Application of next generation sequencing in clinical microbiology and infection prevention.

Autor: Deurenberg RH; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Bathoorn E; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Chlebowicz MA; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Couto N; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Ferdous M; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., García-Cobos S; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Kooistra-Smid AM; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands; Certe, Department of Medical Microbiology, Groningen, The Netherlands., Raangs EC; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Rosema S; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Veloo AC; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Zhou K; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China., Friedrich AW; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands., Rossen JW; Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands. Electronic address: j.w.a.rossen@rug.nl.
Jazyk: angličtina
Zdroj: Journal of biotechnology [J Biotechnol] 2017 Feb 10; Vol. 243, pp. 16-24. Date of Electronic Publication: 2016 Dec 29.
DOI: 10.1016/j.jbiotec.2016.12.022
Abstrakt: 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™ (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.
(Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
Externí odkaz: