Identification of Nasal Gammaproteobacteria with Potent Activity against Staphylococcus aureus: Novel Insights into the “Noncarrier” State

Abstract

Staphylococcus aureus nasal carriage provides the bacterial reservoir for opportunistic infection. In comparing the nasal microbiomes of culture-defined persistent S. aureus carriers versus noncarriers, we detected S. aureus DNA in all noses, including those with an established history of S. aureus negativity based on culture. Colonization with Gammaproteobacteria, including Klebsiella aerogenes, Citrobacter koseri, Moraxella lincolnii, and select Acinetobacter spp., was associated with S. aureus noncarriage. We next developed physiological competition assays for testing anti-S. aureus activity of isolated nasal species, utilizing medium modeling the nutrient-limited fluid of the nasal mucosa, polarized primary nasal epithelia, and nasal secretions. K. aerogenes from the nose of an S. aureus noncarrier demonstrated >99% inhibition of S. aureus recovery in all assays, even when S. aureus was coincubated in 9-fold excess. Secreted S. aureus inhibitory proteins from K. aerogenes and M. lincolnii were heat-stable and <30 kDa, fitting the profile of antimicrobial peptides. C. koseri, Acinetobacter haemolyticus, Acinetobacter junii, and Acinetobacter schindleri inhibited S. aureus recovery on nasal epithelia in a contact-dependent manner, while several other species either had no effect or promoted S. aureus growth. Collectively, this project is one of the first to identify resident nasal microbial species that impede S. aureus survival, and it implies that detectable nasal S. aureus results from shifts in microbial community composition. IMPORTANCE Nasal carriage of Staphylococcus aureus is a risk factor for infection, but it is not yet understood why some individuals carry nasal S. aureus persistently, intermittently, or seemingly not at all when tested via culture methods. This study compared the nasal microbiomes of established S. aureus carriers and noncarriers, identified species associated with noncarriage, and tested them for anti-S. aureus activity using assays developed to model the nutrient-limited nasal mucosa. We determined that all nostril swabs contain S. aureus DNA, even swabs from hosts considered to be long-term noncarriers. Select members of the Gammaproteobacteria class were more prevalent in noncarrier than carrier nostrils and demonstrated potent activity against multiple strains of S. aureus. The results described here provide a better understanding of how the nasal microbiome controls S. aureus growth and viability and may be useful in the design of improved S. aureus decolonization strategies.

Microbiome First Medicine in Health and Safety

“…When Staph A is a predominant colonizer in the nasal passages of infants, those infants are at a higher risk of childhood asthma [ 59 ]. But when the microbiome is healthy, other bacteria can block Staph A from taking up residence via colonization resistance [ 60 , 61 ]. Managing the infant microbiome to optimize colonization resistance against Staph A is one way to reduce the risk of childhood asthma.…”

E-Cigarette Aerosols Promote Oral S. aureus Colonization by Delaying an Immune Response and Bacterial Clearing

“…Our current in vitro model using e-cig aerosols highlights the role IL1β signaling plays in the response to S. aureus carriage ( Figure 6 ). Here, we established co-cultures of normal oral epithelial cells, OKF6, with two strains of S. aureus isolated from non-smoker participants in a previous study [ 30 ]. We observed an inflammatory response elicited by S. aureus , as measured by the secretion of the cytokines IL8, IL1β, IL6, and TNFα ( Figure 6 ), for the 512 strain, which is not as abundant in the oral cavity as the resident 528-11 strain (21).…”

“…Staphylococcus aureus strains 512 (sequence type ST30) and 528-11 (sequence type ST8/t008), 547, S042, and S072 were used in this study [ 30 ]. Strains 512 (sequence type ST30) and 528-11 (sequence type ST8/t008) have been reported to be common isolates from the oral cavity and have been associated with active sites of periodontitis [ 31 ].…”

Microbiome First Approaches to Rescue Public Health and Reduce Human Suffering

“…The infant epithelial lining is particularly susceptible to pathobiont-associated damage because there is decreased production of epithelial-derived antimicrobials in early life [92]. Because antibiotics can often lead to only a short-term benefit with longer term complications as a probable outcome, effective colonization resistance against Staph A in the infant airways is the best benefit-risk strategy [93,94]. As was discussed for the skin, Staph E is a key bacterium in nasal maturation and natural defenses against pathobionts like Staph A [95].…”