@article{f2f081043dbe4b00b560a0d499130375,
title = "An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes",
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.",
keywords = "iNTS, Salmonella, Thermolysates, Whole-genome sequencing",
author = "{The 10KSG consortium} and Perez-Sepulveda, {Blanca M.} and Darren Heavens and Pulford, {Caisey V.} and Predeus, {Alexander V.} and Ross Low and Hermione Webster and Dykes, {Gregory F.} and Christian Schudoma and Will Rowe and James Lipscombe and Chris Watkins and Benjamin Kumwenda and Neil Shearer and Karl Costigan and Baker, {Kate S.} and Feasey, {Nicholas A.} and Hinton, {Jay C.D.} and Neil Hall and Perez-Sepulveda, {Blanca M.} and Darren Heavens and Pulford, {Caisey V.} and Acu{\~n}a, {Mar{\'i}a Teresa} and Dragan Antic and Martin Antonio and Baker, {Kate S.} and Johan Bernal and Hilda Bola{\~n}os and Marie Chattaway and John Cheesbrough and Angeziwa Chirambo and Karl Costigan and Saffiatou Darboe and Paula D{\'i}az and Pilar Donado and Carolina Duarte and Francisco Duarte and Dean Everett and S{\'e}amus Fanning and Feasey, {Nicholas A.} and Patrick Feglo and Ferreira, {Adriano M.} and Rachel Floyd and Gavil{\'a}n, {Ronnie G.} and Gordon, {Melita A.} and Neil Hall and Hernandes, {Rodrigo T.} and Gabriela Hern{\'a}ndez-Mora and Hinton, {Jay C.D.} and Daniel Hurley and Kasumba, {Irene N.}",
note = "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{\'i}a Teresa Acu{\~n}a, Dragan Antic, Martin Antonio, Kate S. Baker, Johan Bernal, Hilda Bola{\~n}os, Marie Chattaway, John Cheesbrough, Angeziwa Chirambo, Karl Costigan, Saffiatou Darboe, Paula D{\'i}az, Pilar Donado, Carolina Duarte, Francisco Duarte, Dean Everett, S{\'e}amus Fanning, Nicholas A. Feasey, Patrick Feglo, Adriano M. Ferreira, Rachel Floyd, Ronnie G. Gavil{\'a}n, Melita A. Gordon, Neil Hall, Rodrigo T. Hernandes, Gabriela Hern{\'a}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{\~n}o, Cristiano Gallina Moreira, Jaime Moreno, Dechamma Mundanda Muthappa, Satheesh Nair, Chris M. Parry, Chikondi Peno, Jasnehta Permala-Booth, Jelena Petrovi{\'c}, Alexander V. Predeus, Jos{\'e} 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{\c c}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. 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. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = dec,
doi = "10.1186/s13059-021-02536-3",
language = "British English",
volume = "22",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central Ltd.",
number = "1",
}