Laura De Nies (University Of Oxford)

Summary of presentation:
Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are critical priority antibiotic-resistant pathogens associated with high mortality rates. Plasmid-encoded ESBLs frequently spread via conjugation between Enterobacteriaceae species within the intestine of colonised patients, but we currently understand little about the fundamental mechanisms driving this dissemination and lack strategies to prevent it. Under normal conditions commensal anaerobes vastly outnumber Enterobacteriaceae within the gastrointestinal tract and the physical contact between donor and recipient bacteria required for conjugative transfer is limited. However, antibiotic treatment can lead to ‘blooms’ of otherwise low-abundant Enterobacteriaceae, increasing the encounter rate between donor and recipient.
Here, we investigated antibiotic-driven mechanisms underlying horizontal gene transfer (HGT) of a conjugative plasmid carrying a single ESBL gene (blaCTX-M-14) between donor and recipient E. coli. Using complementary in vitro and in vivo approaches, we examined how antibiotic class and microbiome composition influence Enterobacterial expansion and conjugation. In vitro, we established three distinct human-derived microbial communities and performed high-throughput screening across a broad antibiotic panel. Selected conditions were validated in vivo using specific-pathogen-free mice (n=8) to capture the complexity of the mammalian gut environment.
In minimally perturbed microbiomes, donor and recipient E. coli exhibited limited growth and no detectable conjugation. Antibiotics directly selecting for the ESBL plasmid, e.g. ampicillin and amoxicillin, promoted expansion of the resistant donor but eliminated susceptible recipients, thereby suppressing HGT. In contrast, antibiotics not directly selecting for the plasmid, including clindamycin and oxacillin, disrupted the commensal microbiota and promoted co-blooming of donor and recipient strains, facilitating conjugation. Oxacillin treatment in vivo produced variable levels of overgrowth and HGT, with metagenomic analyses revealing that baseline microbiome composition and intrinsic susceptibility determined the extent of perturbation and transfer.
Together, these findings demonstrate that preservation of microbiota integrity limits Enterobacterial overgrowth and constrains ESBL plasmid dissemination, highlighting indirect antibiotic effects as key drivers of resistance spread.