An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

Blanca M. Perez-Sepulveda, Darren Heavens, Caisey V. Pulford, Alexander V. Predeus, Ross Low, Gregory F. Dykes, Christian Schudoma, Will Rowe, James Lipscombe, Chris Watkins, Neil Shearer, Karl Costigan, Kate S. Baker, Nicholas A. Feasey, Jay C. D. Hinton, Neil Hall, The 10KSG consortium

Research output: Contribution to journalArticlepeer-review

Abstract

We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. Following the optimization of a logistics pipeline that involved shipping isolates as thermolysates in ambient conditions, the project assembled a diverse collection of 10,419 isolates from low- and middle-income countries. The genomes were sequenced using the LITE pipeline for library construction, with a total reagent cost of less than USD$10 per genome. Our method can be applied to other large bacterial collections to underpin global collaborations.

Original languageEnglish
Article number349
JournalGenome Biology
Volume22
Issue number1
DOIs
Publication statusPublished - 21 Dec 2021

Keywords

  • Salmonella
  • Thermolysates
  • Whole-genome sequencing
  • iNTS

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