Microbiome-Sparing Antimicrobial Therapy: Ecological Prescribing Strategies to Prevent Antimicrobial Resistance Selection

Antimicrobial stewardship has traditionally focused on selecting effective treatment while limiting toxicity, unnecessary exposure, and resistance in the organism being treated. Less attention has been given to the ecological consequences of treatment for commensal microbial communities and to whether these consequences influence subsequent infection or resistance risk. Although antimicrobial-associated microbiome disruption is well documented, its clinical and therapeutic significance remains uncertain. The extent and persistence of disruption vary according to antimicrobial exposure, treatment duration, site of action, and characteristics of the patient’s baseline microbiome. However, validated ecological markers that can guide treatment decisions are still lacking. The principal unresolved questions are which microbiome or resistome changes predict clinically relevant outcomes, which patients are most susceptible to persistent disruption, and whether microbiome-informed prescribing provides a measurable advantage over current stewardship practice.The primary goal of this Research Topic is to identify when microbiome and resistome measurements can provide actionable information for antimicrobial prescribing.We particularly encourage comparative studies evaluating the ecological consequences of different antimicrobial regimens, including differences in community composition, microbiome recovery, colonization resistance, and resistance gene dynamics. Studies may compare antimicrobial agents or examine modifications in dose, route, or treatment duration. The collection also welcomes studies evaluating microbiome or resistome biomarkers in patients at risk of persistent disruption, resistant-organism colonization, or recurrent infection. Candidate biomarkers and predictive models should be assessed using prespecified ecological endpoints and validated against relevant microbiological or clinical outcomes. Where feasible, prospective evaluation or validation in an independent population is encouraged. The collection aims to identify reproducible and clinically relevant ecological measurements that can be incorporated into antimicrobial trials or stewardship programs.We welcome mechanistic, translational, computational, and clinical studies examining how the ecological effects of antimicrobial treatment can inform prescribing, drug development, and antimicrobial stewardship. Relevant sub-topics include: • comparative effects of antimicrobial agents, routes, doses, or treatment durations on the microbiome and resistome• relationships between antimicrobial-associated microbiome disruption, colonization resistance, and the expansion of resistant organisms• microbiome or resistome biomarkers for treatment selection, patient stratification, or monitoring • studies linking multi-omics or culture-based measurements with treatment response, resistance emergence, recurrent infection, or other clinical outcomes • models that predict microbiome disruption, delayed recovery, or the risk of colonization by resistant organisms• narrow-spectrum, pathogen-targeted, phage-based, anti-virulence, or other microbiome-sparing interventions• ecological endpoints and outcome measures for antimicrobial trials• strategies to preserve colonization resistance or support microbiome recovery after treatmentIn this collection we welcome the following article types: FAIR² DATA Direct Submission, FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, Technology and Code. Topic editors: Carlo Genovese, Floriana D'Angeli, Parul Grover Source: https://www.frontiersin.org/research-topics/84750/microbiome-sparing-antimicrobial-therapy-ecological-prescribing-strategies-to-prevent-antimicrobial-resistance-selection