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

Blanca M. Perez-Sepulveda; Darren Heavens; Caisey V. Pulford; Alexander V. Predeus; Ross Low; Hermione Webster; Gregory F. Dykes; Christian Schudoma; Will Rowe; James Lipscombe; Chris Watkins; Benjamin Kumwenda; Neil Shearer; Karl Costigan; Kate S. Baker; Nick Feasey; Jay C.D. Hinton; Neil Hall; 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; Nick 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; Brenda Kwambana; Christopher Parry

doi:10.1186/s13059-021-02536-3

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

Blanca M. Perez-Sepulveda, Darren Heavens, Caisey V. Pulford, Alexander V. Predeus, Ross Low, Hermione Webster, Gregory F. Dykes, Christian Schudoma, Will Rowe, James Lipscombe, Chris Watkins, Benjamin Kumwenda, Neil Shearer, Karl Costigan, Kate S. Baker, Nick Feasey, Jay C.D. Hinton, Neil Hall, Blanca M. Perez-Sepulveda, Darren HeavensCaisey 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, Nick 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, Brenda Kwambana, Christopher Parry

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

32 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
Pages (from-to)	e349
Journal	Genome Biology
Volume	22
Issue number	1
Early online date	21 Dec 2021
DOIs	https://doi.org/10.1186/s13059-021-02536-3
Publication status	E-pub ahead of print - 21 Dec 2021

Keywords

iNTS
Salmonella
Thermolysates
Whole-genome sequencing

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10.1186/s13059-021-02536-3Licence: CC BY

PMC8690886Final published version, 1.06 MBLicence: CC BY

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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., Hinton, J. C. D., Hall, N., Perez-Sepulveda, B. M., ... Parry, C. (2021). An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. Genome Biology, 22(1), e349. Article 349. Advance online publication. https://doi.org/10.1186/s13059-021-02536-3

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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.",

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

author = "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 Nick Feasey 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 Nick Feasey 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 Brenda Kwambana and Christopher Parry",

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doi = "10.1186/s13059-021-02536-3",

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Perez-Sepulveda, BM, Heavens, D, Pulford, CV, Predeus, AV, Low, R, Webster, H, Dykes, GF, Schudoma, C, Rowe, W, Lipscombe, J, Watkins, C, Kumwenda, B, Shearer, N, Costigan, K, Baker, KS, Feasey, N, Hinton, JCD, Hall, N, Perez-Sepulveda, BM, Heavens, D, Pulford, CV, Acuña, MT, Antic, D, Antonio, M, Baker, KS, Bernal, J, Bolaños, H, Chattaway, M, Cheesbrough, J, Chirambo, A, Costigan, K, Darboe, S, Díaz, P, Donado, P, Duarte, C, Duarte, F, Everett, D, Fanning, S, Feasey, N, Feglo, P, Ferreira, AM, Floyd, R, Gavilán, RG, Gordon, MA, Hall, N, Hernandes, RT, Hernández-Mora, G, Hinton, JCD, Kwambana, B & Parry, C 2021, 'An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.', Genome Biology, vol. 22, no. 1, 349, pp. e349. https://doi.org/10.1186/s13059-021-02536-3

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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, Nick

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, Nick

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 - Kwambana, Brenda

AU - Parry, Christopher

PY - 2021/12/21

Y1 - 2021/12/21

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 - iNTS

KW - Salmonella

KW - Thermolysates

KW - Whole-genome sequencing

U2 - 10.1186/s13059-021-02536-3

DO - 10.1186/s13059-021-02536-3

M3 - Article

SN - 1474-7596

VL - 22

SP - e349

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

Keywords

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