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

The 10KSG consortium

doi:10.1186/s13059-021-02536-3

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

The 10KSG consortium

Gastrointestinal Bacteria WGS

Research output: Contribution to journal › Article › peer-review

19 Citations (Scopus)

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 language	English
Article number	349
Journal	Genome Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02536-3
Publication status	Published - Dec 2021

Bibliographical 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, María Teresa Acuña, Dragan Antic, Martin Antonio, Kate S. Baker, Johan Bernal, Hilda Bolaños, Marie Chattaway, John Cheesbrough, Angeziwa Chirambo, Karl Costigan, Saffiatou Darboe, Paula Díaz, 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 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:
© 2021, The Author(s).

Keywords

Salmonella
Thermolysates
Whole-genome sequencing
iNTS

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10.1186/s13059-021-02536-3

Cite this

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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 = "Salmonella, Thermolysates, Whole-genome sequencing, iNTS",

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 Satheesh Nair",

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 = "English",

volume = "22",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "1",

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TY - JOUR

T1 - An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

AU - The 10KSG consortium

AU - Perez-Sepulveda, Blanca M.

AU - Heavens, Darren

AU - Pulford, Caisey V.

AU - Predeus, Alexander V.

AU - Low, Ross

AU - Webster, Hermione

AU - Dykes, Gregory F.

AU - Schudoma, Christian

AU - Rowe, Will

AU - Lipscombe, James

AU - Watkins, Chris

AU - Kumwenda, Benjamin

AU - Shearer, Neil

AU - Costigan, Karl

AU - Baker, Kate S.

AU - Feasey, Nicholas A.

AU - Hinton, Jay C.D.

AU - Hall, Neil

AU - Perez-Sepulveda, Blanca M.

AU - Heavens, Darren

AU - Pulford, Caisey V.

AU - Acuña, María Teresa

AU - Antic, Dragan

AU - Antonio, Martin

AU - Baker, Kate S.

AU - Bernal, Johan

AU - Bolaños, Hilda

AU - Chattaway, Marie

AU - Cheesbrough, John

AU - Chirambo, Angeziwa

AU - Costigan, Karl

AU - Darboe, Saffiatou

AU - Díaz, Paula

AU - Donado, Pilar

AU - Duarte, Carolina

AU - Duarte, Francisco

AU - Everett, Dean

AU - Fanning, Séamus

AU - Feasey, Nicholas A.

AU - Feglo, Patrick

AU - Ferreira, Adriano M.

AU - Floyd, Rachel

AU - Gavilán, Ronnie G.

AU - Gordon, Melita A.

AU - Hall, Neil

AU - Hernandes, Rodrigo T.

AU - Hernández-Mora, Gabriela

AU - Hinton, Jay C.D.

AU - Hurley, Daniel

AU - Nair, Satheesh

N1 - 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, María Teresa Acuña, Dragan Antic, Martin Antonio, Kate S. Baker, Johan Bernal, Hilda Bolaños, Marie Chattaway, John Cheesbrough, Angeziwa Chirambo, Karl Costigan, Saffiatou Darboe, Paula Díaz, 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 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: © 2021, The Author(s).

PY - 2021/12

Y1 - 2021/12

N2 - 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.

AB - 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.

KW - Salmonella

KW - Thermolysates

KW - Whole-genome sequencing

KW - iNTS

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DO - 10.1186/s13059-021-02536-3

M3 - Article

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AN - SCOPUS:85121643916

SN - 1474-7596

VL - 22

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 349

ER -

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

Abstract

Bibliographical note

Keywords

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