Rxivist logo

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. ### Competing Interest Statement The authors have declared no competing interest.

Download data

  • Downloaded 637 times
  • Download rankings, all-time:
    • Site-wide: 49,947
    • In microbiology: 3,062
  • Year to date:
    • Site-wide: 25,146
  • Since beginning of last month:
    • Site-wide: 28,498

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide