Genome sequencing in clinical microbiology : Nature Biotechnology : Nature Publishing Group

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Genome sequencing in clinical microbiology : Nature Biotechnology : Nature Publishing Group

Genome sequencing in clinical microbiology

• Jacqueline Z-M Chan,¹
• Mark J Pallen,^{1, 2}
• Beryl Oppenheim^{1, 2}
• & Chrystala Constantinidou^{1, 2}

• Affiliations
• Corresponding author

Journal name:

Nature Biotechnology

Volume:

30,

Pages:

1068–1071

Year published:

(2012)

DOI:

doi:10.1038/nbt.2410

Published online

08 November 2012

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High-throughput sequencing is being adopted to characterize microbial pathogens and track their evolution and spread.

The remit of the clinical microbiology laboratory encompasses analysis of samples, detection and identification of microorganisms associated with infection, determination of antibiotic susceptibilities and monitoring of pathogen spread. Although several new molecular approaches, such as nucleic acid amplification, mass spectrometry and sequence typing, have been adopted to varying extents, many of the techniques in use today would have been familiar to a nineteenth-century microbiologist. Now, as shown in a spate of recent papers (Table 1), clinical microbiology is on the cusp of a major transformation driven by high-throughput genome sequencing, used as an adjunct, or even an alternative, to traditional diagnostic approaches (Fig. 1). In addition, sequencing technology is shedding light on the unseen world of unculturable microorganisms and enhancing our ability to track the evolution and spread of pathogens and resistance genes in our hospitals and communities.