Human-associated microbiota suppress invading bacteria even under disruption by antibiotics

Abstract

In light of their adverse impacts on resident microbial communities, it is widely predicted that broad-spectrum antibiotics can promote the spread of resistance by releasing resistant strains from competition with other strains and species. We investigated the competitive suppression of a resistant strain of Escherichia coli inoculated into human-associated communities in the presence and absence of the broad and narrow spectrum antibiotics rifampicin and polymyxin B, respectively. We found strong evidence of community-level suppression of the resistant strain in the absence of antibiotics and, despite large changes in community composition and abundance following rifampicin exposure, suppression of the invading resistant strain was maintained in both antibiotic treatments. Instead, the strength of competitive suppression was more strongly associated with the source community (stool sample from individual human donor). This suggests microbiome composition strongly influences the competitive suppression of antibiotic-resistant strains, but at least some antibiotic-associated disruption can be tolerated before competitive release is observed. A deeper understanding of this association will aid the development of ecologically-aware strategies for managing antibiotic resistance.

3D-Printed Dip Slides Miniaturize Bacterial Identification and Antibiotic Susceptibility Tests Allowing Direct Mastitis Sample Analysis

“…Recently, significant focus has turned to the resistome and the relationship between the complex microbiome and its interaction with pathogen behavior, and whether the overall resistance of mixtures of bacteria found in the site of infection might affect the effectiveness of antibiotic treatment [13,30]. In this study, we explore the possibility of an alternative approach to the phenotype-based method that determines the MIC value directly from mixed bacterial population in a sample [3,9,31]. Whilst this may not provide the same standardized measure of antibiotic susceptibility of each individual strain present in the sample, it will be important to continue researching the link between "mixed MIC" found from direct susceptibility testing Our assay is simpler than many microfluidic devices, and the open source 3D-printed frame design is flexible and customizable.…”

Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota

“…Although ampicillin and E.coli are undoubtedly of high real-world relevance, generalizing our results to other species/antibiotics should be done with caution. A recent study by Letten et al [ 48 ] with a similar setup, but different antibiotics, samples and focal strain, found little evidence that antibiotics released an invading strain from competition with resident microbiota. This difference may be explained by different antibiotics having different effects on resident microbiota, variation among focal resistant strains, or other differences between experiments (e.g.…”

“…This difference may be explained by different antibiotics having different effects on resident microbiota, variation among focal resistant strains, or other differences between experiments (e.g. baseline competition with resident microbiota was relatively strong in Letten et al [ 48 ]). Conversely, a past experiment also using this study system showed an ampicillin-resistance plasmid conferred a relatively large fitness benefit to its host when embedded in a gut microbiota and exposed to ampicillin [ 16 ], consistent with our results here.…”

Managing host-parasite interactions in humans and wildlife in times of global change

“…the manner in which host population structures and host resistance drive parasite spread and make parasite control feasible beyond a limited range of targeted host individuals. Moving beyond this, incorporation of systematic monitoring and understanding the movement of drug resistant genomes within the parasite population (Ndiaye et al 2021 ) and the invasion success of drug resistant parasite in host microbial and parasite assemblages (Letten et al 2021 ) will be key for informed drug use in parasite control. The advent of affordable and fast in-field genomic technologies makes this approach more feasible.…”