title: Genomics and metagenomics in medical microbiology.
abstract: Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd. Jean Moulin, 13005 Marseille, France.
authors.forename: Roshan
authors.initials: R
authors.lastname: Padmanabhan
authors.forename: Ajay Kumar
authors.initials: AK
authors.lastname: Mishra
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
mesh_terms: D003141:Communicable Diseases / Q000175:diagnosis*; D006801:Humans; D056186:Metagenomics / Q000379:methods* / Q000639:trends; D008828:Microbiological Techniques / Q000379:methods* / Q000639:trends
keywords: Clinical microbiology; Genomics; Metagenomics; Next-generation sequencing