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

The 10KSG consortium

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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
Number of pages18
JournalGenome Biology
Volume22
Issue number1
DOIs
Publication statusPublished - Dec 2021

Bibliographical note

Funding Information:
The project was supported by both a Global Challenges Research Fund (GCRF) data & resources grant BBS/OS/GC/000009D and the BBSRC Core Capability Grant to the Earlham Institute BB/CCG1720/1 and Core Strategic Programme Grant BBS/E/T/000PR9817. This project was partly supported by the Wellcome Trust Senior Investigator Award (106914/Z/15/Z) to Jay C. D. Hinton.

Funding Information:
Next-generation sequencing and library construction were delivered via the BBSRC National Capability in Genomics and Single Cell (BB/CCG1720/1) at Earlham Institute, by members of the Genomics Pipelines Group. Each of the following Earlham Institute staff and alumni made an enormous contribution to the project: Dr Helen Chapman, Mr. Jake Collins, and Miss Sophie Stephenson. We are grateful to the Centre for Genomic Research, University of Liverpool (UK) for computing support. The 10KSG consortium: Blanca M. Perez-Sepulveda, Darren Heavens, Caisey V. Pulford, Mar?a Teresa Acu?a, Dragan Antic, Martin Antonio, Kate S. Baker, Johan Bernal, Hilda Bola?os, Marie Chattaway, John Cheesbrough, Angeziwa Chirambo, Karl Costigan, Saffiatou Darboe, Paula D?az, Pilar Donado, Carolina Duarte, Francisco Duarte, Dean Everett, S?amus Fanning, Nicholas A. Feasey, Patrick Feglo, Adriano M. Ferreira, Rachel Floyd, Ronnie G. Gavil?n, Melita A. Gordon, Neil Hall, Rodrigo T. Hernandes, Gabriela Hern?ndez-Mora, Jay C. D. Hinton, Daniel Hurley, Irene N. Kasumba, Benjamin Kumwenda, Brenda Kwambana-Adams, James Lipscombe, Ross Low, Salim Mattar, Lucy Angeline Monta?o, Cristiano Gallina Moreira, Jaime Moreno, Dechamma Mundanda Muthappa, Satheesh Nair, Chris M. Parry, Chikondi Peno, Jasnehta Permala-Booth, Jelena Petrovi?, Alexander V. Predeus, Jos? Luis Puente, Getenet Rebrie, Martha Redway, Will Rowe, Terue Sadatsune, Christian Schudoma, Neil Shearer, Claudia Silva, Anthony M. Smith, Sharon Tennant, Alicia Tran-Dien, Chris Watkins, Hermione Webster, Fran?ois-Xavier Weill, Magdalena Wiesner and Catherine Wilson. The review history is available as Additional file 3. Kevin Pang was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher Copyright:
© 2021, The Author(s).

Keywords

  • iNTS
  • Salmonella
  • Thermolysates
  • Whole-genome sequencing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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