Mechanisms of Prophage-Mediated Virulence Driving Community-Acquired MRSA Contagion

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PROJECT SUMMARY Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is known to cause severe bacterial infections and spreads rapidly, creating outbreaks that are public health emergencies. CA-MRSA often contain bacteriophage genetic material, but unless the phage encodes for a known secreted toxin, their contribution to virulence and strain fitness is largely unknown. In this proposal, we will fill this knowledge gap by leveraging an epidemic CA-MRSA clone to identify phage-encoded gene(s) and mechanism(s) of bacteria-phage interaction underlying CA-MRSA contagion. We recently characterized an evolved CA-MRSA strain (USA300-BKV) causing an epidemic of severe skin infection involving a community of predominantly healthy children in Brooklyn, NY. Sequencing revealed the major change antecedent to the dispersion of USA300-BKV was acquisition of a prophage containing a mosaic block of novel genes (mΦ11). We engineered isogenic strains and showed mΦ11 produced significantly larger skin abscesses in mice than strains containing wild type Φ11 or control strain without phage. However, mΦ11 does not encode for any known virulence factors and the presence of mΦ11 did not affect in vitro growth, cytotoxicity, exoprotein production, or transcriptional profiles. Subsequent preliminary studies showed that deletion of a mΦ11-encoded methyltransferase (MTase) decreased the size of the skin abscesses to that of control strain. Based on these observations, we hypothesize that 1) a mΦ11-encoded MTase is activated during infection to cause increased virulence and 2) MTase and/or additional mΦ11 gene(s) enhance CA-MRSA virulence through regulation of bacterial virulence factors. To test these hypotheses, we will identify the bacteriophage gene(s) responsible for enhanced virulence (Specific Aim 1) by 1) complementing MTase into the deletion clone to confirm the functional relevance of MTase, 2) constructing a phage induction repressor mutant to evaluate the effect of induction in vivo, and 3) creating deletion clones in USA300-BKV to examine the effect of the clinical genetic background on the skin infection phenotype. To define the phage- mediated virulence mechanism (Specific Aim 2), we will 1) compare alpha toxin production of mΦ11 lysogens to wild type CA-MRSA during mouse skin infection, 2) perform in vivo transcription profiling using RNA sequencing to identify additional mΦ11 candidate regulatory targets, and 3) delete and complement candidate regulatory targets, with a focus on known virulence and regulatory pathways, for testing in a mouse skin infection model. We expect the independent but complementary Specific Aims will reveal a prophage-encoded mechanism of virulence in a clinically relevant strain causing an epidemic of CA-MRSA. The results will broaden our understanding of phage interactions with the host-bacterial genome and strengthen the paradigm that phages impact virulence in more complex ways than acting as simple toxin carriers. Importantly, identifying the prophage-encoded gene(s) and mechanisms contributing to CA-MRSA contagion promises to inform outbreak surveillance measures and discover novel therapeutic targets to combat this substantial pathogen.