Oral Presentation 15th Lorne Infection and Immunity 2025

Rifaximin prophylaxis and the de novo emergence of near-pan resistant Enterococcus faecium (#27)

Adrianna M Turner 1 , Lucy Li 1 , Ian R Monk 1 , Jean YH Lee 1 , Danielle J Ingle 1 , Stephanie Portelli 2 , Norelle L Sherry 1 3 , Torsten Seemann 1 3 , Liam K Sharkey 1 , Calum J Walsh 1 , Gavin E Reid 4 , Shuai Nie 4 , Bart A Eijkelkamp 5 , Natasha E Holmes 6 , Brennan Collis 6 , Sara Vogrin 6 , Andreas Hiergeist 7 , Daniela Weber 8 , Andre Gessner 7 , Ernst Holler 8 , David B Ascher 2 , Sebastian Duchene 1 9 , Nichollas E Scott 1 , Tim P Stinear 1 , Jason C Kwong 1 6 , Claire L Gorrie 1 3 , Benjamin P Howden 1 3 6 , Glen P Carter 1
  1. Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
  2. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
  3. Microbiological Diagnostic Unit, University of Melbourne, Melbourne, VIC, Australia
  4. Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
  5. Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
  6. Department of Infectious Diseases & Immunology, Austin Health, Melbourne, Victoria, Australia
  7. Institute of Clinical Microbiology and Hygiene, University Medical Center Regensburg, Regensburg, Bavaria, Germany
  8. Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Regensburg, Bavaria, Germany
  9. Dept of Computational Biology, Institut pasteur, Paris, France

Background: Vancomycin-resistant Enterococcus faecium (VREfm) poses a significant threat to public health due to its extensive antimicrobial resistance (AMR). Daptomycin, a last-resort antibiotic, is crucial for treating VREfm infections. The rise of daptomycin resistance necessitates an urgent investigation into its underlying mechanisms and drivers. This study aimed to elucidate the molecular basis and clinical factors leading to daptomycin-resistant VREfm.

Methods: We analysed 1,000 Australian clinical VREfm using daptomycin susceptibility testing and whole-genome sequencing. A genome-wide association study identified novel resistance-associated mutations, which were confirmed using molecular approaches. Patient cohort studies explored the association between daptomycin resistance and rifaximin exposure. A murine VREfm gut colonisation model studied daptomycin-resistant VREfm emergence following rifaximin use. Multi-omics defined the molecular mechanism of resistance. 

Results: Daptomycin resistance was observed in 18.9% of VREfm. Novel rpoB mutations, typically associated with rifamycin resistance, were found to confer cross-resistance to daptomycin. These mutations were globally distributed (5 continents and 20 countries) and emerged shortly after clinical approval of rifaximin, an antimicrobial used prophylactically to prevent hepatic encephalopathy in liver disease patients. Clinical data revealed a strong association between recent rifaximin exposure and the carriage of daptomycin-resistant VREfm. Mouse model data confirmed that rifaximin caused de novo emergence of daptomycin-resistant VREfm within the gut. Multi-omics analyses showed that the rpoB mutations resulted in transcriptional upregulation of a previously uncharacterised operon (prdRAB), causing VREfm cell membrane remodelling, reduced daptomycin binding, and resistance.

Conclusions: This study identified a novel, globally prevalent mechanism of daptomycin resistance in VREfm, driven by rifaximin-induced rpoB mutations. Our findings highlight the unintended consequences of prophylactic rifaximin use and its potential to undermine daptomycin therapy. This work challenges the assumption that rifaximin is 'low-risk' for AMR development and shows how unanticipated antibiotic cross-resistance can undermine global strategies designed to preserve the use of critical antibiotics.