Suh, W. S. | Search bioRxiv

bioRxiv2024

Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition

The oral microbiome has been understudied as a reservoir for clinical pathogens, including drug-resistant strains. Understanding how alterations in microbiome functioning render this site vulnerable to colonization is essential, as multidrug-resistant organisms (MDRO) carriage is a major risk factor for developing serious infections. To advance our knowledge of oral MDRO carriage and protection against pathogen colonization conferred by native microbiota, we examined microbiomes from individuals colonized by MDROs (n=33) and non-colonized age-matched controls (n=30). Shotgun metagenomic analyses of oral swabs from study participants revealed significant differences in microbial communities with depletion of Streptococcus spp. among those colonized by multidrug-resistant gram-negative bacilli (RGNB), compared to non-carriers. We utilized metagenomic sequencing to characterize the oral resistome and find antimicrobial resistance genes are present in higher abundance among RNGB carriers versus non-carriers. High-throughput co-culture screening revealed oral bacteria isolated from MDRO non-carriers demonstrate greater inhibition of gram-negative pathogens, compared to isolates from carriers. Moreover, biosynthetic gene clusters from streptococci are found in higher abundance from non-carrier microbiomes, compared to RGNB carrier microbiomes. Bioactivity-guided fractionation of extracts from Streptococcus isolate SID2657 demonstrated evidence of strong E. coli and A. baumannii inhibition in a murine model of infection. Together, this provides evidence that oral microbiota shape this dynamic microbial community and may serve as an untapped source for much-needed antimicrobial small-molecules.

microbiology↗

bioRxiv2023

Bacillus subtilis derived lipopeptides disrupt quorum sensing and biofilm assembly in Staphylococcus aureus

Multidrug-resistant Staphylococcus aureus is one of the most clinically important pathogens in the world with infections leading to high rates of morbidity and mortality in both humans and animals. S. aureus ability to form biofilm protects individual cells from antibiotics and promotes the transfer of antibiotic resistance genes. Therefore, new strategies aimed to inhibit biofilm growth and disassemble mature biofilms are urgently needed. Probiotic species, namely Bacillus subtilis, are gaining interest as a potential therapeutic against S. aureus for their ability to reduce S. aureus colonization and virulence. Here, we collected and screened 1123 Bacillus strains obtained from a variety of agricultural environments in search of isolates with strong antibiofilm activity against clinical multi-drug resistant S. aureus. We selected a single strain, B. subtilis 6D1, based on its ability to inhibit biofilm growth, disassemble mature biofilm, and improve antibiotic sensitivity of S. aureus biofilms through an Agr quorum sensing interference mechanism. Biochemical and molecular networking analysis of an active organic fraction revealed multiple surfactin isoforms and an uncharacterized compound were both driving this antibiofilm activity. Furthermore, when compared against commercial HPLC grade surfactin obtained from B. subtilis, this active fraction inhibited biofilm formation against all four S. aureus Agr backgrounds and prevented S. aureus-induced cytotoxicity when applied to HT29 human intestinal cell lines better than the commercial standard. Our results demonstrate the mixture of compounds produced by B. subtilis 6D1 can mitigate S. aureus virulence through multiple mechanisms. Contribution to the FieldThe biofilm formation capability of bacterial pathogens, such as Staphylococcus aureus, increases these microorganisms virulence potential and decreases the efficacy of common antibiotic regiments. Probiotics possess a variety of strain-specific strategies to reduce biofilm formation in competing organisms, however, the mechanisms and compounds responsible for these phenomena often go uncharacterized. In this study, we identified a mixture of small probiotic-derived peptides capable of Agr quorum sensing interference as one of the mechanisms driving antibiofilm activity against S. aureus. This collection of peptides also improved antibiotic killing and protected human gut epithelial cells from S. aureus-induced toxicity by stimulating an adaptive immune response. We conclude that purposeful strain screening and selection efforts can be used to identify unique probiotic strains that possess specially desired mechanisms of action. This information can be used to further improve our understanding of the ways in which probiotic and probiotic-derived compounds can be applied to prevent bacterial infections in clinical and agricultural settings.

microbiology↗