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Genome Sequencing and Interrogation of Genome Databases: A Guide to Neisseria meningitidis Genomics

  • Holly B. Bratcher
  • Odile B. HarrisonEmail author
  • Martin C. J. Maiden
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1969)

Abstract

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.

Key words

DNA extraction Next-generation sequencing De novo assembly PubMLST Strain designation GenomeComparator GrapeTree ClonalFrameML Artemis 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Holly B. Bratcher
    • 1
  • Odile B. Harrison
    • 1
    Email author
  • Martin C. J. Maiden
    • 1
  1. 1.Department of ZoologyUniversity of OxfordOxfordUK

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