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

Methods Mol Biol. 2017;1520:331-356. doi: 10.1007/978-1-4939-6634-9_20.


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.

Keywords: Antibiotic resistance; Gene finding; High-throughput sequencing; Microbial typing; Online databases.

MeSH terms

  • Bacteria / genetics*
  • Drug Resistance, Microbial / genetics*
  • Epidemiological Monitoring*
  • Genes, Bacterial
  • High-Throughput Nucleotide Sequencing / methods*
  • Multilocus Sequence Typing / methods*
  • Software