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



Perez-Sepulveda, Blanca ORCID: 0000-0002-2891-4010, Heavens, Darren, Pulford, Caisey ORCID: 0000-0003-2500-9119, Predeus, Alexander ORCID: 0000-0002-2750-1599, Low, Ross ORCID: 0000-0002-0956-2822, Webster, Hermione, Schudoma, Christian, Rowe, Will ORCID: 0000-0003-0384-4463, Lipscombe, James, Watkins, Chris
et al (show 8 more authors) (2020) An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.

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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. By optimising a logistics pipeline that collected isolates as thermolysates, permitting shipment in ambient conditions, the project assembled a diverse collection of 10,419 clinical and environmental isolates from low- and middle-income countries in less than one year. The bacteria were obtained from 51 countries/territories dating from 1949 to 2017, with a focus on Africa and Latin-America. All isolates were collected in barcoded tubes and genome sequenced using an optimised DNA extraction method and the LITE pipeline for library construction. After Illumina sequencing, the total reagent cost was less than USD$10 per genome. Our method can be applied to genome-sequence other large bacterial collections at a relatively low cost, within a limited timeframe, to support global collaborations.

Item Type: Article
Uncontrolled Keywords: The 10KSG consortium
Depositing User: Symplectic Admin
Date Deposited: 29 Jul 2020 13:28
Last Modified: 05 Oct 2022 22:03
DOI: 10.1101/2020.07.22.200840
Open Access URL: https://www.biorxiv.org/content/10.1101/2020.07.22...
URI: https://livrepository.liverpool.ac.uk/id/eprint/3095442