Genome DNA analysis and genotyping of clinical isolates of Helicobacter pylori

The genotype of genome DNA from seventeen clinical isolates of Helicobacter pylori by pulsed-field gel electrophoresis (PFGE) and arbitrarily primed polymerase chain reaction (AP-PCR) was determined. Three restriction enzymes, Apa I, Kpn I and Not I, were found to produce distributions of DNA fragments which were useful for analysis of the chromosome-sized DNA from H. pylori NCTC11637T by PFGE. Many of the isolates of H. pylori could not be genotyped by PFGE after digestion reaction with Apa I, Kpn I, and Not I. When AP-PCR with a ten-nucleotide primer was performed using the chromosomal genomic DNA from the isolates as templates, fifteen distinctly different profiles were obtained from the seventeen isolates. Thus, genotyping of the isolates was possible where PFGE profiles had not previously been informative. The results suggest that AP-PCR is more suitable for genotyping of clinical isolates of H. pylori in Japan than PFGE.