An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
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 NA., 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 NA., Feglo P., Ferreira AM., Floyd R., Gavilán RG., Gordon MA., Hall N., Hernandes RT., Hernández-Mora G., Hinton JCD., Hurley D., Kasumba IN., Kumwenda B., Kwambana-Adams B., Lipscombe J., Low R., Mattar S., Montaño LA., Moreira CG., Moreno J., Muthappa DM., Nair S., Parry CM., Peno C., Permala-Booth J., Petrović J., Predeus AV., Puente JL., Rebrie G., Redway M., Rowe W., Sadatsune T., Schudoma C., Shearer N., Silva C., Smith AM., Tennant S., Tran-Dien A., Watkins C., Webster H., Weill F-X., Wiesner M., Wilson C.
AbstractWe 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.