title: Application of next generation sequencing in clinical microbiology and infection prevention.
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.
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Ruud H
authors.initials: RH
authors.lastname: Deurenberg
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Bathoorn
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Monika A
authors.initials: MA
authors.lastname: Chlebowicz
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Natacha
authors.initials: N
authors.lastname: Couto
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Mithila
authors.initials: M
authors.lastname: Ferdous
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Silvia
authors.initials: S
authors.lastname: García-Cobos
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands; Certe, Department of Medical Microbiology, Groningen, The Netherlands.
authors.forename: Anna M D
authors.initials: AM
authors.lastname: Kooistra-Smid
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Erwin C
authors.initials: EC
authors.lastname: Raangs
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Sigrid
authors.initials: S
authors.lastname: Rosema
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Alida C M
authors.initials: AC
authors.lastname: Veloo
authors.affiliation: 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.
authors.forename: Kai
authors.initials: K
authors.lastname: Zhou
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Friedrich
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands. Electronic address: j.w.a.rossen@rug.nl.
authors.forename: John W A
authors.initials: JW
authors.lastname: Rossen
mesh_terms: D000818:Animals; D001424:Bacterial Infections / Q000175:diagnosis / Q000235:genetics* / Q000517:prevention & control* / Q000635:transmission; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D004196:Disease Outbreaks / Q000517:prevention & control; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D056186:Metagenomics; D008828:Microbiological Techniques / Q000379:methods*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D015047:Zoonoses / Q000235:genetics / Q000517:prevention & control
chemical_list: D004269:DNA, Bacterial
keywords: Clinical microbiology; Infection prevention; Ion PGM(™); MiSeq; Next generation sequencing; Whole genome sequencing