How New Zealand’s ESR and Awanui Labs achieve ultrafast outbreak detection with Solu and Nanopore sequencing

Kia ora! Read how New Zealand’s Institute of Environmental Science and Research (ESR) and Awanui Labs Wellington are changing the game by pairing Oxford Nanopore sequencing with Solu, a cloud-based bioinformatics platform, to detect and respond to outbreaks faster.

Key takeaways

• Solu’s cloud-based platform reduced bioinformatics turnaround times from weeks to minutes.
• Awanui Labs Wellington's and ESR's approach shows that combining nanopore sequencing with automated analytics is feasible for ultra-rapid outbreak detection.
• This model has global implications, offering a scalable solution for hospitals and public health agencies worldwide.

Need for speed: the Wellington region approach

In the race against infectious disease outbreaks, every hour counts. Hospitals and public health teams often have the tools to sequence pathogens, but analyzing that data can take weeks – time they don’t have during an outbreak.

Awanui Labs Wellington, which provides services to Wellington Regional Hospital, implemented real-time Nanopore sequencing to enhance its outbreak detection capabilities [1]. With rapid library preparation methods, this could speed up outbreak investigations. However, they faced a significant limitation: off-site data analysis could take weeks to complete.

ESR saw an opportunity to cut through this bottleneck by piloting an ultrafast outbreak detection system that utilizes fast, easy-to-use bioinformatics tools. They sought an automated, cloud-based solution that could deliver rapid on-site analysis without requiring specialized expertise.

How Solu enables same-day outbreak investigation

Solu, a cloud-based bioinformatics platform, turned out to be exactly what they needed. It’s designed to be simple – it has a drag-and-drop interface for sequencing files, and no specialized expertise is needed. The microbiology lab staff on-site at the hospital can upload basecalled sequencing reads, and Solu’s automated workflow delivers results in minutes. This means that the lab could identify outbreaks faster, enabling timely action to prevent further spread.

"When paired with ONT sequencing, which allows utilisation of sequence data in real-time, this analysis model would potentially allow same-day high-resolution outbreak investigation."

Benchmarking Solu against traditional bioinformatics

To validate Solu’s effectiveness, Awanui Labs Wellington and ESR conducted a series of tests by revisiting ‘real-world’ nanopore sequence data from two neonatal unit outbreaks: a MRSA outbreak in 2023 [2] and a Klebsiella variicola outbreak in 2024 [3]. Here’s what they found:

• The median time-to-results with Solu was 13 minutes for S. aureus and 20 minutes for K. variicola, faster than the manual workflow.
• Single-nucleotide variant (SNV) distances showed general agreement with traditional bioinformatics approaches; using Solu would provide a rapidly actionable approach for infection prevention and control (IPC) management.
• Because Solu is automated, it didn’t require a team of bioinformatics experts to run.

These tests showed that Solu isn’t just fast—it’s also practical to use for hospitals and labs. The full results are currently available as a preprint.

Real-world implementation of this approach has already begun, with Solu, ESR, and Awanui Labs Wellington working together to continuously refine and optimize the processes. "We're now entering an exciting phase where actual usage data will help us make the system even faster and more efficient," says Sam Sihvonen, co-founder and CEO of Solu.

While Solu can significantly streamline the bioinformatics process, it's important to note that interpreting whole genome sequencing results still requires personnel familiar with WGS outputs. The platform works best within a hub-and-spoke model where hospital laboratories can quickly generate and analyze data while maintaining a connection to centralized bioinformatics expertise (such as national reference laboratories) for advanced analysis and oversight.

This model is particularly effective because Solu's data-sharing capabilities enable seamless collaboration between local laboratories and central expertise. Hospital labs can maintain their rapid response capabilities while benefiting from the guidance of experienced bioinformaticians when needed.

Implications for global outbreak response

Awanui Labs Wellington’s and ESR's success with Solu and Nanopore sequencing demonstrates a highly accessible model for healthcare facilities worldwide. The combination of portable nanopore sequencers and cloud-based Solu means that genomic surveillance can be implemented almost anywhere. Here's why:

• Minimal setup required: Oxford Nanopore Technologies' compact sequencing devices and Solu's cloud platform eliminate the need for extensive lab space or computing infrastructure.
• Cost-effective entry: The relatively small investment needed for nanopore equipment, combined with Solu's cloud-based pricing, makes genomic surveillance accessible even for facilities with limited resources.
• Fast turnaround: The combination of rapid nanopore sequencing and Solu's analysis speed allows for quick results from small sample volumes, enabling faster outbreak detection.

The bottom line

The future of outbreak detection is fast, automated, and cloud-powered. Awanui Labs Wellington's and ESR's work with Solu and Nanopore sequencing shows what’s possible when you combine cutting-edge tools with a focus on speed and accessibility. For hospitals and labs looking to step up their outbreak response, the message is clear: tools like Solu can turn weeks of waiting into minutes of action.

Ready to transform your outbreak detection capabilities? Start analyzing samples for free or contact our team to learn how Solu can help your organization respond faster to infectious disease outbreaks.

References

1. Bloomfield, M., Hutton, S., Velasco, C., Burton, M., Benton, M., & Storey, M. (2024). Oxford nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians. Pathology, 56(3), 444-447. https://doi.org/10.1016/j.pathol.2023.07.014

2. White, R. T., Bakker, S., Burton, M., Castro, M. L., Couldrey, C., Dyet, K., Eustace, A., Harland, C., Hutton, S., Macartney-Coxson, D., Tarring, C., Velasco, C., Voss, E. M., Williamson, J., & Bloomfield, M. (2024). Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing. Microbial genomics, 10(7), 001273. https://doi.org/10.1099/mgen.0.001273

3. White, R.T., Balm, M., Burton, M. et al. The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing. Antimicrob Resist Infect Control 14, 6 (2025). https://doi.org/10.1186/s13756-025-01529-2

‍