Two Novel Amino Acid Insertions in the Helicobacter pylori rdxA Gene Detected in Gastric Paraffin Biopsies

 The biggest problem in the management of patients with Helicobacter pylori infections is resistance to the first-line antibiotic drug metronidazole. Several mechanisms underlie the resistance of H. pylori to metronidazole, and one of them is mutations in the rdxA gene encoding the nicotinamide adenine dinucleotide phosphate (NADPH) protein. Therefore, we characterized the rdxA gene amplified by PCR from gastric paraffin biopsies.

 This is an explorative study using 34 gastric paraffin biopsies that were H. pylori positive in a real-time PCR assay. To analyze the rdxA gene, we conducted nested PCR of a gene fragment, followed by DNA sequencing to analyze amino acid changes and protein structure analysis.

 Of the 34 H. pylori-positive paraffin biopsies, 5 were positive for the rdxA gene fragment. The amino acid change analysis showed that the NADPH protein had substitutions, insertions, frameshifts, and premature stop codons. Two novel amino acid insertions were found. The protein structure analysis showed that the NADPH protein with substitutions had amino acid changes forming 2 pockets for active sites. The NAPDH protein with substitutions and the 2 novel insertions showed the loss of one pocket.

 The present study reports on the genetic analysis of the rdxA gene showing DNA sequence diversity. Two amino acid insertions in the NADPH gene are a unique finding, and their effect on antibacterial-resistant phenotype needs to be investigated in future studies.