High-throughput sequencing (NGS) in molecular epidemiology

Résumé

This book explains how next-generation sequencing supports molecular epidemiology by enabling high-resolution pathogen typing, outbreak investigation, genomic surveillance, and detection of resistance and virulence genes. It compares major sequencing platforms, describes the full WGS workflow from sample to annotated genome, and examines cgMLST and SNP-based phylogeny. The book also highlights practical applications in public health and One Health, while discussing technical limits, bioinformatics challenges, standardization, and interpretation issues, especially in resource-limited settings.