Nasal microbiome-derived antimicrobial factors to inhibit Staphylococcus aureus colonization - Staphylococcus aureus (SA) is a seemingly benign member of the human microbiota, colonizing most people transiently throughout life. SA nasal carriage (SANC) is the reservoir for spread of this bacterium, since clinical strains nearly always match the patient’s own nasally carried strain. SA is also one of the most commonly isolated pathogens from infected wounds and surgical sites, and cases of severe pneumonia. The global economic toll of SA infections is enormous and multi-drug resistant strains continue to emerge. Therefore, new approaches to decolonize carriers of SA are urgently needed. To better understand the dynamics of SANC, we monitored hundreds of healthy subjects longitudinally and observed that nearly half of our cohort never produced an SA-positive swab as determined by culture. However, when we analyzed nasal swabs using a shotgun metagenomic approach, we detected SA DNA in all noses. This led us to hypothesize that noncarriers’ nasal microbiota elaborate a defense against SA that prevents expansion and persistence upon exposure. We identified and isolated species that associate with SA culture-negative noses and developed physiological competition assays for testing anti-SA activity. While several members of the Gammaproteobacteria class exhibited anti-SA activity, nasal Klebsiella spp. potently inhibited (>99%) SA survival in a contact-independent manner. For multiple nasal isolates of K. aerogenes from our donor cohort, this inhibition was attributed to a small, cationic, proteinaceous molecule(s). Our preliminary findings provide a strong basis for our proposed studies to evaluate whether these noncarrier-associated microbes may be exploited to suppress or eliminate SANC. In Aim 1, we will purify and identify anti-SA proteins and polypeptides from the conditioned medium of Klebsiella cultures, which are easily prepared at large scale. Next, we will determine the potency of purified proteins against diverse SA strains, and evaluate the mechanism(s) by which lead proteins inhibit SA growth and survival. In Aim 2, we will determine the effect of lead anti-SA proteins on nasal epithelial barrier permeability, intracellular signaling, inflammatory factor and host defense peptide secretion, and chemotaxis. We will measure the stability of lead SA inhibitors in nasal tissue, in the presence of mucosal proteases, and when mixed with SANC secretions. We will determine whether nasal SA can develop resistance to lead proteins, and we will assess off-target effects of lead proteins against prevalent and potentially beneficial nasal (non-SA) bacterial species. Understanding how noncarriers combat SA will promote the development of novel topical agents to bolster nasal immunity and reduce SANC and subsequent transmission and infection by SA.
