Omics of antimicrobials and antimicrobial resistance

ABSTRACT

Introduction: The development of new antimicrobials has become an urgent priority because of a global challenge emerging from the rise of antimicrobial resistant pathogens.

Areas covered: In this review, the authors discuss the opportunities offered by modern omics approaches to address the challenge and the use of this approach in antimicrobial development. Specifically, the authors focus on the role of omics technologies and bioinformatics for the revelation of the effects of antimicrobials in a variety of microbial cellular processes, as well as the identification of potential cellular targets, the mechanisms of antimicrobial resistance, and the development of new antimicrobials.

Expert opinion: Prevention of antimicrobial resistance does not only depend on rational drug design such as narrow-spectrum antimicrobials but on several factors. It is the opinion of the authors that the use of a multi-omics bioinformatics approach should become an integral part of antimicrobial drug discovery as well as in the prevention of antimicrobial resistance.

KEYWORDS:

• Antimicrobials
• antimicrobial resistance mechanisms
• novel antimicrobials
• genomics
• transcriptomics
• proteomics
• metabolomics

Acknowledgements

We thank N.B. Baranova (Kazan Institute of Biochemistry and Biophysics) for help with figures and Dr. Anthony J. Travis (University of Aberdeen) for proofreading the manuscript.

Article highlights

• Transcriptomic, proteomic, and metabolomic analyses of bacterial responses to antimicrobial treatment revealed that resistance to antimicrobials may involve multiple pathways in the cell including central metabolism.

• Investigation of antimicrobial effects on bacterial cells with the use of omics technologies uncovered the multiple physiological effects imposed by antimicrobials.

• Analysis of pathways affected by various antimicrobials opens the possibility for identification of new targets for antimicrobials.

• The complexity of responses to antimicrobials allows identifying targets for synergistically acting antimicrobials.

• Prevention of antimicrobial resistance includes not only rational drug design such as narrow-spectrum antimicrobials but also depends on a number of other factors.

This box summarizes key points contained in the article.

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

The authors are supported by a grant from the Russian Foundation for Basic Research (Award No. 18-04-00660).