Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology.

JWA Rossen, AW Friedrich, J Moran-Gilad

Research output: Contribution to journalArticlepeer-review


In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories.
Original languageEnglish
Pages (from-to)355-360
Number of pages6
JournalClin Microbiol Infect
Issue number4
StatePublished - Apr 2018


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