Molecular strain typing has become an essential tool for the analysis of bacterial pathogens obtained during investigations of epidemiologic outbreaks, laboratory contamination, and recurrent infection. A wide variety of strain typing methods have been described using contemporary DNA-based technologies. However, developing methods and generating data have proven easier than defining robust approaches for interpreting the results. Clinical and Laboratory Standards Institute document MM11-A—Molecular Methods for Bacterial Strain Typing; Approved Guideline examines the biology behind molecular strain typing and the process of characterizing and validating typing systems. The prevalent methods are described with particular attention to pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Specific issues in analyzing typing data derived from these methods are discussed. The guideline offers a general approach, suitable for use in the situations commonly encountered in clinical laboratories, for interpreting and reporting molecular typing results. For selected bacterial pathogens, the application of molecular typing systems and the insights derived are considered in detail.

Bacterial strain typing is now performed in a wide range of venues, including hospital-based clinical microbiology laboratories; federal, state, and local reference laboratories; as well as industrial and commercial laboratories. Similarly, the results of bacterial strain typing are now used in many different contexts, including clinical care settings; public health investigations, particularly of emerging infections; the food and pharmaceutical industries; and environmental analyses. 

The goal of this guideline is to provide a framework that will facilitate consistency in reporting bacterial strain typing and will assist both the laboratories performing these studies and the professionals applying the results. A general approach to the analysis of molecular typing data will be presented, as well as specific criteria for interpreting typing results obtained with the most commonly used methods. This guideline will focus on techniques that analyze bacterial chromosomal DNA, particularly pulsed-field gel electrophoresis (PFGE) and nucleotide sequencing; phenotypic techniques (e.g., serotyping, phage typing) and plasmid-based methods will not be addressed.