Global lessons from metagenomics for future critical care and pathogen surveillance

Respiratory infections often present diagnostic and analytical challenges, even when standard microbiology methods suggest a clear causative organism. Metagenomic sequencing offers a way to characterise microbial diversity directly from samples, without the constraints of targeted or culture-based approaches.

In this session, two researchers share complementary perspectives:

Gowtham Thakku presents results from evaluating Oxford Nanopore metagenomic workflows using spike-in controls and a range of real-world specimen types. Drawing on experience from global infectious disease training programmes, he discusses practical considerations for implementation and how these insights support capacity building for future pathogen genomic surveillance.

Georgios Kitsios describes how applying Oxford Nanopore metagenomic sequencing to culture-positive pneumonia samples reveals unexpected microbial complexity. His work highlights extensive diversity within the lung microbiome, frequent co-infections, and links between pathogen profiles, host inflammation, and disease biology.

Together, the talks illustrate how real-time nanopore sequencing can extend respiratory infection research beyond pathogen identification alone.

What you will learn:

• Limitations of conventional culture-based methods in severe pneumonia research
• How metagenomic sequencing can uncover microbial diversity in culture-positive respiratory samples
• Relationships between pathogen abundance, community composition, and host inflammatory responses
• Practical considerations for implementing Oxford Nanopore metagenomic workflows, including optimisation and training in research and surveillance settings