A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens

Gautam, Sanjay S. and KC, Rajendra and Leong, Kelvin WC and Mac Aogáin, Micheál and O’Toole, Ronan F. (2019) A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens. Journal of Biological Methods, 6 (1). p. 110. ISSN 2326-9901

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Official URL: http://dx.doi.org/10.14440/jbm.2019.276

Abstract or 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.

Item Type:Journal article
Keywords that describe the item:genome sequencing, human bacterial pathogens
Subjects:Q Science > QR Microbiology
R Medicine > RA Public aspects of medicine
Divisions:Schools > Centre for Health & Social Practice
ID Code:7188
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Deposited On:11 Feb 2020 01:28
Last Modified:06 May 2020 21:11

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