title: Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections.
abstract: The term 'shotgun metagenomics' is applied to the direct sequencing of DNA extracted from a sample without culture or target-specific amplification or capture. In diagnostic metagenomics, this approach is applied to clinical samples in the hope of detecting and characterizing pathogens. Here, I provide a conceptual overview, before reviewing several recent promising proof-of-principle applications of metagenomics in virus discovery, analysis of outbreaks and detection of pathogens in contemporary and historical samples. I also evaluate future prospects for diagnostic metagenomics in the light of relentless improvements in sequencing technologies.
authors.affiliation: Division of Microbiology and Infection,Warwick Medical School, University of Warwick,Coventry CV4 7AL,UK.
authors.forename: M J
authors.initials: MJ
authors.lastname: Pallen
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001424:Bacterial Infections / Q000175:diagnosis* / Q000453:epidemiology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics; D010271:Parasites / Q000235:genetics / Q000302:isolation & purification; D010272:Parasitic Diseases / Q000175:diagnosis*; D017422:Sequence Analysis, DNA; D014777:Virus Diseases / Q000175:diagnosis*; D014780:Viruses / Q000235:genetics / Q000302:isolation & purification