Phage-mediated adaptation of Staphylococcus aureus to the avian innate immune response

Staphylococcus aureus is an important human and livestock pathogen. An S. aureus prophage (Avβ) inserted into the chromosome at the β-toxin gene (β-converting phage) is present in approximately 90% of human strains and is known to contribute to human-specific innate immune evasion. Comparative genomic analysis of S. aureus isolates from infected poultry has recently revealed an avian-specific subfamily of β-converting phages. Population analysis revealed that 80% of avian isolates tested carry prophage Avβ and that the genes encoded on its putative immune evasion cluster are conserved, suggesting a role in avian host-adaptation. A φAvβ-deficient avian S. aureus strain was used to investigate the role of prophage Avβ in avian host-pathogen interactions. Compared to the wild type, the φAvβ-deficient strain has increased susceptibility to chicken bone-marrow derived macrophage killing. Further investigation using GFP-expressing bacteria has revealed that the φAvβ-deficient strain exhibits reduced phagocytosis compared to the wild type and is associated with decreased killing of macrophages. PCR analysis revealed that prophage Avβ is capable of excision from the chromosome, leading to restoration of β-toxin expression and therefore an intact β-toxin could influence S. aureus-macrophage interactions. To further dissect whether prophage Avβ mediates immune evasion, deletion mutants of three candidate phage effector genes were constructed. No difference in bacterial survival or phagocytosis was observed by single gene deletion mutants compared to the wild type. Finally, RNA-seq analysis was used to decipher the general response of chicken bone-marrow derived macrophages to S. aureus. Toll-like receptor signalling pathways, NF-κB and the type I interferon response are the main drivers of the early chicken macrophage response to S. aureus. Importantly, the transcriptomic analysis of infected macrophages revealed that the presence of prophage Avβ (or β-toxin due to prophage Avβ excision), is associated with an inhibition of avian antimicrobial peptide gene expression. Overall, these data provide new insights into innate immune evasion of avian S. aureus and mechanisms of bacterial host-adaptation.