Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory Review uri icon


MeSH Major

  • Bacteriological Techniques
  • Genome, Bacterial
  • High-Throughput Nucleotide Sequencing
  • Molecular Diagnostic Techniques


  • The identification and/or prediction of the antimicrobial resistance of microorganisms in clinical materials solely by molecular means in the diagnostic microbiology laboratory is not novel. However, the ability to sequence multitudes of bacterial genomes and deliver and interpret the resultant sequence information in near "real-time" is the basis of next-generation sequencing (NGS) technologies. There have been numerous applications and successes of NGS applications in the clinical and public health domain. However, none have, as yet, delivered perhaps the most sought after application, i.e., the generation of microbial sequence data for "real-time" patient management. In this review, we discuss the use of NGS and whole-genome sequencing (WGS) of microorganisms as a logical next step for the routine diagnosis of infection and the prediction of antimicrobial susceptibility in the clinical microbiology laboratory.

publication date

  • August 2012



  • Review



  • eng

Digital Object Identifier (DOI)

  • 10.1007/s10096-012-1641-7

PubMed ID

  • 22678348

Additional Document Info

start page

  • 1719

end page

  • 26


  • 31


  • 8