Episode 18: Panel - Has Nanopore rendered onsite Illumina obsolete?

The microbinfie podcast explores the evolving landscape of sequencing technologies, focusing on the potential of nanopore sequencing to transform microbial genomics research, particularly in resource-limited settings.

The panel discussion was held at the MRC Gambia about SARS-CoV-2, part of The London School of Hygiene and Tropical Medicine, in January 2020. This event was recorded in front of a live audience of scientists, just as SARS-CoV-2 was beginning to be reported as an emerging infectious disease.

Panelists

• Andrew Page - Quadram Institute
• David Baker - Quadram Institute
• Ozan Gundogdu - London School of Hygiene and Tropical Medicine (UK)
• Abdul Sesay - London School of Hygiene and Tropical Medicine (Gambia)
• Nick Loman - University of Birmingham

Chair: Suzie Hingley-Wilson, University of Surrey

Participants

• Mark Pallen - Quadram Institute
• Muna Anjum - APHA
• Arnoud van Vliet - University of Surrey
• Martin Antonio - London School of Hygiene and Tropical Medicine
• Archie Worwui - London School of Hygiene and Tropical Medicine

Extra notes

• Long-Read Sequencing vs. Short-Read Sequencing:

  • The discussion emphasizes the shift from short-read sequencing platforms like Illumina to long-read sequencing using technologies such as Oxford Nanopore and PacBio.
  • Oxford Nanopore, due to its high data output and ability to provide long contigs, appears to be favored for complex metagenomic samples over Illumina.

• Challenges and Limitations:

  • A significant challenge for nanopore technology is its error rate, which is higher compared to Illumina or PacBio. Efforts exist to improve or circumvent these issues with current methodological advancements.
  • While nanopore can handle a large portion of sequencing tasks, there will still be specific applications needing the high accuracy offered by Illumina or PacBio.

• Technological Adoption:

  • The accessibility and cost-effectiveness of the nanopore platform may lead to broader adoption, especially in resource-limited settings like Africa, where accessibility to Illumina is more challenging.
  • Some institutions are transitioning to hybrid sequencing approaches, leveraging both MinION Nanopore and Illumina for more comprehensive results.

• Methodology Adjustments:

  • Analysis pipelines used for nanopore data differ from those used with Illumina due to inherent differences in error profiles and data output. This necessitates custom bioinformatics solutions and ongoing optimization.
  • There is a mention of hybrid assemblies, where long and short reads are combined, though this requires conversions and isn't straightforward.

• Outbreak and Pathogen Detection:

  • Nanopore is valued for its potential in direct sequencing applications to detect pathogens quickly, bypassing culture steps. However, its accuracy may still limit its use for detailed epidemiological tracking.
  • A hybrid approach of initial screening with nanopore followed by detailed Illumina sequencing is suggested for specific cases needing precision.

• Strategic Considerations:

  • Institutions may adopt core sequencing facilities with both platforms as nanopore becomes more prevalent, creating flexibility for long-read and short-read techniques.
  • Cost considerations remain crucial, particularly with high-throughput applications, impacting technology choices in public health and surveillance contexts.

• Future Outlook:

  • PacBio is noted for its high accuracy, but cost and accessibility challenges hinder its wider adoption compared to the flexible and portable nature of Oxford Nanopore. The potential for an all-in-one solution combining the strengths of current platforms is hinted as a desirable future advancement.

Overall, the episode underscores the evolution in microbial bioinformatics driven by advancements in sequencing technology, emphasizing the importance of adapting methodologies to leverage new data capabilities while managing existing limitations.