Publication

Application of next generation sequencing in clinical microbiology and infection prevention

Deurenberg, R. H., Bathoorn, E., Chlebowicz, M. A., Couto, N., Ferdous, M., Garcia-Cobos, S., Kooistra-Smid, A. M. D., Raangs, E. C., Rosema, S., Veloo, A. C. M., Zhou, K., Friedrich, A. W. & Rossen, J. W. A., 10-Feb-2017, In : Journal of Biotechnology. 243, p. 16-24 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM (TM) (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. (C) 2016 The Author(s). Published by Elsevier B.V.

Original languageEnglish
Pages (from-to)16-24
Number of pages9
JournalJournal of Biotechnology
Volume243
Early online date29-Dec-2016
Publication statusPublished - 10-Feb-2017

    Keywords

  • Infection prevention, Ion PGM (TM), Clinical microbiology, MiSeq, Next generation sequencing, Whole genome sequencing, KLEBSIELLA-PNEUMONIAE, BACTERIAL-MENINGITIS, GENOME SEQUENCE, TYPING METHODS, CHICKEN MEAT, METAGENOMICS, NETHERLANDS, ENTEROBACTERIACEAE, IDENTIFICATION, VISUALIZATION

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