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Whole genome sequencing (WGS) has revolutionized molecular microbiology, allowing the population biology of bacterial pathogens to be examined with greater accuracy and detail. The study of Neisseria meningitidis isolates, in particular, has benefitted from the availability of WGS data allowing outbreak cases, hyper-invasive lineages, molecular epidemiology, and vaccine coverage to be determined. Here, we describe a suite of protocols for the optimum recovery and analysis of WGS data, including a brief overview of methods for N. meningitidis DNA extraction, sequencing, and analysis. Downstream analysis tools are described including a step-by-step guide to the use of PubMLST.org/neisseria . This freely accessible website provides a resource for the Neisseria community allowing the diversity of the meningococcal population to be extracted and exploited.

Original publication

DOI

10.1007/978-1-4939-9202-7_4

Type

Journal article

Journal

Methods Mol Biol

Publication Date

2019

Volume

1969

Pages

51 - 82

Keywords

Artemis, ClonalFrameML, DNA extraction, De novo assembly, GenomeComparator, GrapeTree, Next-generation sequencing, PubMLST, Strain designation, DNA, Bacterial, Databases, Genetic, Genome, Bacterial, Genomics, Humans, Neisseria meningitidis, Whole Genome Sequencing