Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology

作者：Mathew A. Beale, Vignesh Shetty, Kirsty Ambridge, George Lacey, Sam Dougan, William Roberts-Sengier, Beth Sampher, Florent Lassalle, Matthew J. Dorman, Mahlape P. Mahlangu, Johanna M. E. Venter, Bianca Da Costa Dias, Martha Chipinduro, Tendai Washaya, Luanne Rodgers, Beauty Makamure, Ethel Dauya, Michael Marks, Étienne Muller, Rashida A. Ferrand, Nicholas R. Thomson · 发表于：Nature Communications · 年份：2026 · DOI：10.1038/s41467-026-75002-y · 被引用次数：2 · 研究领域：Genetics, Bioinformatics, and Biomedical Research、Biomedical Text Mining and Ontologies、Genomics and Phylogenetic Studies

Genomic pathogen surveillance is a powerful tool for public health and research, but is costly and unachievable in low-resource settings. Most sub-genomic typing methods sacrifice resolution whilst remaining costly. We developed "Phylo-Plex", a novel approach that identifies information-rich genomic regions to maximise phylogenetic information whilst minimising the number of regions. Applied to Treponema pallidum and Neisseria gonorrhoeae, we designed a high-resolution multiplex PCR sequencing scheme for lineage tracking pathogens with different extremes of genome variation. For Treponema pallidum, we also designed and evaluated the Phylo-Plex scheme in the laboratory and field settings by sequencing 72 clinical samples using MinION Flongle cells. Our T. pallidum scheme comprising 59 multiplex amplicons achieved high discrimination of fine-scale sublineages comparable to those defined using whole genomes, and demonstrating a qPCR detection limit ≤Ct 32. Variant calls from MinION amplicon sequencing were highly correlated with Illumina whole genome sequencing. We successfully deployed the method in a low-resource laboratory in Zimbabwe, costed at <£300/24 samples (£12.47/sample). Phylo-Plex enables low-cost tracking of priority pathogenic lineages in low resource settings and at scale.