Introducing cgMLST: a second way to compare your samples

Genomic surveillance comes down to one question. How similar is this group of samples? Answer it well and you can see who infected whom, catch transmission early, and tell related cases from background noise.

Solu has always answered that question with a peer-reviewed, SNP-based phylogeny. Today we're adding a second way to compare your samples: core-genome multilocus sequence typing (cgMLST). It is built on established community schemes (Pasteur and PubMLST) and fully deterministic across runs and workspaces. We find the allelic profiles from the uploaded genomes that are directly comparable across institutions, so you can find out whether the same or similar pathogen is also present at another facility.

How it works

Using cgMLST on Solu is a simple, drag-and-drop workflow.

1. Upload your samples to the platform.
2. Allelic profiles are computed for each sample, for every supported species.
3. Profiles of the same species are compared against each other.
4. Results are visualized in a phylogenetic tree, and clusters are formed automatically.
5. Allelic profiles can be downloaded and shared easily, so other organizations can compare results against them.

Solu shows SNP-based phylogeny by default; to use cgMLST instead, switch the method per species in your workspace settings, where the choice applies to everyone on the team.

cgMLST is currently available for:

• Klebsiella pneumoniae, K. variicola, K. quasipneumoniae, K. quasivariicola, and K. africana
• Mycobacteroides abscessus
• Staphylococcus aureus
• Vibrio cholerae
• Listeria monocytogenes
• Campylobacter jejuni and C. coli

We are continually adding new species. If you work with one that isn't supported yet, reach out to our team and we're glad to assist you.

Validated clustering results

Our whitepaper documents how Solu platform implements cgMLST and shows that it produces valid clustering results across seven core-genome MLST schemes. Here's what stood out.

1. We recovered published outbreaks. We re-ran the authors' raw reads from six published studies, across Klebsiella, Mycobacteroides abscessus, Staphylococcus aureus, Listeria, Vibrio cholerae, and Campylobacter, and recovered the clusters they reported.

2. It closely matches our peer-reviewed SNP pipeline. Because Solu already provides a validated SNP-based phylogeny, we compared the two methods on the same isolates across all six datasets. The results agreed closely throughout.

3. It's built on community schemes, and it's fully reproducible. cgMLST uses the curated Pasteur and PubMLST schemes the community already relies on, keeping results comparable across institutions. The validation datasets are public, so the results can be independently reproduced.

Who it's for

cgMLST is built for people doing genomic surveillance who either aren't familiar with SNP-based approaches or simply consider cgMLST the better fit for their work.

It is especially useful for teams that need to share results across organizations. The allelic profiles are comparable from one organization to the next, making it easy to tell whether the same or similar pathogen has appeared at another site.

Try it today

cgMLST is live in the Solu platform now. Log in and switch any supported species over to cgMLST in your workspace settings. New to Solu? Start a free trial and see it in action.

Want the full technical details, such as the schemes, the thresholds or the per-dataset metrics? Read the complete validation white paper.