Research Article

Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection

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Science  29 Mar 2019:
Vol. 363, Issue 6434, eaat9691
DOI: 10.1126/science.aat9691

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Phage subverts immune response

Pseudomonas aeruginosa (Pa) is a multidrug-resistant Gramnegative bacterium commonly found in health care settings. Pa infections frequently result in considerable morbidity and mortality. Sweere et al. found that a type of temperate filamentous bacteriophage that infects and integrates into Pa is associated with chronic human wound infections. Likewise, wounds in mice colonized with phage-infected Pa were more severe and longer-lasting than those colonized by Pa alone. Immune cell uptake of phage-infected Pa resulted in phage RNA production and inappropriate antiviral immune responses, impeding bacterial clearance. Both phage vaccination and transfer of antiphage antibodies were protective against Pa infection.

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Structured Abstract


We have identified previously unsuspected, directly pathogenic roles for bacteriophage (phage) virions in bacterial infections. In particular, we report that internalization of phage by human and murine immune cells triggers maladaptive viral pattern recognition receptors and suppressed bacterial clearance from infected wounds.


Bacteriophage are abundant at sites of bacterial infection, but their effect on mammalian immunity is unclear. To investigate this, we studied Pseudomonas aeruginosa (Pa), a major human pathogen associated with chronic wounds and other infections, and Pf, a filamentous phage produced by Pa. Notably, Pf is lysogenic and its production does not typically destroy its bacterial host, unlike the lytic phage used in phage therapy for bacterial infections. Previous work had suggested that Pf phage are important in the pathogenesis of Pa infections, although the underlying mechanisms were unclear. Here, we have examined the impact of Pf on Pa wound infections in humans and in animal models.


We report that Pf bacteriophage were present in 25 of 37 (68%) Pa-infected wounds in our cohort. Furthermore, wounds infected with Pf-positive strains were significantly older than wounds infected with Pf-negative strains, and Pf was more commonly found in chronic, nonhealing wounds. Consistent with this finding, in a murine wound infection model, Pf-positive strains of Pa required an average of 50 times fewer bacteria than Pf-negative strains to establish wound infections. Additionally, mice infected with Pf-positive strains of Pa exhibited greater morbidity and mortality than mice infected with Pf-negative strains.

Mechanistically, these effects were associated with endocytosis of Pf phage by mammalian immune cells, both in vivo and in vitro. We found that uptake of Pf phage resulted in the production of phage RNA, which, in turn, triggered Toll-like receptor 3 (TLR3)– and TIR domain–containing adapter-inducing interferon-β (TRIF)–dependent type I interferon production, the inhibition of tumor necrosis factor production, and the suppression of phagocytosis. These data suggest that a natural (unmodified) bacteriophage may be able to produce mRNA within human cells.

Consistent with a pathogenic role for Pf phage, we report that a vaccine against Pf phage protects against Pa wound infections. Passive immunization of mice with monoclonal antibodies against Pf was likewise effective in protecting against Pa infection by enhancing the opsonization of Pa bacteria.


These results reveal direct, pathogenic roles for phage virions in bacterial infections. Building upon these insights, we report that vaccination against phage virions represents a potential therapeutic strategy for the prevention of infections by antibiotic-resistant Pa. These findings may have broad utility and impact beyond the pathophysiology of chronic wound infections. Pa is a major pathogen in other clinical settings as well, including lung infections in cystic fibrosis. Moreover, many other Gram-negative bacteria, including Klebsiella pneumoniae, Salmonella enterica, Vibrio cholerae, and Escherichia coli, have the capacity to harbor similar filamentous phage (genus Inovirus). Indeed, several of these phage are known to contribute to the virulence potential of their host bacteria. We propose that filamentous phage may be relevant to human interactions with a broad range of pathogenic and commensal bacteria and that these viruses may have profound, direct effects on human health and disease.

Internalization of Pf bacteriophage within a mammalian cell.

Endocytosis of Pf by dendritic cells and other leukocytes triggers viral pattern recognition receptors, which suppress bacterial clearance. This three-dimensional image was generated by using confocal microscopy and z-stacked images (purple, actin stain; blue, DAPI (4′,6-diamidino-2-phenylindole) stain; green, Alexa Fluor 488–labeled Pf4).


Bacteriophage are abundant at sites of bacterial infection, but their effects on mammalian hosts are unclear. We have identified pathogenic roles for filamentous Pf bacteriophage produced by Pseudomonas aeruginosa (Pa) in suppression of immunity against bacterial infection. Pf promote Pa wound infection in mice and are associated with chronic human Pa wound infections. Murine and human leukocytes endocytose Pf, and internalization of this single-stranded DNA virus results in phage RNA production. This triggers Toll-like receptor 3 (TLR3)– and TIR domain–containing adapter-inducing interferon-β (TRIF)–dependent type I interferon production, inhibition of tumor necrosis factor (TNF), and the suppression of phagocytosis. Conversely, immunization of mice against Pf prevents Pa wound infection. Thus, Pf triggers maladaptive innate viral pattern-recognition responses, which impair bacterial clearance. Vaccination against phage virions represents a potential strategy to prevent bacterial infection.

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