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URL: https://dx.doi.org/10.17504/protocols.io.4xxgxpn

Authors: Sanjay Gautam, Rajendra KC, Kelvin WC Leong, Micheál Mac Aogáin, Ronan F. O’Toole

Summary: Bacterial whole genome sequencing (WGS) is becoming a widely-used technique in research, clinical diagnostic, and public health laboratories. It enables high resolution characterization of bacterial pathogens in terms of properties that include antibiotic resistance, molecular epidemiology, and virulence. The introduction of next-generation sequencing instrumentation has made WGS attainable in terms of costs. However, the lack of a beginner’s protocol for WGS still represents a barrier to its adoption in some settings. Here, we present detailed step-by-step methods for obtaining WGS data from a range of different bacteria (Gram-positive, Gram-negative, and acid-fast) using the Illumina platform. Modifications have been performed with respect to DNA extraction and library normalization to maximize the output from the laboratory consumables invested. The protocol represents a simplified and reproducible method for producing high quality sequencing data. The key advantages of this protocol include simplicity of the protocol for users with no prior genome sequencing experience and reproducibility of the protocol across a wide range of bacteria.

Affiliations: School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Australia, School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Australia, School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Australia, Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, Ireland, School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Australia

External URL: http://www.jbmethods.org/jbm/article/view/276/247

Version: 1

Publication Date: 2019

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