文档介绍：METHODS IN MOLECULAR BIOLOGY TM
Volume 266
Genomics,
Proteomics,
and Clinical
Bacteriology
MethodsMethods andand ReviewsReviews
Edited by
Neil Woodford
Alan P. Johnson
Bacterial Genomes for the Masses 3
1
Bacterial Genomes for the Masses
Relevance to the Clinical Laboratory
Mark J. Pallen
Summary
Bacterial genome sequencing has revolutionized the research landscape and promises to
deliver important changes to the clinical microbiology laboratory, through the identification of
novel diagnostic targets and through the birth of a new discipline or “genomic epidemiology.”
Current progress and future prospects for exploitation of genome sequences in clinical bacteri-
ology are reviewed.
Key Words: Genome sequencing; bacteriology; genomics; molecular epidemiology; genomic
epidemiology; diagnosis.
1. Introduction
“All changed, changed utterly:
A terrible beauty is born.”
W. B. Yeats—Easter 1916
The world of bacterial genome sequencing “changed utterly” when the first
plete bacterial genome sequences were published by scientists at The
Institute for Genomic Research (TIGR) in Maryland in 1995 (1–3). Sequenc-
ing of the Haemophilus influenzae genome was followed quickly by that of
Mycoplasma genitalium—both using a whole-genome shotgun sequencing
strategy that shattered the dogma that genomes should be sequenced using a
top-down approach, where detailed mapping and creation of an ordered library
had to precede genome sequencing. Consequently, aside from a handful of
From: Methods in Molecular Biology, vol. 266: Genomics, Proteomics, and Clinical Bacteriology:
Methods and Reviews
Edited by: N. Woodford and A. Johnson © Humana Press Inc., Totowa, NJ
3
4 Pallen
projects already underway in 1995, nearly all other bacterial genome sequenc-
ing projects have relied on the quick, easy, and efficient approach of making a
random shotgun library, automatically sequencing tens of thousands of clones,
and then puter power to a