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
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