From Command Line to Real-Time: How Akershus Updated their Genomic Surveillance workflow

It started as a simple tip: “There’s a hospital in Akershus doing excellent work with Solu.”

So, we boarded a flight to Oslo, travelled to Akershus University Hospital, and sat down with Cecilie Sveen-Ekre, a seasoned biomedical laboratory scientist with an M.Sc. in molecular medicine and 15 years of experience in microbiology.

Last year, in 2024, the Akershus team responded to a vancomycin-resistant E. faecium outbreak in Oslo. The outbreak originated in 2023 and created a potential threat to patient safety, as Akershus is located close to the capital. To rule out local spread, Cecilie and the team whole genome sequenced E. faecium isolates from the patients.

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The challenge of managing complex results.

After sequencing the VRE isolates, the team ran into a bottleneck: organizing and keeping track of files and results. As Cecilie and the Akershus team worked to investigate the outbreak, poor data organization became a limiting factor. This led to unnecessary increases in turnaround time.

We used command-line tools… results were in separate folders… finding the analysis took forever. I used two computers simultaneously to keep track of the results.

Cecilie recognized that generating actionable insights under timely pressure required proper, real-time analysis tools. This led her and the team to adopt Solu.

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Solu’s impact:

First time logging in, I drag & dropped the files, and got results in minutes. It was like magic.

Unlike with burdensome procedures with multi-computer SNP analysis and Excel, Cecilie and her team were able to focus on the results with Solu. They could detect real-time clusters, compare new isolates, and review them with infection control, all within minutes of upload. The change resulted in a holistic view of the outbreak, even including vital findings that the team was previously unaware of. No command line required.

It saves time and strengthens the quality of our work.

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Next steps:

Looking ahead, Cecilie and the team plan to establish Solu as a central communication tool between the laboratory and the infection control team. They want to leverage the platform not only for analysis, but also for communicating results clearly and efficiently.

Solu is an intuitive platform that makes it easy to track genomic data, understand clusters, and detect high-risk isolates quickly.

We left Akershus with a strong cup of Norwegian coffee, a thank you, and a reminder: real-time genomic surveillance is needed. Especially tools that continuously get faster, easier to use, and smarter.