Abstract
Recent advances in DNA sequencing technologies have the potential to transform the field of clinical and public health microbiology, and in the last few years numerous case studies have demonstrated successful applications in this context. Among other considerations, a lack of user-friendly data analysis and interpretation tools has been frequently cited as a major barrier to routine use of these techniques. Here we consider the requirements of microbiology laboratories for the analysis, clinical interpretation and management of bacterial whole-genome sequence (WGS) data. Then we discuss relevant, existing WGS analysis tools. We highlight many essential and useful features that are represented among existing tools, but find that no single tool fulfils all of the necessary requirements. We conclude that to fully realise the potential of WGS analyses for clinical and public health microbiology laboratories of all scales, we will need to develop tools specifically with the needs of these laboratories in mind.
Highlights
The recent advent of NGS (Next-Generation (DNA) Sequencing) technologies has revolutionised the field of bacterial genomics
To appreciate the relevant features of whole-genome sequence (WGS) analysis tools we must understand the specific types of analyses that are required for clinical/public health microbiology investigations
Fricke and Rasko described the bioinformatic challenges associated with the application of bacterial WGS data in clinical settings, highlighting the need for standardisation, appropriate management of computing resources, data integration and storage [20]
Summary
The recent advent of NGS (Next-Generation (DNA) Sequencing) technologies has revolutionised the field of bacterial genomics. Traditional bacterial characterisation comprises multiple species-specific phenotypic and molecular tests, requiring several days or even weeks for completion [8,12] Such characterisation can be achieved through the analysis of WGS data. Microbiology laboratories must characterise isolates of a large number of different species, each of which may require a different set of tests This review follows those describing the potential uses of, challenges and impact of WGS technologies for clinical/public health microbiology laboratories [7,8,11,20]. We present an overview of these requirements followed by a discussion of the relevant features, benefits and constraints of a number of existing WGS analysis execution tools Most of these tools were not designed for use in clinical/public health laboratory settings, rather to provide flexible solutions for research purposes. We hope this discussion will inform and inspire clinical/public health microbiologists, bioinformaticians and computer scientists alike, such that we can work together to develop the tools that will make routine WGS use a reality
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