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

Perez-Sepulveda, Blanca M; Heavens, Darren; Pulford, Caisey V; Predeus, Alexander V; Low, Ross; Webster, Hermione; Dykes, Gregory F; Schudoma, Christian; Rowe, Will; Lipscombe, James; +9 more... Watkins, Chris; Kumwenda, Benjamin; Shearer, Neil; Costigan, Karl; Baker, Kate S; Feasey, Nicholas A; Hinton, Jay CD; Hall, Neil; 10KSG consortium; 10KSG consortium; (2021) An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. Genome biology, 22 (1). 349-. ISSN 1474-7596 DOI: https://doi.org/10.1186/s13059-021-02536-3

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.