Application of next generation sequencing in clinical microbiology and infection prevention
Autor: | Natacha Couto, Erwin C. Raangs, Kai Zhou, A.M.D. Kooistra-Smid, Alida Veloo, John W. A. Rossen, Monika A. Chlebowicz, Ruud H. Deurenberg, Alexander W. Friedrich, Erik Bathoorn, Sigrid Rosema, Silvia García-Cobos, Mithila Ferdous |
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Přispěvatelé: | Microbes in Health and Disease (MHD) |
Rok vydání: | 2017 |
Předmět: |
DNA
Bacterial Microbiological Techniques 0301 basic medicine BACTERIAL-MENINGITIS medicine.medical_specialty NETHERLANDS MiSeq Bioengineering Bacterial genome size Computational biology Biology Genome Applied Microbiology and Biotechnology DNA sequencing METAGENOMICS Disease Outbreaks 03 medical and health sciences Medical microbiology TYPING METHODS Species Specificity ENTEROBACTERIACEAE Zoonoses Infection prevention Next generation sequencing medicine Animals Humans Clinical microbiology Whole genome sequencing Genetics Base Sequence IDENTIFICATION Ion PGM (TM) High-Throughput Nucleotide Sequencing Outbreak GENOME SEQUENCE Bacterial Infections Sequence Analysis DNA General Medicine Molecular diagnostics 030104 developmental biology Metagenomics VISUALIZATION KLEBSIELLA-PNEUMONIAE CHICKEN MEAT Genome Bacterial Biotechnology |
Zdroj: | Journal of Biotechnology, 243, 16-24. Elsevier |
ISSN: | 0168-1656 |
DOI: | 10.1016/j.jbiotec.2016.12.022 |
Popis: | 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. |
Databáze: | OpenAIRE |
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