Global lessons from metagenomics for future critical care and pathogen surveillance
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Understanding infection biology — from ICU pneumonia to broader pathogen surveillance — demands approaches that deliver richer information, faster, and with flexibility across sample types and settings.
This webinar will examine how real-time Oxford Nanopore sequencing can support research into respiratory infections, antimicrobial strategy development, and the potential for wider adoption of applied metagenomics in clinical microbiology and public health.
Georgios Kitsios will outline how applying Oxford Nanopore metagenomic sequencing to culture-positive pneumonia samples provides a more detailed picture of microbial community structure, co-infections and host responses. His work demonstrates substantial diversity even in cases considered diagnostically straightforward, using standard clinical methods, thereby offering new perspectives into infection biology and inflammation research.
Gowtham Thakku will share findings from evaluating Oxford Nanopore metagenomic workflows using spike-in standards and varied real-world specimens. He will highlight practical considerations from global infectious disease training programmes and how these experiences are informing capacity building for future pathogen genomic surveillance.
In this webinar, you will learn:
About the limitations of conventional culture methods in severe pneumonia
How metagenomic sequencing reveals microbial complexity even in culture-positive pneumonias.
How pathogen abundance and community composition may relate to host inflammation and potential survival outcomes
Key technical considerations, optimisations, and training insights for implementing Oxford Nanopore metagenomic workflows in research and surveillance settings.
Meet the speakers
In this webinar, we'll share results from exploring the Oxford Nanopore metagenomics workflow using spike-in standards and real-world clinical samples. The talk will cover challenges, optimizations, and insights from our international training programs in genomic surveillance. Key highlights include:
- Insights from evaluating ONT metagenomics workflows across sample types
- Practical strategies for addressing technical challenges
- Lessons from global training workshops in metagenomics sequencing
In this webinar, we'll share results from exploring the Oxford Nanopore metagenomics workflow using spike-in standards and real-world clinical samples. The talk will cover challenges, optimizations, and insights from our international training programs in genomic surveillance. Key highlights include:
- Insights from evaluating ONT metagenomics workflows across sample types
- Practical strategies for addressing technical challenges
- Lessons from global training workshops in metagenomics sequencing
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Gowtham Thakku , Scientist , Chan Zuckerberg BiohubSevere pneumonia in the ICU presents diagnostic challenges: cultures are slow and often negative, driving empiric therapy and clinical uncertainty. While metagenomic sequencing has been proposed to address culture-negative cases and accelerate diagnosis, less attention has focused on microbiologically confirmed pneumonias—cases of presumed diagnostic certainty. This presentation examines Nanopore metagenomic data from culture-positive pneumonias processed through the BugSeq pipeline, revealing unexpected complexity in pathogen abundance and microbial community composition. These metagenomic features correlate with host inflammatory responses and clinical outcomes, identifying a previously underappreciated source of biological heterogeneity with potentially direct implications for antibiotic decision-making and precision treatment strategies.
Learning Objectives:
- Understand the diagnostic limitations of conventional culture methods in severe pneumonia, including delayed results and high rates of culture negativity
- Recognize that even culture-positive pneumonias harbor unexpected microbial complexity when examined by metagenomic sequencing
- Evaluate how pathogen abundance and community composition may relate to host inflammation and survival outcomes
- Apply metagenomic insights with the potential to refine antibiotic strategies and identify biological heterogeneity in critically ill patients with pneumonia
Severe pneumonia in the ICU presents diagnostic challenges: cultures are slow and often negative, driving empiric therapy and clinical uncertainty. While metagenomic sequencing has been proposed to address culture-negative cases and accelerate diagnosis, less attention has focused on microbiologically confirmed pneumonias—cases of presumed diagnostic certainty. This presentation examines Nanopore metagenomic data from culture-positive pneumonias processed through the BugSeq pipeline, revealing unexpected complexity in pathogen abundance and microbial community composition. These metagenomic features correlate with host inflammatory responses and clinical outcomes, identifying a previously underappreciated source of biological heterogeneity with potentially direct implications for antibiotic decision-making and precision treatment strategies.
Learning Objectives:
- Understand the diagnostic limitations of conventional culture methods in severe pneumonia, including delayed results and high rates of culture negativity
- Recognize that even culture-positive pneumonias harbor unexpected microbial complexity when examined by metagenomic sequencing
- Evaluate how pathogen abundance and community composition may relate to host inflammation and survival outcomes
- Apply metagenomic insights with the potential to refine antibiotic strategies and identify biological heterogeneity in critically ill patients with pneumonia
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Georgios Kitsios , Assistant Professor of Medicine , University of Pittsburgh
