From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

Trends Microbiol. 2018 Dec;26(12):1035-1048. doi: 10.1016/j.tim.2018.08.004. Epub 2018 Sep 4.


Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Bacteria / genetics*
  • Bacteria / isolation & purification*
  • Bacteria / pathogenicity
  • Base Sequence
  • Cross Infection / diagnosis
  • Cross Infection / epidemiology
  • Cross Infection / microbiology
  • Diagnostic Tests, Routine / economics
  • Diagnostic Tests, Routine / methods*
  • Drug Resistance, Bacterial
  • Genes, Bacterial
  • Genome, Bacterial*
  • Humans
  • Multilocus Sequence Typing
  • Phenotype
  • Sequence Analysis, DNA
  • Virulence / genetics
  • Virulence Factors / genetics
  • Whole Genome Sequencing / economics
  • Whole Genome Sequencing / methods*


  • Virulence Factors