title: Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing.
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.
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Alameda Da Universidade, Lisbon, 1649-004, Portugal.
authors.forename: Miguel Paulo
authors.initials: MP
authors.lastname: Machado
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Alameda Da Universidade, Lisbon, 1649-004, Portugal.
authors.forename: Bruno
authors.initials: B
authors.lastname: Ribeiro-Gonçalves
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Alameda Da Universidade, Lisbon, 1649-004, Portugal.
authors.forename: Mickael
authors.initials: M
authors.lastname: Silva
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Alameda Da Universidade, Lisbon, 1649-004, Portugal.
authors.forename: Mário
authors.initials: M
authors.lastname: Ramirez
authors.affiliation: Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Alameda Da Universidade, Lisbon, 1649-004, Portugal. jcarrico@fm.ul.pt.
authors.forename: João André
authors.initials: JA
authors.lastname: Carriço
mesh_terms: D001419:Bacteria / Q000235:genetics*; D004352:Drug Resistance, Microbial / Q000235:genetics*; D062665:Epidemiological Monitoring; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058885:Multilocus Sequence Typing / Q000379:methods*; D012984:Software
keywords: Antibiotic resistance; Gene finding; High-throughput sequencing; Microbial typing; Online databases