Bruelisauer, L. | bioRxiv Science

bioRxiv2026

Individual bacterial taxa drive colonisation resistance to methicillin-resistant Staphylococcus aureus in human nasal microbiome samples

Identifying bacterial interactions that determine susceptibility of human microbiomes to colonisation by pathogenic bacteria has important implications for understanding health and disease and, consequently, improving treatment and prevention. Here, we show how microbiome composition of healthy-human nasal passage samples determines susceptibility to colonisation by methicillin-resistant Staphylococcus aureus (MRSA) using a replicated microcosm approach. We find that variable MRSA population growth among samples from different individuals is associated with differences in microbial community composition. To identify individual taxa contributing to in vitro colonisation resistance, we isolate bacteria from inhibitory samples and measure their effects on MRSA in co-culture. This reveals strong MRSA inhibition by multiple Enterobacteriaceae isolates, including some which fully suppress MRSA growth in our system. Finally, by assembling nasal model communities reflecting the composition of natural nasal microbiome samples and combining drop-in and drop-out designs, we show that individual taxa can drive community-level resistance to MRSA growth. Together, our results demonstrate causal links between taxonomic composition of nasal microbiome samples and resistance to S. aureus, informing potential new microbiome-targeted interventions to manage S. aureus colonisation.

microbiology↗

bioRxiv2023

Clinical Antibiotic-Resistance Plasmids Have Small Effects on Biofilm Formation and Population Growth in Escherichia coli in vitro

Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain-dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.

microbiology↗