New Possibilities in Pathogen Detection
Genomic-based diagnostics have emerged as promising alternatives to conventional culture-based methods, offering advantages in speed, accessibility, sensitivity, and precision (*). However, they have a key limitation: they cannot easily determine whether detected DNA originates from viable – and therefore potentially infectious – organisms. This uncertainty affects decisions in clinical microbiology, infection control, and environmental health monitoring.
“Nanopore sequencing gives us much richer data than most other technologies,” says Urban. “The raw signal – produced as DNA passes through the nanopores – has already been used to detect chemical modifications to DNA. We now show, for the first time, that this signal also holds information about whether microbes are alive, which is critical for many of our applications in public health genomics."
AI Models Reveal Microbial Viability
“We show that AI models can be trained to predict whether DNA comes from a dead or alive microorganism,” so Harika Ürel, doctoral researcher at Helmholtz Munich and the first author of the paper. “This is the first time such a prediction has been made using raw sequencing data.”
“Nanopore technology has already transformed genomics with its portability and data richness. What we add here is first evidence that we can infer biological states directly from the sequencing signal, which is important for real-time, genome-based pathogen monitoring,” adds Urban.
(*) as previously demonstrated by the Urban team at Helmholtz Munich (see Sauerborn et al., 2024, Nature Communications; and Perlas et al., 2025, Virus Evolution).
Original publication
Ürel et al., 2025: Nanopore- and AI-empowered microbial viability inference. GigaScience. DOI: 0.1093/gigascience/giaf100
About the scientist
Prof. Lara Urban is a Principal Investigator at Helmholtz AI, where she leads research at the intersection of artificial intelligence and genomics. She also holds a position on the professorship track at the University of Zurich, where her work contributes to One Health research – an integrated approach that explores the links between human, animal, and environmental health. Contact: lara.urban@helmholtz-munich.de
Funding information
The research was supported by a Helmholtz Principal Investigator Grant awarded to Lara Urban at Helmholtz AI and brought together expertise from microbiologists, computational biology, and data science. It was carried out within the interdisciplinary research environment of Helmholtz AI, which focuses on applying AI across the life sciences.
