with <i>P. aeruginosa</i> LPS using electron microscopy. Our findings highlight that both human and avian IAV can bind to bacterial surface components from different host sites, resulting in differential functional interactions early after binding, suggesting the need to study IAV-bacteria interactions at the host range interface.IMPORTANCEThe host range of influenza A virus (IAV) spans humans and numerous animal species, with species specificity governed by multiple viral and host determinants. Human and zoonotic IAV strains that infect different hosts can encounter different bacterial species specific to the host niche that supports replication of these viruses, yet few studies have assessed the role of host bacteria as a potential host range determinant for IAV. Using both live bacteria and microbial glycan arrays, we show that human and avian A(H1N1) viruses can bind to bacterial surface glycans present in the mammalian respiratory tract independent of sialic acid binding preferences. Coincubation of viruses with lipopolysaccharides sourced from distinct host niches revealed both strain-specific and bacterial polysaccharide-specific interactions with functional consequences on virion stability and infectivity. Our findings suggest that public health needs to further investigate IAV-bacteria interactions, in both human and animal populations, enabling identification of emerging threats and timely public health responses.