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PCR-based genotyping of Helicobacter pylori of Gambian children and adults directly from biopsy specimens and bacterial cultures

Ousman Secka1*, Martin Antonio1, Mary Tapgun1, Douglas E Berg3, Christian Bottomley4, Vivat Thomas1, Robert Walton1, Tumani Corrah1, Richard A Adegbola15 and Julian E Thomas2

Author Affiliations

1 Bacterial Diseases Programme, Medical Research Council Laboratories, The Gambia

2 School of Clinical Medical Sciences, Newcastle University, Newcastle upon Tyne, UK

3 Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA

4 London School of Hygiene and Tropical Medicine, London, UK

5 Bill & Melinda Gates Foundation, Seattle, USA

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Gut Pathogens 2011, 3:5  doi:10.1186/1757-4749-3-5

Published: 20 April 2011



Helicobacter pylori is an important agent of gastroduodenal disease in Africa and throughout the world. We sought to determine an optimum method for genotyping H. pylori strains from children and adults in The Gambia, West Africa.


Virulence genes were amplified in 127 of 190 cases tested (121 adults and 6 children); each of 60 bacterial cultures, and 116 from DNA extracted directly from biopsies. The proportion of biopsies that were cagA+, the ratio of vacAs1/s2, and vacAm1/m2, and the proportion of mixed strain populations in individual subjects changed with age. Strains lacking virulence cagA and vacA genes and with apparently homogeneous (one predominant strain) infections were more common among infants than adults.


In order to detect the range of bacterial genotypes harbored by individual patients, direct PCR proved slightly superior to isolation of H. pylori by biopsy culture, but the techniques were complementary, and the combination of both culture and direct PCR produced the most complete picture. The seemingly higher virulence of strains from adult than infant infections in The Gambia merits further analysis.

Genotyping; Helicobacter pylori; biopsy specimens; bacterial cultures