Recently, many bacterial genomes have been fully sequenced, and analysis of the sequenced genomes has revealed the presence of variable proportions of repeats, including tandem repeats. Short repeat motifs undergo frequent variation in the number of repeated units. MLVA is an appropriate method for bacterial typing and identification, for determining genetic diversity, and for the tracing-back of highly mono-morphological species [12–14]. The MLVA typing was reported to have a high-quality species identification capability and a high discriminatory power. The method has been used in the analysis of many bacteria [15–18], but little research has been carried out in H. pylori. Therefore, this study established the H. pylori MLVA system and applied to type clinical strains.
The H. pylori genome has a number of repeat sequences, and their repeat number results in divergence. The 12 loci identified were distributed throughout the genome. These loci had different variations in different isolates and were able to typing H. pylori successfully.
The H. pylori MTs were clustered with ethnic groups, consistent with the previous reports [19, 20]. The Han strains were selected from Southern China and had little relationship to Mongolian strains from Northern China or Tibetan strains from Western China. It may demonstrate an apparent cluster tendency in different regions and ethnic groups, but there were some exceptions, which may because, unlike other Asian countries with relatively homogeneous populations, China has a heterogeneous population from various ethnic groups. Therefore, there may be more opportunity for DNA transfer between strains of different genotypes in China than other countries. While Tibet is a relatively closed region, H. pylori strains from this area have a good cluster.
The H. pylori genome shows a high degree of genetic diversity among strains [21, 22], but weakly clonal groupings of different diseases were detected, and these could be superimposed on a pattern of free recombination. And the relationship between particular H. pylori genotype and related disease has not been sure.
MLVA is a useful molecular tool for epidemiological investigations and recognition of laboratory cross-contamination [23–25]. VNTR analysis thus provides multiple independent characteristics for phylogenetic analysis. Studies have indicated that MLVA is sufficient to resolve closely related isolates. In contrast, combining loci with lower variability values is suitable for establishing clear phylogenetic patterns among strains that have evolved over a longer time period. Theoretically, the greater the number of loci used, the higher the discriminatory power that can be achieved, and subtler phylogenetic relationships among bacterial strains can be established.
At the present time, the MLVA was established and applied to examine the clonal relationships between H. pylori isolates from China and Japan. The loci used in this study provided high discriminatory power and successfully separated isolates of different strains from different geographical areas. And there was a particularly evident of H. pylori from Tibet, a relatively closed region, which showed better cluster than other ethnic groups. The data will aid in the development of a genomic polymorphism database of H. pylori. We have established a preliminary profile of MLVA but more information is required for a comprehensive profile.
China is a large country containing 56 ethnic groups and a large population. Therefore, further studies are required including isolates from more regions and over several more time-frames.