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. 2018 Dec 18;115(51):12902-12910.
doi: 10.1073/pnas.1717163115.

Microbiome as a tool and a target in the effort to address antimicrobial resistance

David A Relman  1   2   3 , Marc Lipsitch  4   5   6
Affiliations

Microbiome as a tool and a target in the effort to address antimicrobial resistance

David A Relman et al. Proc Natl Acad Sci U S A. .

Abstract

Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.

Keywords: antibacterial agents; drug resistance; horizontal gene transfer; immune system; microbiota.

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Conflict of interest statement

Conflict of interest statement: D.A.R. holds stock in or stock options from Seres Therapeutics, Evelo Biosciences, ProDermIQ, and Second Genome. M.L. has received consulting/honoraria payments from Merck, Pfizer, Antigen Discovery, and Affinivax and grant funding from Pfizer through the Harvard T. H. Chan School of Public Health.

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