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.
Highlights
Whole-genome sequencing (WGS) is an important tool that has revolutionized our understanding of bacterial disease over the past decade [1,2,3,4]
We optimized the logistics of specimen collection and the transport of materials to the sequencing center in the University of Warwick (UK)
To facilitate large-scale low-cost whole-genome sequencing, we developed the LITE (Low Input, Transposase Enabled; Fig. 2) pipeline, a low-cost high-throughput library construction protocol based on the Nextera kits (Illumina)
Summary
Whole-genome sequencing (WGS) is an important tool that has revolutionized our understanding of bacterial disease over the past decade [1,2,3,4]. Recognizing the immense advantages that WGS data provides for surveillance, functional genomics, and population dynamics, both public health and research communities have adopted genomebased approaches. Large-scale bacterial genome projects could only be performed in a handful of sequencing centers around the world. The high demand for sequencing human genomes has driven down the costs of sequencing reagents to below USD$1000 per sample [5,6,7]. The genome sequencing of thousands of microorganisms has remained expensive, largely due to costs associated with sample transportation and library construction
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