Advanced Techniques in Diagnostic Microbiology

26
Molecular Strain Typing Using
Repetitive Sequence–Based PCR
STACIE R. FRYE AND MIMI HEALY
Introduction
Microbial strain typing is increasingly important in routine clinical microbiology
laboratories as a method to track hospital-acquired infections. Although many
methods can be used, this chapter focuses on one particular method used for typing
of bacteria and fungi: repetitive sequence–based PCR (rep-PCR). A number of
valuable reviews are available for more in-depth discussion of other technologies
(Olive and Bean, 1999; Soll, 2000; Zaidi et al., 2003). The technology behind
rep-PCR will be introduced with a review of traditional, manual rep-PCR. The
latest advances will be highlighted with a discussion of the DiversiLab System,
Bacterial Borcodes, Inc., Athens, GA, which is an automated rep-PCR technology.
Additionally, we describe a comparison of the technologies, current applications
in clinical microbiology laboratories, and future potential of rep-PCR as a routine
clinical test.
Principles of Rep-PCR and the DiversiLab System
Microbial Typing
With the rising spread of antibiotic-resistant organisms, clinical laboratories must
focus more and more on the epidemiology of hospital-acquired infections. Strain
typing is an extremely useful tool in tracking the spread of nosocomial infections
(Watterson and Drobniewski, 2000; Taha, 2002; Wu and Della-Latta, 2002). In
addition to tracking the source of hospital-associated infections, strain typing is
useful for studying community-acquired infections, discriminating between recurrent
infections caused by new exposure or by colonization, and investigations to
determine the presence of single source; multiple-site infections or other environmental
source. Finally, strain typing can be a useful tool to identify and pinpoint
laboratory contamination. Because of its many uses, strain typing has become a
common procedure in many clinical laboratories. This has required clinical laboratories
to shift from using solely phenotypic methods to using genotypic methods
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