Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique

Abstract Two genotyping methods were performed on bacterial suspensions of the human pathogen Helicobacter pylori . A total of 29 clinical isolates were analysed by sequencing of a 294-bp PCR-derived internal segment of the essential ureC/glmM gene of H. pylori , and by random amplified polymorphic DNA (RAPD) using a single 11-bp oligonucleotide made up of an arbitrary nucleotide sequence. Each isolate exhibited a distinct sequence over a 210-bp stretch of the ureC/glmM gene. Similarly, the isolates bore different profiles when tested by RAPD fingerprinting. Successive strains arising from patients who relapsed following antibiotic treatment and strains isolated from two patients institutionalized in the same care centre had identical ureC/glmM gene sequences and RAPD profiles. Both methods were found to be discriminatory. However, PCR sequencing of the ureC/glmM gene appeared to be more reproducible and more reliable for distinguishing between strains than the RAPD technique.