Distribution of open reading frames of plasticity region of strain J99 in Helicobacter pylori strains isolated from gastric carcinoma and gastritis patients in Costa Rica

The plasticity region of Helicobacter pylori strain J99 is a large chromoso mal segment containing 33 strain-specific open reading frames (ORFs) with c haracteristics of a pathogenicity island. To study the diversity of the pla sticity region, 22 probes corresponding to 20 ORFs inside the plasticity re gion and two ORFs on its boundaries were hybridized to genomic DNA isolated from clinical strains of H. pylori from patients with gastritis or gastric adenocarcinoma, Highly variable hybridization patterns were observed. The majority of the clinical strains presented a hybridization profile similar to that of J99; thus, these ORFs are not J99 strain specific. No associatio n was found between a particular hybridization pattern and the clinical ori gin of the strain. Nevertheless, two single ORFs (JHP940 and JHP947) were m ore likely to be found in gastric cancer strains. They may be new pathogeni city markers. An in vitro expression study of these ORFs was also performed for the J99 strain, under different conditions. Thirteen ORFs were consist ently expressed, six were consistently shut off and three were expressed di fferentially. Most of the constitutionally expressed genes were located on the 3' part of the plasticity region. Our results show that the plasticity region, rather than being considered a pathogenicity island per se, should be considered a genomic island, which represents a large fragment of foreig n DNA integrated into the genome and not necessarily implicated in the path ogenic capacity of the strain.