Mycobacterial Strain Genotyping
Historically, the microbiological tools used to differentiate or subspeciate clinical isolates of Mycobacterium tuberculosis were based on phage and/or drug susceptibility patterns (1). The comparison of strains has evolved from analysis of protein products (phenotyping) to the analysis of genetic content (genotyping). DNAbased fingerprinting of M. tuberculosis was introduced in 1990. In the ensuing years, more than 30,000 strains have been analyzed and cataloged, and thousands of unique patterns have been identified. Molecular fingerprinting is used in a wide range of epidemiological, clinical, and basic studies to demonstrate foci of transmission in cites (6-8), nosocomial outbreaks (9-11), and congregate settings (12-14); to study transmission among high-risk populations such as HIV-positive and homeless persons (16,17); to evaluate cross-contamination in the clinical laboratory (18-20); and to analyze sequence changes as they reflect rates of molecular evolution (21,22).