Microbial sequence typing in the genomic era
Cargando...
Archivos
Fecha
2018-09
Profesor/a Guía
Facultad/escuela
Idioma
en
Título de la revista
ISSN de la revista
Título del volumen
Editor
Elsevier B.V.
Nombre de Curso
Licencia CC
Licencia CC
Resumen
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology. © 2017 Elsevier B.V.
Notas
Indexación Scopus
Palabras clave
Salmonella Enterica, Serotype, Whole Genome Sequencing
Citación
Infection, Genetics and Evolution Volume 63, Pages 346 - 359September 2018
DOI
10.1016/j.meegid.2017.09.022