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Journal article

Rapid bacterial genome sequencing: methods and applications in clinical microbiology.

  • Bertelli C Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
  • Greub G
  • 2013-04-23
Published in:
  • Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. - 2013
Antibiotic resistance
bacterial genome
diagnostic
high-throughput sequencing
virulence factor
Bacterial Infections
Bacterial Typing Techniques
DNA, Bacterial
Disease Outbreaks
Drug Resistance, Microbial
Escherichia coli
Genome, Bacterial
High-Throughput Nucleotide Sequencing
Host-Pathogen Interactions
Humans
Metagenomics
Mycobacterium tuberculosis
Virulence Factors
English The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.
Language
  • English
Open access status
bronze
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/105889
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