Variability in presence-absence scoring of AP PCR fingerprints affects computer matching of bacterial isolates

Sources of variation in scoring bands in arbitrarily primed PCR (AP PCR) fingerprints of bacterial isolates were identified, and their effect on computer matching of fingerprints was determined. E. coli and five Salmonella serotypes were fingerprinted. PCR reactions and gel electrophoresis analysis of PCR products were replicated, including comparisons in the same gel and in different gels. Bands in the images were assigned by two different people on a presence-absence basis. Variations in scoring the images occurred at all levels, and prevented correct identification of isolates. E. coli was distinguished from Salmonella, but discrimination among different Salmonella serotypes and between two isolates of the same serotype was poor. Our results suggest that computer analysis of AP PCR fingerprints scored on a presence absence basis may not correctly match isolates. Side-by-side visual comparison of isolates is recommended.