With novel (previously undescribed diversity), it functions more like a highly sensitive MLST - randomly occurring SNPs will occur by chance in amplicons, but we have many more amplicons than a typical MLST scheme so we have more opportunity to detect novelty. - ThreadSky

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typemat12.bsky.social • 92 days ago

With novel (previously undescribed diversity), it functions more like a highly sensitive MLST - randomly occurring SNPs will occur by chance in amplicons, but we have many more amplicons than a typical MLST scheme so we have more opportunity to detect novelty.

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typemat12.bsky.social•92 days ago

We designed a 59-amplicon multiplex primer scheme which performs with high sensitivity (

typemat12.bsky.social•92 days ago

And we then deployed the method to a low-resource laboratory with our collaborators @thruzim.bsky.social BRTI in Zimbabwe as part of an ongoing genital ulcer study. The final assay can be performed in <2 days and costs <£13/sample.

typemat12.bsky.social•92 days ago

We also built a @nextflow.io pipeline for rapid data processing, and a prototype shiny app for interactive data interpretation.

typemat12.bsky.social•92 days ago

Although here we have used T. pallidum as a model, we think this approach has broad applications for larger pathogen genomes (bacterial, fungal, parasite), and we hope others can make use of these approaches for different pathogens.

typemat12.bsky.social•92 days ago

And @carmcdhume.bsky.social recently did a blog about our field work using this method in Zimbawe https://sangerinstitute.blog/2025/02/17/syphilis-surprises-with-a-worldwide-comeback/

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