Francesc Coll, PhD, Institute of Biomedicine of Valencia, Spanish National Research Council (IBV-CSIC), Spain
Margo Diricks, PhD, Research Center Borstel, Leibniz Lung Center, Germany
Koji Yahara, PhD, National Institute of Infectious Diseases, Japan Institute for Health Security, Japan
Francesc Coll, PhD, Institute of Biomedicine of Valencia, Spanish National Research Council (IBV-CSIC), Spain
Francesc Coll is a principal investigator (cientÃfico titular) at the Institute of Biomedicine of Valencia, Spanish National Research Council (IBV-CSIC), where he leads the Applied Microbial Genomics Unit. Before that he was a senior Staff Scientist at the Wellcome Sanger Institute (UK), and an Assistant Professor at the London School of Hygiene & Tropical Medicine (LSHTM), supported by an Institutional Strategic Support Fund Fellowship (ISSF), funded by Wellcome & LSHTM. He joined LSHTM in July 2016 as an Research Fellow (postdoc) funded by a Sir Henry Wellcome Postdoctoral Fellowship, after joining the research group led by Prof. Sharon Peacock at the University of Cambridge, UK. In October 2014, he completed his PhD at LSHTM under the supervision of Prof. Taane Clark, which focused on strain genotyping and drug resistance in Mycobacterium tuberculosis using whole genome sequencing.
Francesc is a computational biologist with expertise in bacterial genomics, antibiotic resistance, and applied bacteriology. His research focuses on the applications of whole-genome sequencing as a tool for basic research, surveillance, and diagnostics for bacterial infections. He employs advanced population-genomics approaches, such as Genome-Wide Association Studies (GWAS), to characterize the genetic basis of bacterial phenotypes and adaptation. He conducted genomic surveillance studies to map the spread of nosocomial pathogens such as MRSA and VRE. He has also worked in the development of bioinformatics analysis pipelines, standards for genome analyses and interpretation, and in the identification of genetic markers for the surveillance and diagnosis of bacterial pathogens. More recently, he has conducted studies to characterize mutational adaptation of commensal and pathogenic bacteria.
Overall, he has over 14 years of experience in his field and have published over 50 peer-reviewed papers, including 14 as the main author (first, last or corresponding author).
Margo Diricks, PhD, Research Center Borstel, Leibniz Lung Center, Germany
Dr. ir. Margo Diricks is a bioengineer who completed her PhD in the field of biocatalysis at the University of Ghent, Belgium. After working for three years at a bioinformatics company, she joined the Research Center Borstel (RCB) – Leibniz Lung Center in 2020 as a postdoctoral researcher.
At RCB, Margo has focused on developing and applying bioinformatic tools and pipelines to analyze, interpret, and visualize genomic data of emerging drug-resistant lung pathogens, such as non-tuberculous mycobacteria, Haemophilus influenzae, and Stenotrophomonas maltophilia, in order to study their transmission dynamics, population structure, and the evolution of antimicrobial resistance (AMR). She is the curator of the publicly available 7-loci MLST and core genome MLST (cgMLST) typing schemes for Mycobacterium abscessus on pubMLST, which provide global reference frameworks for molecular surveillance and transmission analysis.
Based on her scientific achievements, her work has been recognized with multiple Best Paper of the Month awards as well as the BD Research Award. Alongside her scientific work, she is dedicated to supporting early-career researchers, mainly providing guidance to PhD students on challenges that extend beyond the scope of their direct supervision.
She is also actively engaged in large-scale international collaborations and professional networks, including the Pan-Africa Network for Genomic Surveillance of Poverty-Related Diseases and Emerging Pathogens, the European Society for Mycobacteriology, NTM-net (the international network to promote clinically oriented research on non-tuberculous mycobacterial diseases), the One Health Platform (OHP), and the German Society for Hygiene and Microbiology. In addition, she contributes to the ESGEM-AMR working group coordinated by the ESCMID Study Group for Epidemiological Markers (ESGEM), where she is a member of the Haemophilus subgroup.
Koji Yahara, PhD, National Institute of Infectious Diseases, Japan Institute for Health Security, Japan
Dr Koji Yahara, Group Leader at the Antimicrobial Resistance (AMR) Research Center, National Institute of Infectious Diseases, Japan Institute for Health Security, is a biomedical informatician with a PhD in Biostatistics, obtained through a collaborative program bridging biostatistics and infectious disease epidemiology.
A primary focus of his work has been the statistical analysis of both genomic/metagenomic and epidemiological data related to infectious diseases, as well as the development and management of information technology programs and databases in the fields of life science and medicine. In 2012, he began a long-term research visit to Germany and the UK as a government-funded JSPS Research Fellow at the University of Tokyo, conducting international projects that he later expanded upon after returning to Japan.
In April 2016, he joined the National Institute of Infectious Diseases, where he assumed responsibility for information technology of the Japan Nosocomial Infections Surveillance (JANIS), a national comprehensive AMR surveillance program in Japan . Since 2020, he has been a leader in national genomic surveillance linked to JANIS, as well as in the use of the international version of JANIS to promote international cooperation as part of the activities of the WHO Collaborating Center for AMR Surveillance and Research.
He received an award from the Society for Genome Microbiology, Japan, in recognition of his contributions to population genomic studies on microbial recombination, phylogeny, and population structure. He was a main organizer of SMBE Satellite Workshop on Pathogen Pangenome Evolution Between and Within their Hosts in 2024. He has corresponding or first-author publications in Nature Communications, Genome Medicine, Molecular Biology and Evolution, Journal of Hospital Infection and has been an editor of Microbial Genomics.
The emergence of drug resistance, tolerance and persistence in pathogenic microorganisms is a pressing global health challenge. The alarming rise of multidrug-resistant pathogens threatens to render many existing treatments ineffective. Recent advances in genomic technologies, such as whole genome sequencing (including the latest long read sequencing), have provided new insights into the genetic and functional aspects of drug resistance. By identifying resistance mechanisms and their evolutionary trajectories, researchers can contribute to the design of novel therapeutic interventions, thereby enhancing our capacity to combat infections and reduce the burden of antimicrobial resistance.
This Collection aims to explore the biology underlying resistance mechanisms across bacteria, viruses, and fungi, focusing on molecular mechanisms, genetic factors, and evolutionary dynamics.
We welcome submissions on various genomic studies regarding antimicrobial resistance, in particular those focusing on:
All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.
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This Collection welcomes submission of original Research, Method, Short Report, Review, and Database article types. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Biology of drug resistance and tolerance in bacteria, viruses, fungi" from the dropdown menu.
All manuscripts submitted to this journal, including those submitted to collections and special issues, are assessed in line with our editorial policies and the journal’s peer review process. Reviewers and editors are required to declare competing interests and can be excluded from the peer review process if a competing interest exists.