Harnessing diversity and antagonism within the pig skin microbiota to identify novel mediators of colonization resistance to methicillin-resistant Staphylococcus aureus

Abstract

The microbiota mediate multiple aspects of skin barrier function, including colonization resistance to pathogens such as Staphylococcus aureus . The endogenous skin microbiota limits S. aureus colonization via competition and direct inhibition. Novel mechanisms of colonization resistance are promising therapeutic targets for drug-resistant infections, such as those caused by methicillin-resistant S. aureus (MRSA). Here, we developed and characterized a swine model of topical microbiome perturbation and MRSA colonization. As in other model systems, topical antimicrobial treatment had a little discernable effect on community diversity though the overall microbial load was sensitive to multiple types of intervention, including swabbing. In parallel, we established a porcine skin culture collection and screened 7,700 isolates for MRSA inhibition. Using genomic and phenotypic criteria, we curated three isolates to investigate whether prophylactic colonization would inhibit MRSA colonization in vivo . The three-member consortium together, but not individually, provided protection against MRSA colonization, suggesting cooperation and/or synergy among the strains. Inhibitory isolates were represented across all major phyla of the pig skin microbiota and did not have a strong preference for inhibiting closely related species, suggesting that relatedness is not a condition of antagonism. These findings reveal the porcine skin as an underexplored reservoir of skin commensal species with the potential to prevent MRSA colonization and infection. IMPORTANCE The skin microbiota is protective against pathogens or opportunists such as S. aureus , the most common cause of skin and soft tissue infections. S. aureus can colonize normal skin and nasal passages, and colonization is a risk factor for infection, especially on breach of the skin barrier. Here, we established a pig model to study the competitive mechanisms of the skin microbiota and their role in preventing colonization by MRSA. This drug-resistant strain is also a livestock pathogen, and swine herds can be reservoirs of MRSA carriage. From 7,700 cultured skin isolates, we identified 37 unique species across three phyla that inhibited MRSA. A synthetic community of three inhibitory isolates provided protection together, but not individually, in vivo in a murine model of MRSA colonization. These findings suggest that antagonism is widespread in the pig skin microbiota, and these competitive interactions may be exploited to prevent MRSA colonization.

An exploration of mechanisms underlyingDesemzia incertacolonization resistance to methicillin-resistantStaphylococcus aureuson the skin

“…This result differs from our previously reported data, where precolonization by D. incerta was not sufficient to reduce MRSA colonization but showed a trend toward statistical significance 24 . In our previous model we used a lower inoculum of D. incerta (10 8 CFU) on a different genetic background (SKH1 hairless mice).…”

“…In both models, 10 9 CFU D. incerta was applied daily for 2 days and 10 8 CFU USA300 MRSA was applied daily for one day. We found that precolonization with D. incerta reduced subsequent MRSA colonization by 60%, but decolonization with D. incerta did not have a noticeable effect on MRSA bacterial burden.This result differs from our previously reported data, where precolonization by D. incerta was not sufficient to reduce MRSA colonization but showed a trend toward statistical significance 24 . In our previous model we used a lower inoculum of D. incerta (10 8 CFU) on a different genetic background (SKH1 hairless mice).…”

“…In our previous model we used a lower inoculum of D. incerta (10 8 CFU) on a different genetic background (SKH1 hairless mice). Altogether, the data suggests that mono-colonization with D. incerta exhibits colonization resistance against MRSA at high innocula, and using a consortia of bacteria as described previously 24 may increase this anti-MRSA effect.…”

“…We previously cultured 3 bacterial isolates from porcine skin, A. viridans , R. aerolata, and D. incerta that exhibited inhibitory activity against MRSA in vitro , and together in vivo 24 . To examine the individual mechanisms of inhibition, we tested whether these three isolates secreted antimicrobial molecules.…”

The Porcine Skin Microbiome Exhibits Broad Fungal Antagonism

“…Consistent with previous works characterizing porcine skin microbial communities (Wareham- Mathiassen et al, 2023; Wei et al, 2023), bacterial communities are dominated by taxa within the Bacillota phyla and Aerococcus and Streptococcus genera ( Fig. 1E-F ).…”