Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England

Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India.
BMC Microbiology (Impact Factor: 2.73). 03/2005; 5(32):1-10. DOI: 10.1186/1471-2180-5-32
Source: OAI


Background . Genomic diversity of H. pylori from many different human populations is largely unknown. We compared genomes of 65 H. pylori strains from Nottingham, England. Molecular analysis was carried out to identify rearrangements within and outside the cag -pathogenicity-island ( cag PAI) and DNA sequence divergence in candidate genes. Phylogenetic analysis was carried out based on various high-resolution genotyping techniques.

Results . Analyses of virulence genes ( cag T, cag E, cag A, vac A, ice A, oip A and bab B) revealed that H. pylori strains from England are genetically distinct from strains obtained from other countries. The toxigenic vac A s1m1 genotype was found to be less common and the plasticity region cluster was found to be disrupted in all the isolates. English isolates showed a predominance of ice A1 alleles and a functional proinflammatory oip A gene. The English H. pylori gene pool revealed several Asian/oriental features. This included the predominance of cag A – glr ( cag A right junction) motif types III and II (up to 42%), presence of vac A m1c alleles and phylogenetic affinity towards East Asian / Amerindian gene pools based on fluorescent amplified fragment length polymorphism (FAFLP) analysis and glm M sequence analysis.

Conclusion . Overall, our results demonstrated genetic affinities of H. pylori in England with both European and the Asian gene pools and some distinctive genetic features of virulence genes that may have evolved in this important European population.

Download full-text


Available from: Leonardo A Sechi,
    • "In England, a study found the predominance of iceA1 alleles, cagA, and vacAs1m2 strains in patients with ulcers. The study also showed genetic affinities of H. pylori in England with both European and Asian gene pools.[44] "
    [Show abstract] [Hide abstract]
    ABSTRACT: Helicobacter pylori is recognized as a major cause of gastritis, peptic ulcer, gastric cancer, and mucosa-associated lymphoma. Infection with this gram-negative microaerophile has been treated using combination of antibiotics and proton pump inhibitors for different gastrointestinal diseases. The most commonly used treatment is triple therapy which consists of administration of a proton pump inhibitor, clarithromycin, and amoxicillin. Many factors contribute to treatment failure, but one of the main reasons is development of bacterial antibiotic resistance. The percent prevalence of antibiotic resistance varies among different countries; it appears to be partly determined by the geographic factors and its ability to undergo frequent homologous recombination. The aim of this paper is to review the prevalence of H. pylori infection, association of clinical outcomes with H. pylori genotypes, and current status of antibiotic resistance in H. pylori in Saudi Arabia. It also discusses the different alternative approaches for the treatment of H. pylori using antibiotics. In addition, association of antibiotic resistance with H. pylori virulent genotypes in Saudi population and its underlying resistance mechanism will also be discussed.
    Saudi Journal of Gastroenterology 07/2014; 20(4):212-218. DOI:10.4103/1319-3767.136935 · 1.12 Impact Factor
    • "For molecular confirming of H. pylori colonies, the glmM gene was identified by PCR using specific primer pairs: forward 5’ GGATAAGCTTTTAGGGGTGTTAGGGG-3’ and reverse 5’ GCTTACTTTCTAACACTAACGCGC-3’ with a 296-bp size product.[10] The PCR was performed in a final volume of 25 μl containing 10 X PCR buffer, 500 nM of each primer, 2 mM MgCl2; 200 μM each deoxyribonucleotide triphosphate (dNTP), 1.5 U Taq DNA polymerase, and 200 ng DNA sample. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Helicobacter pylori is an important pathogen for gastroduodenal diseases. Infection with H. pylori can be limited by regimens of multiple antimicrobial agents. However, antibiotic resistance is a leading cause of treatment failure. The aim of this study has been to determine the resistance patterns of H. pylori strains isolated from gastric biopsies of patients with dyspepsia by agar dilution method, in Tehran, Iran. PATIENTS AND METHODS : H. pylori isolates from patients with gastrointestinal diseases were evaluated for susceptibility testing by agar dilution method. Susceptibility testing was performed to commonly used antibiotics including clarithromycin, tetracycline, amoxicillin, metronidazole and ciprofloxacin. Among 92 patients with dyspepsia, H. pylori strains were isolated from 42 patients. Seventeen (40.5%) of the isolates were resistant to metronidazole (MICs ≥ 8 μg/l), whereas one isolate (2.4%) was resistant to amoxicillin (MICs ≤ 0. 5 μg/ml) and ciprofloxacin (MICs ≤ 1μg/ml). The resistance rates to other antibiotics in H. pylori isolates are recorded as follows: clarithromycin 6 (14.3 %), tetracycline 2 (4.8%). In 5 of 42 resistant cases, combined resistance was found. These data suggest that metronidazole should be used among Iranian patients in first-line therapy with caution, and ciprofloxacin in association with amoxicillin and a proton pump inhibitor is more recommended.
    Saudi Journal of Gastroenterology 03/2011; 17(4):261-4. DOI:10.4103/1319-3767.82581 · 1.12 Impact Factor
  • Source
    • "Recently, a novel putative virulence factor has been identified, the oipA (outer inflammatory protein) gene, which encodes one of the outer membrane proteins and is an inflammation-related gene located approximately 100 kb from the cag PAI on the H. pylori chromosome [20]. oipA induces IL-8 secretion by epithelial cells and active OipA protein production may be "on" or "off" depending on the number of CT dinucleotide repeats in the signal sequence of the oipA gene (HP0638) [21]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Distinct virulence factors of H. pylori have been described: the vaculating cytotoxin (vacA), the cytotoxin associated gene (cagA), the induced by contact with epithelium factor Antigen (iceA gene) and the outer membrane protein oipA. In Tunisia, there are no data regarding the pattern of H. pylori genotypes; therefore, this prospective and multicentre study was the first to be done in Tunisia and aimed to investigate the prevalence of the vacA, cagA, iceA and oipA genotypes of H. pylori isolates from Tunisian patients with peptic ulceration, gastric cancer, MALT lymphoma and gastritis. H. pylori was cultured from endoscopic biopsies obtained from 281 Tunisian patients. The vacA alleles, cagA, iceA and oipA genotypes were determined by PCR. The vacA s1m1, s1m2 and s2m2 were respectively found in 10.7%, 12.5% and 45.6% of strains. The s2m1 genotype was not detected in our study. The cagA was found in 61.6% of isolates. The iceA1 and the iceA2 genotypes were respectively isolated in 60.2% and in 16% of strains. The oipA genotype was detected in 90.8% of strains. Considering the vacA and iceA genotypes, the presence of multiple H. pylori strains in a single biopsy specimen was found respectively in 31.4% and 23.8%. The comparison between strains isolated from antrum and fundus showed that Tunisian patients were infected with two or more strains of different cagA, vacA, iceA and oipA genotypes and the discordance was respectively in 9.6%, 4.6%, 8.9% and 8.5% of strains. Our results showed that in 46% (131 strains among 281), the H. pylori strains were highly virulent in relation of the three or four virulent factors they could carry. These finding were described before in the literature. Tunisian patients were colonized by one or multiple strains of H. pylori in the same time in relation of presence of vacA m1/m2 and iceA1/iceA2 in the same biopsy. The discordance between strains isolated from antrum and fundus was high, and it is in favour of multicolonization.
    Annals of Clinical Microbiology and Antimicrobials 03/2010; 9(1):10. DOI:10.1186/1476-0711-9-10 · 2.19 Impact Factor
Show more