Advances in Microbial Genomics in the AMR Field

Dear Colleagues,

The global dissemination of antimicrobial resistance (AMR) is among the most serious challenges to public health, food production, and ecological integrity. In recent years, the integration of microbial genomics and high-throughput sequencing has transformed our ability to detect, monitor, and predict resistance patterns across ecosystems. Genomic sciences are rapidly enhancing our understanding of microbial resistance mechanisms, the evolution of AMR in pathogens, and the emergence of novel resistance pathways under selective pressure. Additionally, advances in bioinformatics, artificial intelligence, and functional genomics are providing new opportunities for targeted intervention and therapeutic innovation. Phage therapy, CRISPR-based tools, and genome-informed surveillance strategies represent promising alternatives to conventional antibiotics. At the same time, international collaborative platforms and databases are enabling real-time global monitoring and data sharing, representing key elements for effective AMR control under a One Health approach. Despite these advances, gaps remain in translating genomic data into actionable insights, especially in low-resource settings, where AMR surveillance is often limited.

This Special Issue of Microorganisms aims to gather original research and review articles that present recent advances in the genomics of antimicrobial resistance (AMR), including novel approaches for its study, monitoring, and control. We welcome contributions that explore new technologies, analytical methods, and applications of microbial genomic data across clinical, agricultural, and environmental contexts.

The scope of this Special Issue includes, but is not limited to, innovations in AMR surveillance, the application of CRISPR technologies and phages in AMR control, AI-based genomic analysis, the development of global platforms and databases for AMR research, and international collaborative strategies aligned with the One Health framework.

Prof. Dr. Rosalba Troncoso-Rojas
Guest Editor

Dr. María Elena Báez-Flores
Guest Editor Assistant

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.