Scholarlink

<p>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 <i>Treponema pallidum</i> and <i>Neisseria gonorrhoeae</i>, we designed a high-resolution multiplex PCR sequencing scheme for lineage tracking pathogens with different extremes of genome variation. For <i>Treponema pallidum</i>, 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 <i>T. pallidum</i> 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 &lt;£300/24 samples (£12.47/sample). Phylo-Plex enables low-cost tracking of priority pathogenic lineages in low resource settings and at scale.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月9日

查看全文
  • Mathew A. Beale,
  • Vignesh Shetty,
  • Kirsty E. 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 M. Washaya,
  • Luanne Rodgers,
  • Beauty Makamure,
  • Ethel Dauya,
  • Michael Marks,
  • Etienne E. Müller,
  • Rashida A. Ferrand,
  • Nicholas R. Thomson

摘要

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.