Clinical Review

Microbial genome sequencing—beyond the double helix

BMJ 1998; 317 doi: https://doi.org/10.1136/bmj.317.7172.1568 (Published 05 December 1998) Cite this as: BMJ 1998;317:1568
  1. Peter J Jenks, Wellcome research fellow (pjenks@pasteur.fr)
  1. Unité de Pathogénie Bactérienne des Muqueuses, Institut Pasteur, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France

    Considerable advances in automated DNA sequencing and bioinformatics have made the sequencing of entire microbial genomes a reality (see fig 1). Researchers have been quick to recognise the scientific value of microbial sequence data, and there is now a frantic rush to sequence a wide range of important micro-organisms. The continuing release of data from these projects, combined with advances in techniques used to investigate pathogenesis, will lead to an unprecedented understanding of micro-organisms and how they cause disease.

    In this article I discuss how this sequence information will affect the practice of clinical microbiology and the management of infectious diseases. In particular, I examine how the large scale study of the entire genetic complement of micro-organisms should result in the provision of more rapid and efficient diagnostic techniques, as well as the development of new antimicrobial strategies.

    Microbial genome sequencing

    In the past few years a large number of clinically important bacteria, parasites, and fungi have been sequenced, and genomic data for many human pathogens will be available by the turn of the century (see box). Because many of the early sequencing efforts were funded by private industry, concerns were raised about ownership and freedom of access to the data generated by these projects. As sequencing technology has become more refined and efficient, however, the cost of such projects has fallen, and funding is increasingly being provided by government agencies and medical charities. This has greatly improved access to microbial sequence information, and data from most projects are deposited, often on a daily basis, on websites on the internet.

    A comprehensive catalogue of all genome sequencing projects is provided by the Magpie Genome Sequencing Project List (www.mcs.anl.gov), and links to individual projects are also available at this site. Other useful resources include the website of the Institute for Genomic Research (www.tigr.org), which …

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