4.4 Article

Microbial sequence typing in the genomic era

Journal

INFECTION GENETICS AND EVOLUTION
Volume 63, Issue -, Pages 346-359

Publisher

ELSEVIER
DOI: 10.1016/j.meegid.2017.09.022

Keywords

Bacteria; Epidemiology; MLST; Pathogen; Typing; WGS

Funding

  1. District of Columbia Developmental Center for AIDS Research [P30AI087714]
  2. George Washington University
  3. Margaret Q. Landenberger Research Foundation
  4. K12 Career Development Program award [5 K12 HL119994]
  5. Spanish Government [RYC-2015-18241]
  6. CONICYT + PAI/CONCURSO NACIONAL APOYO AL RETORNO DE INVESTIGADORES/AS DESDE EL EXTRANJERO, CONVOCATORIA 2014 + FOLIO [82140008]
  7. FONDECYT de iniciacion [11160905]
  8. NATIONAL HEART, LUNG, AND BLOOD INSTITUTE [K12HL119994] Funding Source: NIH RePORTER
  9. NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES [P30AI087714, P30AI117970] Funding Source: NIH RePORTER

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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.

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