The resistance of H. pylori to clarithromycin is one of the major causes of eradication failure. In H. pylori, clarithromycin resistance is due to point mutation in 23S rRNA. The aims of this study were to investigate the mutation of 23S rRNA and to examine the association of cagA, vacA genotype and clarithromycin resistant genes.

H. pylori DNA was extracted from antral biopsy specimens from 27 children with H. pylori infection. Specific polymerase chain reaction (PCR) assays were used for cagA and vacA. Mutations associated with clarithromycin resistance were detected by using PCR restriction fragment length polymorphism (RFLP) analysis of 23S rRNA gene.

A2143G mutation was detected in one case and A2144G in 4, indicating 18.5% were clarithromycin resistant. Among the total of 27, cagA was present in 25 (93%), vacA s1a/m1 in 6 (22%), s1a/m2 in 3 (11%), s1c/m1 in 16 (59%), and s1c/m2 in 1 (4%). All of the 5 clarithromycin resistant strains were cagA (+), among which 2 were s1a/m1 and 2 were s1c/m1. There was no relation between genotypes and clarithromycin resistant genes.

Detection of H. pylori resistance to clarithromycin using PCR RFLP from biopsy specimens might be useful for the selection of antibiotics. Clarithromycin resistant genes are not associated with genotypes of cagA and vacA.