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J Biotechnol. 2017 Feb 10;243:16-24. doi: 10.1016/j.jbiotec.2016.12.022. Epub 2016 Dec 29.

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

Author information

1
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
2
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands; Certe, Department of Medical Microbiology, Groningen, The Netherlands.
3
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.
4
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands. Electronic address: j.w.a.rossen@rug.nl.

Abstract

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.

KEYWORDS:

Clinical microbiology; Infection prevention; Ion PGM(™); MiSeq; Next generation sequencing; Whole genome sequencing

PMID:
28042011
DOI:
10.1016/j.jbiotec.2016.12.022
[Indexed for MEDLINE]
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