Rethinking antimicrobial stewardship paradigms in the context of the gut microbiome

Abstract

Ongoing concerns over the presence and persistence of antimicrobial resistance (AMR), particularly in Gram-negative bacteria, continue to have significant global health impacts. The gastrointestinal tract, or ‘gut’, environment amplifies AMR in the human gut microbiome, even in the absence of antibiotics. It constitutes a complex and diverse community of organisms, and patterns and alterations within it are increasingly being found to be associated with states of health and disease. Our understanding of the effects of routes of administration of antimicrobials on the gut microbiome is still lacking despite recent advances in metagenomics. In this article we review current evidence for antibiotic effects on gut microbiota and explore possible prescribing and stewardship approaches that would seek to minimize these effects. If we are to preserve existing and new antimicrobials, we need to consider their use in the context of their effect on gut ecology, and the human microbiome in general.

Harnessing the microbiome to prevent global biodiversity loss

“…The treatment and management of microbial disruptions have traditionally focused on administering antimicrobials 38 , with little consideration for the maintenance of the beneficial constituents…”

Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year

“…Scientific developments have enabled the possibility of personalised medicine at this time more than any other. In an age where antimicrobial resistance (AMR) is a global concern, insights into the gut microbiome, a known 'amplifier' of AMR 1 , may in the future aid clinicians in tailoring therapy for their patients to reduce this and other health risks. However, for patients, providing faecal samples can be an uncomfortable experience 2 , and the cost of sequencing individual patients' gut microbiomes, both in terms of time and resource, still remains prohibitive.…”

Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year

“…Scientific developments have enabled the possibility of personalised medicine at this time more than any other. In an age where antimicrobial resistance (AMR) is a global concern, insights into the gut microbiome, a known ‘amplifier’ of AMR 1 , may in the future aid clinicians in tailoring therapy for their patients to reduce this and other health risks. However, for patients, providing faecal samples can be an uncomfortable experience 2 , and the cost of sequencing individual patients’ gut microbiomes, both in terms of time and resource, still remains prohibitive.…”