Aims: Helicobacter pylori is a causative agent of gastroduodenal diseases in Bangladesh as well as throughout the world. This study aimed to determine the H. pylori cagA, vacA and iceA virulent genotypes by PCR directly in gastric biopsies from dyspeptic patients of Chittagong, Bangladesh and evaluating the association of these genotypes with clinical manifestations. Methodology and results: CLO (Campylobacter-Like Organism) test and Hp16s PCR (16S rRNA based H. pylori specific PCR) was performed to confirm H. pylori infection. Among 111 patients, H. pylori infection was found in 60 patients by CLO test, while Hp16s PCR revealed that 54 patients were H. pylori positive. PCR amplification of the H. pylori virulence genes was successful in 35 gastric biopsies amongst the 54 Hp16s PCR positive biopsies. The positive rates for the cagA, vacAs1, vacAs2, vacAm1, vacAm2, iceA1, iceA2 genes were 34.3%, 71.4%, 8.6%, 62.9%, 28.6%, 20% and 11.4%, respectively. The allelic variant vacAs1m1 had a predominant percentage with 51.4%, followed by vacAs1m2, vacAs2m2 and vacAs1m1m2 with 14.3%, 5.7% and 2.9%, respectively. Among the subtypes of vacAs1, only s1a was detected in 54.3% of biopsies while none of the cases showed the s1b and s1c genotypes. However, there was no statistically significant association (p>0.05) observed between the virulent genotypes and clinical conditions. Conclusion, significance and impact of study: We found that cagA, vacAs1m1 and iceA1 were the most frequent H. pylori genotypes in severe clinical outcomes of the infection. The data in this study would provide a basis for understanding the diverse virulence pattern of this bacterium in Bangladeshi dyspeptic patients.
Helicobacter pylori

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.
Anti-Bacterial Agents ; Bacteria ; Binding Sites ; Colonic Neoplasms ; Colorectal Neoplasms ; Computer Simulation* ; Drug Delivery Systems ; Drug Discovery ; Fusobacterium nucleatum* ; Fusobacterium* ; Genes, Essential ; Genome ; Genome, Human ; Genomics ; Humans ; Ligands ; Mass Screening ; Mining* ; Proteome*