e-Article
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
Document Type
Academic Journal
Author
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; Watkins, Chris; Kumwenda, Benjamin; Shearer, Neil; Costigan, Karl; Baker, Kate S.; Feasey, Nicholas A.; Hinton, Jay C. D.; Hall, Neil; Acuéa, María Teresa; Antic, Dragan; Antonio, Martin; Bernal, Johan; Bolaéos, Hilda; Chattaway, Marie; Cheesbrough, John; Chirambo, Angeziwa; Darboe, Saffiatou; Díaz, Paula; Donado, Pilar; Duarte, Carolina; Duarte, Francisco; Everett, Dean; Fanning, Séamus; Feglo, Patrick; Ferreira, Adriano M.; Floyd, Rachel; Gavilán, Ronnie G.; Gordon, Melita A.; Hernandes, Rodrigo T.; Hernández-Mora, Gabriela; Hurley, Daniel; Kasumba, Irene N.; Kwambana-Adams, Brenda; Mattar, Salim; Montaéo, Lucy Angeline; Moreira, Cristiano Gallina; Moreno, Jaime; Muthappa, Dechamma Mundanda; Nair, Satheesh; Parry, Chris M.; Peno, Chikondi; Permala-Booth, Jasnehta; PetroviÄ, Jelena; Puente, José Luis; Rebrie, Getenet; Redway, Martha; Sadatsune, Terue; Silva, Claudia; Smith, Anthony M.; Tennant, Sharon; Tran-Dien, Alicia; Weill, François-Xavier; Wiesner, Magdalena; Wilson, Catherine
Source
Genome Biology (Online Edition). December 21, 2021, Vol. 22 Issue 1
Subject
Language
English
Abstract
Author(s): Blanca M. Perez-Sepulveda[sup.1], Darren Heavens[sup.2], Caisey V. Pulford[sup.1], Alexander V. Predeus[sup.1], Ross Low[sup.2], Hermione Webster[sup.1], Gregory F. Dykes[sup.1], Christian Schudoma[sup.2], Will Rowe[sup.1,3], James Lipscombe[sup.2], Chris Watkins[sup.2], Benjamin Kumwenda[sup.4], Neil [...]
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. Keywords: Thermolysates, Salmonella, Whole-genome sequencing, iNTS
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. Keywords: Thermolysates, Salmonella, Whole-genome sequencing, iNTS