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

Abstract

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.

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Acknowledgment

The authors would like to thank Dr. George Weinstock for his insightful discussions on the current cost and throughput of the whole-genome sequencing (WGS) analysis.

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Correspondence to W. M. Dunne Jr.

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Review Editor: Alex van Belkum, no conflict of interest.

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Dunne, W.M., Westblade, L.F. & Ford, B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31, 1719–1726 (2012). https://doi.org/10.1007/s10096-012-1641-7

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Keywords

  • cagA
  • Tigecycline
  • mecA Gene
  • Human Microbiome
  • Clinical Microbiology Laboratory