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

2021; BioMed Central; Volume: 22; Issue: 1 Linguagem: Inglês

10.1186/s13059-021-02536-3

1474-760X

Blanca M. Perez-Sepulveda, Darren Heavens, Caisey V. Pulford, Alexander V. Predeus, Ross Low, Hermione J. Webster, Gregory F. Dykes, Christian Schudoma, Will Rowe, James Lipscombe, Christopher B. Watkins, Benjamin Kumwenda, Neil Shearer, Karl Costigan, Kate S. Baker, Nicholas Feasey, Jay C. D. Hinton, Neil Hall, Blanca M. Perez-Sepulveda, Darren Heavens, Caisey V. Pulford, María Teresa Acuña, Dragan Antić, Martín Antonio, Kate S. Baker, Johan Fabian Bernal, Hilda Bolaños, Marie Anne Chattaway, J. Cheesbrough, Angeziwa Chunga Chirambo, Karl Costigan, Saffiatou Darboe, Paula Díaz, Pilar Donado, Carolina Duarte, Francisco Duarte-Martínez, Dean Everett, Séamus Fanning, Nicholas Feasey, Patrick Kwame Feglo, Adriano Mota Ferreira, Rachel Floyd, Ronnie G. Gavilán, Melita A. Gordon, Neil Hall, Rodrigo T. Hernandes, Gabriela Hernández-Mora, Jay C. D. Hinton, Daniel Hurley, Irene N Kasumba, Benjamin Kumwenda, Brenda Kwambana-Adams, James Lipscombe, Ross Low, Salim Máttar, Lucy Angeline Montaño, Cristiano G. Moreira, Jaime Moreno, Dechamma Mundanda Muthappa, Satheesh Nair, Chris M. Parry, Chikondi Peno, Jasnehta Permala-Booth, Jelena Petrović, Alexander V. Predeus, José L. Puente, Getenet Rebrie, Martha Redway, Will Rowe, Teruê Sadatsune, Christian Schudoma, Neil Shearer, Claudia Silva, Anthony M. Smith, Sharon M. Tennant, Alicia Tran-Dien, Christopher B. Watkins, Hermione J. Webster, François‐Xavier Weill, Magdalena Wiesner, Catherine N. Wilson,

Probiotics and Fermented Foods

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.