High-throughput sequencing for the study of bacterial pathogen biology

Graphical abstract

Highlights

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  High throughput sequencing (HTS) is revolutionizing research into bacterial pathogens.

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  HTS reveals that bacterial pathogens may undergo considerable diversification during infection.

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  HTS can allow tracing of outbreak origin and transmission.

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  HTS offers advantages over existing transcriptomic technologies for understanding global gene expression in bacteria.

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  Transposon mutagenesis and HTS is a powerful combination for identifying bacterial determinants required for in vivo survival.

Abstract

A revolution in sequencing technologies in recent years has led to dramatically increased throughput and reduced cost of bacterial genome sequencing. An increasing number of applications of the new technologies are providing broad insights into bacterial evolution, epidemiology, and pathogenesis. For example, the capacity to sequence large numbers of bacterial isolates is enabling high resolution phylogenetic analyses of bacterial populations leading to greatly enhanced understanding of the emergence, adaptation, and transmission of pathogenic clones. In addition, RNA-seq offers improved quantification and resolution for transcriptomic analysis, and the combination of high-throughput sequencing with transposon mutagenesis is a powerful approach for the identification of bacterial determinants required for survival in vivo. In this concise review we provide selected examples of how high throughput sequencing is being applied to understand the biology of bacterial pathogens, and discuss future technological advances likely to have a profound impact on the field.