How Sequencing is Reshaping Infectious Disease Genomics

This content was funded by Oxford Nanopore Technologies. 

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Antimicrobial resistance, outbreak investigation, and pathogen surveillance present growing challenges for clinical microbiology laboratories worldwide. In this video series, leading experts share how Oxford Nanopore sequencing technologies can be integrated into real-world diagnostic workflows, from targeted resistance profiling and pneumococcal surveillance to continental-scale malaria genomics and respiratory metagenomics. 

• Three whole-genome sequencing programmes were unified into a single diagnostic model, covering 24-hour reflex sequencing for antimicrobial resistance, pneumococcal genotyping to inform vaccination policy, and a stepwise outbreak triage framework 
• A decentralised surveillance network across multiple African countries uses a nanopore protocol delivering results in approximately five hours at under $25 per sample, targeting drug resistance genes, diagnostic antigens, and vaccine targets 
• Three Swedish university hospitals jointly evaluated the beta SQK-MAB114.24 kit across 98 clinical samples, 15 specimen types, and defined mock samples, achieving detection as low as 15 CFU/mL 
• NHS Lothian traces its sequencing journey from SARS-CoV-2 and poliovirus surveillance through mpox outbreak response, RSV whole-genome sequencing, and antimicrobial resistance monitoring in Neisseria gonorrhoeae 

1. Microbiology, Virology, and Immunology Laboratories, AdventHealth Orlando, Florida, USA
2. Sahlgrenska University Hospital, Gothenburg, Sweden
3. Max Planck Institute for Infection Biology, Berlin, Germany
4. NHS Lothian, UK