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Abstract
This study tested the Suppressive Subtractive Hybridisation (SSH) method by extracting the strain specific genes from H. pylori strain, 10700. Nine clones were identified as 10700-specific clones; 16 clones as the pHPS1-specific sequences; and 137 clones homologous to sequences in 26695 and J99 genomes. The high recovery of divergent genes suggested that SSH is not suitable for divergent strains.
Seventy eight H. pylori Malaysia isolates in three ethnic backgrounds were analysed by Multilocus Sequence Typing (MLST). STRUCTURE analysis assigned the Malaysian isolates to hpEastAsia, hpAsia2 and hpEurope and revealed a new subpopulation, hspIndia, within hpAsia2. The majority of Malay isolates were found to be grouped together with Indian isolates. Therefore, the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive.
DNA microarrays were employed to analyse 10 Malaysian isolates, comprising three Chinese, three Indian and four Malay isolates. However, 217 oligonucleotides were identified with non-specific bindings and were excluded from subsequent analysis. The remaining oligonucleotides were classified as common gene oligonucleotides, Strain Specific Genes (SSGs), and common but non-homologous oligonucleotides (CNHOs). Microarray analysis has also revealed 99.6% of common genes, 73.5% of SSGs and 89.9% of CNHOs universally present in the 10 Malaysian isolates. However, higher number of genes was detected among the Malaysian isolates than the global isolates. This may due to the different microarrays used between microarray studies. In addition, 268 genes variably present among hspIndia and hspLadakh; 259 genes were shown to be variably present among the three Malaysian and six global isolates. Then again, the 10 Malaysian isolates were not clustered together according to the population structure established by MLST studies. Therefore, Microarrays data does not reflect the evolutionary history of H. pylori but can be used to provide information on gene acquisition and loss between populations established by MLST.