Title
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
Date Issued
01 December 2021
Access level
open access
Resource Type
journal article
Author(s)
Perez-Sepulveda B.M.
Heavens D.
Pulford C.V.
Predeus A.V.
Low R.
Webster H.
Dykes G.F.
Schudoma C.
Rowe W.
Lipscombe J.
Watkins C.
Kumwenda B.
Shearer N.
Costigan K.
Baker K.S.
Feasey N.A.
Hinton J.C.D.
Hall N.
Perez-Sepulveda B.M.
Heavens D.
Pulford C.V.
Acuña M.T.
Antic D.
Antonio M.
Baker K.S.
Bernal J.
Bolaños H.
Chattaway M.
Cheesbrough J.
Chirambo A.
Costigan K.
Darboe S.
DÃaz P.
Donado P.
Duarte C.
Duarte F.
Everett D.
Fanning S.
Feasey N.A.
Feglo P.
Ferreira A.M.
Floyd R.
Gordon M.A.
Hall N.
Hernandes R.T.
Hernández-Mora G.
Hinton J.C.D.
Hurley D.
Kasumba I.N.
Kumwenda B.
Kwambana-Adams B.
Lipscombe J.
Low R.
Mattar S.
Montaño L.A.
Moreira C.G.
Moreno J.
Muthappa D.M.
Nair S.
Parry C.M.
Peno C.
Permala-Booth J.
Petrović J.
Predeus A.V.
Puente J.L.
Rebrie G.
Redway M.
Rowe W.
Sadatsune T.
Schudoma C.
Shearer N.
Silva C.
Smith A.M.
Tennant S.
Tran-Dien A.
Watkins C.
Webster H.
Weill F.X.
Wiesner M.
Wilson C.
Publisher(s)
BioMed Central Ltd
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.
Volume
22
Issue
1
Language
English
OCDE Knowledge area
BiologÃa celular, MicrobiologÃa
Genética, Herencia
Subjects
Scopus EID
2-s2.0-85121643916
PubMed ID
Source
Genome Biology
ISSN of the container
14747596
Sponsor(s)
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, MarÃa Teresa Acuña, Dragan Antic, Martin Antonio, Kate S. Baker, Johan Bernal, Hilda Bolaños, Marie Chattaway, John Cheesbrough, Angeziwa Chirambo, Karl Costigan, Saffiatou Darboe, Paula DÃaz, Pilar Donado, Carolina Duarte, Francisco Duarte, Dean Everett, Séamus Fanning, Nicholas A. Feasey, Patrick Feglo, Adriano M. 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 Mattar, Lucy Angeline Montaño, Cristiano Gallina Moreira, Jaime Moreno, Dechamma Mundanda Muthappa, Satheesh Nair, Chris M. Parry, Chikondi Peno, Jasnehta Permala-Booth, Jelena Petrović, Alexander V. Predeus, José 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, François-Xavier Weill, Magdalena Wiesner and Catherine Wilson.
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.
Sources of information:
Directorio de Producción CientÃfica
Scopus