Background and objectives

Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen Escherichia coli. 

Methodology

Using anaerobic gut microcosms comprising E. coli embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. 

Results

While cross-protection gave an advantage to antibiotic-susceptible E. coli in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant E. coli in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). 

Conclusions and implications

Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be key for slowing the spread of resistance. 

Briefly our dataset was collected via three different experiements. 

Experiment 1: LB competition experiment

We assessed whether cross protection could occur in a well mixed LB lab media. We competed antibiotic resistant and susceptible strains of E. coli MG1655 either alone or in a 1:1 mix, in LB media with or without ampicillin. Growth rates were caluclated as malthusian parameters for each strain (m; log(final density/starting density)). 

Experiment 2: Anaerobic gut microcosm competition experiment

We determined the relative importance of cross protection and competive release in anaerobic gut microcoms containing a natural faecal community. 

We competed antibiotic resistant and susceptible strains of E. coli MG1655 either alone or in a 1:1 mix, in LB media with or without ampicillin, and in the presence versus absence of the microbiota. Growth rates were caluclated as malthusian parameters for each strain (m; log(final density/starting density)). 

Experiment 3: Supernatant addition experiment 

We tested whether population growth of focal resistant E. coli varied upon exposure to supernatants extracted from cultures including (i) focal E. coli, (ii) the resident microbiota or (iii) no bacteria. Supernatant was obtained by inoculating microcosms of basal medium containing 7.2μg/ml ampicillin with: (1) resistant E.coli (2) susceptible E.coli_, (3) microbiota only (4) microbiota + resistant E. coli or (5) microbiota + susceptible E. coli. We also included two control tubes containing sterile basal medium. One control tube was treated with ampicillin, the second was not. Focal resistant E. coli were grown in these supernatants and the final abundance of our focal strain was determined using flow cytometry. 

Full details of methods are outlined in the manuscript.