Antibiotics pp 331-356 | Cite as

Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing

  • Miguel Paulo Machado
  • Bruno Ribeiro-Gonçalves
  • Mickael Silva
  • Mário Ramirez
  • João André Carriço
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1520)

Abstract

High-Throughput Sequencing (HTS) technologies transformed the microbial typing and molecular epidemiology field by providing the cost-effective ability for researchers to probe draft genomes, not only for epidemiological markers but also for antibiotic resistance and virulence determinants. In this chapter, we provide protocols for the analysis of HTS data for the determination of multilocus sequence typing (MLST) information and for determining presence or absence of antibiotic resistance genes.

Key words

High-throughput sequencing Microbial typing Gene finding Online databases Antibiotic resistance 

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Miguel Paulo Machado
    • 1
  • Bruno Ribeiro-Gonçalves
    • 1
  • Mickael Silva
    • 1
  • Mário Ramirez
    • 1
  • João André Carriço
    • 1
  1. 1.Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa, Alameda Da UniversidadeLisbonPortugal

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