DOI: 10.5061/dryad.1rn8pk0tt
title: Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota

description: 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. 
description: Briefly our dataset was collected via three different
 experiements.  <strong>Experiment 1: LB
 competition experiment</strong> We assessed
 whether cross protection could occur in a well mixed LB lab media. We
 competed antibiotic resistant and susceptible strains of <em>E.
 coli</em> 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 (<em>m</em>; log(final density/starting
 density)).  <strong>Experiment 2: Anaerobic gut
 microcosm competition experiment</strong> 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 <em>E. coli </em>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 (<em>m</em>; log(final
 density/starting density)).  <strong>Experiment
 3: Supernatant addition experiment </strong>
 We tested whether population growth of focal
 resistant <i>E. coli</i> varied upon exposure to supernatants
 extracted from cultures including (i) focal <i>E. coli</i>,
 (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<sub>, </sub>(3) microbiota only (4)
 microbiota + resistant E. coli or (5)<sub> </sub>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 <i>E. coli </i>were grown in these
 supernatants and the final abundance of our focal strain was determined
 using flow cytometry.   
 <em>Full details of methods are outlined in the manuscript.
 </em>