Performance criteria of DNA fingerprinting methods for typing of Helicobacter pylori isolates: Experimental results and meta-analysis

Typing systems are used to discriminate between isolates of Helicobacter py lori for epidemiological and clinical purposes. Discriminatory power and ty peability are important performance criteria of typing systems. Discriminat ory power refers to the ability to differentiate among unrelated isolates; it is quantitatively expressed by the discriminatory index (DI). Typeabilit y refers to the ability of the method to provide an unambiguous result for each isolate analyzed; it is quantitatively expressed by the percentage of typeable isolates. We evaluated the discriminatory power and the typeabilit y of the most currently used DNA fingerprinting methods for the typing of H . pylori isolates: ribotyping, PCR-based restriction fragment length polymo rphism (PCR-RFLP) analysis, and random amplified polymorphism DNA (RAPD) an alysis. Forty epidemiologically unrelated clinical isolates were selected t o constitute a test population adapted to the evaluation of these performan ce criteria. A meta-analysis of typeability and discriminatory power was co nducted retrospectively with raw data from published studies in which ribot yping, PCR-RFLP, RAPD, repetitive extragenic palindromic DNA sequence-based PCR (REP-PCR), or pulsed-field gel electrophoresis (PFGE) was used. Experi mental results and the meta-analysis demonstrated the optimal typeability ( 100%) and the excellent discriminatory powers of PCR-based typing methods: RAPD analysis, DIs, 0.99 to 1; REP-PCR, DI, 0.99; and PCR-RFLP analysis, DI s, 0.70 to 0.97). Chromosome restriction-based typing methods (ribotyping a nd PFGE) are limited by a low typeability (12.5 to 75%) that strongly decre ases their discriminatory powers: ribotyping, DI, 0.92; PFGE, DIs, 0.24 to 0.88. We do not recommend the use of ribotyping and PFGE for the typing of H. pylori isolates. We recommend the use of PCR-based methods.