Use of molecular typing in infection control.

Molecular typing is an important epidemiologic tool in infection control. Molecular tools now commonly supplement traditional epidemiologic comparative methods. In determining genetic relatedness by examining DNA at a molecular level, these tools have ultimately led to a better understanding of patterns of colonization and pathogen distribution. Molecular methods are used both for outbreak investigations and for surveillance of emerging and multidrug resistant organisms. By better understanding these patterns, hospitals, governments, and other stakeholders can design rational infection control programs and allocate resources efficiently. Historically, the typing of pathogens in infection control relied on phenotypic methods such as serotyping and phage typing. Genotypic methods have essentially replaced phenotypic methods because they have higher discriminatory power, are useful for a broader category of organisms, and can type strains that were nontypeable by phenotypic methods. An ideal molecular typing method should have high discriminatory power between closely related strains and be easily interpretable while remaining reproducible, rapid, and inexpensive. There are many genotypic methods that vary considerably in their discriminatory power and the proportion of the genome that they analyze. Plasmid analysis, one of the first typing methods developed, was useful in outbreaks where there were multiple transmissible resistance or virulence determinants. This phenotypic method lacks reproducibility, as plasmids can be easily acquired and lost and is now essentially obsolete. Pulse field electrophoresis (PFGE) is very reproducible and is usually the method of choice for outbreak investigations. Although it has only moderate discriminatory power, it can analyze a large portion of the genome, which is generally sufficient to determine clonal relationships. Like PFGE, restriction fragment length polymorphism analysis uses restriction enzyme digestion to exploit naturally occurring DNA polymorphisms. restriction fragment length polymorphism analysis (including ribotyping) can be simplified by automation, although it is limited by its reliance on radiolabeled probes to known DNA sequences. Polymerase chain reaction (PCR)-based methods, though highly discriminatory, generally examine only a small portion of the chromosome, which is a limitation if the amplified portion cannot be used to distinguish between individual strains. These methodologies are quick and relatively easy to perform, and can detect a very small quantity of DNA. Unfortunately, they require target sequences in advance and can easily be contaminated leading to false positive results. Examples of PCRbased methods include multiplex PCR, nested PCR, arbitrarily primed PCR, repetitive sequence PCR, amplified fragment length polymorphism, and spoligotyping. A relatively new method, sequence-based molecular typing (single-locus sequence typing and multilocus sequence typing) is promising because it is highly discriminatory, standardized, and interpretable—relying directly on the nucleic code. This feature is important to identify variance in individual genes and can also be used to examine multiple loci. This allows the creation of genomic libraries which can be used for large-scale surveillance. However, currently it is too cumbersome for use in real-time clinical scenarios. The most common use of molecular typing methods is in outbreak investigations, to determine if clonal spread has occurred in a microenvironment, such as an individual neonatal intensive care unit (NICU), identify sources and secondary cases, and then institute appropriate infection control From the *Department of Pediatrics, Columbia University Medical Center, Columbia University; and †Department of Epidemiology, New York-Presbyterian Hospital, New York, NY. Copyright © 2007 by Lippincott Williams & Wilkins ISSN: 0891-3668/07/2606-0527 DOI: 10.1097/INF.0b013e3180600c19 CONTENTS Use of Molecular Typing in Infection Control Autoinflammatory Syndromes Table