Direct RNA sequencing unlocks insights into antibiotic resistance mechanisms and pathogen genomics | LC 25

Biography

Chloé Baum is a molecular biologist specialising in next-generation sequencing (NGS) technologies. After completing her PhD in collaboration with New England Biolabs, she now leads the implementation of Oxford Nanopore Technologies at Biomics, the sequencing core facility of the Pasteur Institute.

With extensive experience in short- and long-read sequencing, Chloé has developed innovative NGS-based methods that have since been applied to microbiology and microbiome research.

Abstract

The increasing threat of arboviral outbreaks and the emergence of novel antibiotic resistance mechanisms highlight the urgent need for innovative genomic approaches. Direct RNA sequencing offered by Oxford Nanopore Technologies, allows the analysis of RNA in real time without the need for reverse transcription or amplification, preserving critical base modifications. Here, we present the application of this technology in two critical areas of pathogen genomics: arbovirus surveillance and antibiotic resistance research. The first project focuses on genomic surveillance of arboviruses in the Pacific region. In collaboration with the Pasteur Institute of New Caledonia, we used direct RNA sequencing to characterize RNA viral genomes such as dengue and chikungunya, revealing insights into mutation dynamics, and sequence diversity. This approach enhances the ability to monitor virus evolution, improve outbreak preparedness, and strengthen genomic surveillance capabilities in the Pacific. The second project investigates a novel antibiotic resistance mechanism driven by an uncharacterized rRNA modification. Using direct RNA sequencing, we identified this modification, shedding light on its role in resistance. Together, these results illustrate the potential of direct RNA sequencing to address global challenges in pathogen genomics, from genomic surveillance to new antimicrobial resistance mechanisms.