An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.
Salmonella
Thermolysates
Whole-genome sequencing
iNTS
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
21 12 2021
21 12 2021
Historique:
received:
10
08
2020
accepted:
21
10
2021
entrez:
21
12
2021
pubmed:
22
12
2021
medline:
15
3
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34930397
doi: 10.1186/s13059-021-02536-3
pii: 10.1186/s13059-021-02536-3
pmc: PMC8690886
doi:
Substances chimiques
DNA, Bacterial
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
349Subventions
Organisme : Wellcome Trust
ID : 106914/Z/15/Z
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/T/000PR9817
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/CCG1720/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/OS/GC/000009D
Pays : United Kingdom
Investigateurs
Blanca M Perez-Sepulveda
(BM)
Darren Heavens
(D)
Caisey V Pulford
(CV)
María Teresa Acuña
(MT)
Dragan Antic
(D)
Martin Antonio
(M)
Kate S Baker
(KS)
Johan Bernal
(J)
Hilda Bolaños
(H)
Marie Chattaway
(M)
John Cheesbrough
(J)
Angeziwa Chirambo
(A)
Karl Costigan
(K)
Saffiatou Darboe
(S)
Paula Díaz
(P)
Pilar Donado
(P)
Carolina Duarte
(C)
Francisco Duarte
(F)
Dean Everett
(D)
Séamus Fanning
(S)
Nicholas A Feasey
(NA)
Patrick Feglo
(P)
Adriano M Ferreira
(AM)
Rachel Floyd
(R)
Ronnie G Gavilán
(RG)
Melita A Gordon
(MA)
Neil Hall
(N)
Rodrigo T Hernandes
(RT)
Gabriela Hernández-Mora
(G)
Jay C D Hinton
(JCD)
Daniel Hurley
(D)
Irene N Kasumba
(IN)
Benjamin Kumwenda
(B)
Brenda Kwambana-Adams
(B)
James Lipscombe
(J)
Ross Low
(R)
Salim Mattar
(S)
Lucy Angeline Montaño
(LA)
Cristiano Gallina Moreira
(CG)
Jaime Moreno
(J)
Dechamma Mundanda Muthappa
(DM)
Satheesh Nair
(S)
Chris M Parry
(CM)
Chikondi Peno
(C)
Jasnehta Permala-Booth
(J)
Jelena Petrović
(J)
Alexander V Predeus
(AV)
José Luis Puente
(JL)
Getenet Rebrie
(G)
Martha Redway
(M)
Will Rowe
(W)
Terue Sadatsune
(T)
Christian Schudoma
(C)
Neil Shearer
(N)
Claudia Silva
(C)
Anthony M Smith
(AM)
Sharon Tennant
(S)
Alicia Tran-Dien
(A)
Chris Watkins
(C)
Hermione Webster
(H)
François-Xavier Weill
(FX)
Magdalena Wiesner
(M)
Catherine Wilson
(C)
Informations de copyright
© 2021. The Author(s).
Références
Curr Opin Microbiol. 2020 Feb;53:61-70
pubmed: 32248056
BMC Bioinformatics. 2010 Dec 10;11:595
pubmed: 21143983
Vaccine. 2015 Jun 19;33 Suppl 3:C8-15
pubmed: 25937611
J Clin Microbiol. 2020 Mar 25;58(4):
pubmed: 31969425
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Science. 2017 Nov 10;358(6364):785-789
pubmed: 29123067
J Clin Microbiol. 2010 Sep;48(9):3403-6
pubmed: 20592143
Nat Rev Genet. 2016 May 17;17(6):333-51
pubmed: 27184599
Wellcome Open Res. 2020 Sep 24;5:223
pubmed: 33614977
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595
pubmed: 28594827
Nat Microbiol. 2021 Mar;6(3):327-338
pubmed: 33349664
Proc Biol Sci. 2015 Dec 22;282(1821):20150488
pubmed: 26702036
Funct Integr Genomics. 2015 Mar;15(2):141-61
pubmed: 25722247
Clin Infect Dis. 2012 Apr;54(7):955-63
pubmed: 22318974
Lancet Infect Dis. 2015 Oct;15(10):1193-1202
pubmed: 26116186
Nat Genet. 2016 Oct;48(10):1211-1217
pubmed: 27548315
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nat Biotechnol. 2012 May;30(5):434-9
pubmed: 22522955
PLoS One. 2016 Jan 22;11(1):e0147101
pubmed: 26800248
Clin Infect Dis. 2021 Aug 16;73(4):631-641
pubmed: 33493332
EBioMedicine. 2019 May;43:338-346
pubmed: 31003929
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
N Engl J Med. 2018 Oct 11;379(15):1403-1415
pubmed: 30280646
Lancet Infect Dis. 2019 Apr;19(4):369-381
pubmed: 30792131
Clin Microbiol Rev. 2017 Oct;30(4):1015-1063
pubmed: 28855266
PLoS Genet. 2018 Apr 5;14(4):e1007261
pubmed: 29621240
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Nat Rev Microbiol. 2012 Sep;10(9):599-606
pubmed: 22864262
PLoS Negl Trop Dis. 2020 Nov 24;14(11):e0008796
pubmed: 33232324
Nat Rev Genet. 2017 Jan;18(1):41-50
pubmed: 27840430
Pathology. 2015 Apr;47(3):199-210
pubmed: 25730631
Nat Med. 2020 Jun;26(6):832-841
pubmed: 32528156
Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15442-7
pubmed: 19720995
Lancet Infect Dis. 2019 Dec;19(12):1312-1324
pubmed: 31562022
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Microb Genom. 2022 Mar;8(3):
pubmed: 35302932
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
PLoS Med. 2015 Dec 03;12(12):e1001921
pubmed: 26633831