Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus
Robert J. Ulrich, Magdalena Podkowik, Rebecca Tierce, Irnov Irnov, Gregory Putzel, Nora M. Samhadaneh, Keenan A. Lacey, Daiane Boff, Sabrina M. Morales, Sohei Makita, Theodora K. Karagounis, Erin E. Zwack, Chunyi Zhou, Randie H. Kim, Karl Drlica, Alejandro Pironti, Harm van Bakel, Victor J. Torres, Bo Shopsin
Robert J. Ulrich, Magdalena Podkowik, Rebecca Tierce, Irnov Irnov, Gregory Putzel, Nora M. Samhadaneh, Keenan A. Lacey, Daiane Boff, Sabrina M. Morales, Sohei Makita, Theodora K. Karagounis, Erin E. Zwack, Chunyi Zhou, Randie H. Kim, Karl Drlica, Alejandro Pironti, Harm van Bakel, Victor J. Torres, Bo Shopsin
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Research Article Infectious disease Microbiology

Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus

Abstract

We recently described the evolution of a community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 variant responsible for an outbreak of skin and soft tissue infections. Acquisition of a mosaic version of the Φ11 prophage (mΦ11) that increases skin abscess size was an early step in CA-MRSA adaptation that primed the successful spread of the clone. The present study shows how prophage mΦ11 exerts its effect on virulence for skin infection without encoding known toxin or fitness genes. Abscess size and skin inflammation were associated with DNA methylase activity of an mΦ11-encoded adenine methyltransferase (designated pamA). pamA increased expression of fibronectin-binding protein A (fnbA; FnBPA), and inactivation of fnbA eliminated the effect of pamA on abscess virulence without affecting strains lacking pamA. Thus, fnbA is a pamA-specific virulence factor. Mechanistically, pamA was shown to promote biofilm formation in vivo in skin abscesses, a phenotype linked to FnBPA’s role in biofilm formation. Collectively, these data reveal a critical mechanism — epigenetic regulation of staphylococcal gene expression — by which phage can regulate virulence to drive adaptive leaps by S. aureus.

Authors

Robert J. Ulrich, Magdalena Podkowik, Rebecca Tierce, Irnov Irnov, Gregory Putzel, Nora M. Samhadaneh, Keenan A. Lacey, Daiane Boff, Sabrina M. Morales, Sohei Makita, Theodora K. Karagounis, Erin E. Zwack, Chunyi Zhou, Randie H. Kim, Karl Drlica, Alejandro Pironti, Harm van Bakel, Victor J. Torres, Bo Shopsin

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Figure 1

Effect of en bloc deletions on the mΦ11-mediated skin abscess phenotype.

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Effect of en bloc deletions on the mΦ11-mediated skin abscess phenotype....
(A) Skin infection workflow. Created with BioRender.com. (B) Map of mΦ11 in strain USA300-BKV, adapted with permission from Copin et al. (5), with en bloc deletion locations. Arrows indicate predicted ORFs and the direction of the transcription of genes within the unique mΦ11 modules. Homologous (red) and nonhomologous (blue) ORFs are shown, compared with prototypical Φ11. Black arrow indicates pamA. Black bars beneath the gene map correspond to the gene blocks deleted from the indicated strain. (C) Representative images of skin abscesses 72 hours after subcutaneous infection with the indicated strains. Scale bar (black): 1 cm. (D) Skin abscess infections with en bloc deletion mutants. Skin abscess area at the indicated times after infection with approximately 107 bacterial CFU of LAC* lysogens containing mΦ11 (blue, n = 20, strain BS989), mΦ11Δ32–43 (purple, n = 16–18, strain RU47), mΦ11Δ44–57 (salmon, n = 20, strain RU108), or mΦ11Δ32–64 (cyan, n = 18–20, strain RU42). Data are pooled from 2 independent experiments and represent mean ± SD. Statistical significance was determined by Kruskal-Wallis and Dunn’s tests, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001.