Clinical metagenomics for infection diagnosis

Schlaberg Robert, Laura Filkins

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations


Clinical metagenomics enables universal pathogen detection by unbiased next-generation sequencing. Recent advances in sequencing and bioinformatics technology have paved the way for increasing adoption of precision diagnostic tests based on metagenomic sequencing. In patients with infectious syndromes that can have many causes (e.g. bloodstream infections, bone and joint infections, meningitis/encephalitis, ocular infections, gastroenteritis, and respiratory tract infections), clinical metagenomics enables comprehensive detection of pathogens and profiling of the local microbiota. In addition, the genetic makeup of pathogens can be characterized in detail informing treatment decisions, infection prevention efforts, and pathogen surveillance. This chapter summarizes technological advances that have enabled integration of clinical metagenomic tests in diagnostic algorithms and discusses remaining challenges that need to be addressed to realize the full potential of this powerful technology.

Original languageEnglish (US)
Title of host publicationGenomic and Precision Medicine
Subtitle of host publicationInfectious and Inflammatory Disease
Number of pages26
ISBN (Electronic)9780128014967
StatePublished - Jan 1 2019


  • Antimicrobial resistance
  • Clinical metagenomics
  • Microbial genomics
  • Next-generation sequencing
  • Precision diagnostics
  • Syndromic testing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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