DNA sequence analysis of South African Helicobacter pylori Vacuolating Cytotoxin Gene (vacA)

Abstract

Sequence diversity and population structures can vary widely among pathogenic bacteria species. In some species, all isolates are highly similar, whereas in others most of the isolates are distinguished easily. H. pylori is known for its wide genetic diversity amongst the various strains most especially in the genes involved in virulence. The aim of this study was to evaluate by PCR and sequence analysis, the genetic profile of H. pylori vacA gene (s1, s2, m1 and m2). We sequenced small DNA segments from 13 vacAs1, 10 vacAm2, 6 vacAm1 and 6 vacAs2 strains which were amplified with amplicon size of 259/286 bp, 290 bp and 352 bp for vacAs1/s2, m1 and m2 respectively. Based on similarities among our strains accession numbers were provided for seven vacAs1 (HQ709109-HQ709115), six vacAs2 (JN848463-JN848468), six vacAm1 (JN848469-JN848474) and six vacAm2 (HQ650801-HQ650806) strains. Amongst the strains studied, 98.07%, 98.58%, 97.38% and 95.41% of vacAs1, vacAs2, vacAm1 and vacAm2 of the strains were conserved respectively. Findings of this study underscores the importance of understanding the virulence composition and diversity of H. pylori in South Africa for enhanced clinico-epidemiological monitoring and pathophysiology of disease.

Keywords: Helicobacter pylori; South Africa; diversity; vacuolating cytotoxin gene (vacA).

Figure 1

Maximum parsimony analysis of vacAs1 sequences from clinical isolates showing that phylogenetic analysis between strains is not distinct. There is clustering between the strains. Branches with significant bootstrap support are indicated; origins of H. pylori strains are labelled with a code: SA—South Africa, USA—USA, Col—Colombia, Thai—Thailand, Alas—Alaska, Ari—Arizona, Japan-Japan; Bar indicates 2 nucleotide substitution per site. Our vacAs1 sequences were compared with (AB057218.1, AB057223.1, AB057222.1, AB057221.1 AB057219.1, AB057214.1, AB057216.1, AB057217.1, AB057211.1, AB057215.1, AB057190.1, AB057188.1, AB057187.1, AB057185.1, AB057178.1, AB057175.1, AB057184.1, AB057182.1, AB057167.1, AB057164.1, AB057166.1, AB057140.1, AB057139.1).

Figure 2

Maximum parsimony analysis of vacAm2 sequences from clinical isolates showing that phylogenetic analysis between strains is not distinct. There is clustering between the strains. Branches with significant bootstrap Support are indicated; origins of H. pylori strains are labelled with a code: SA—South Africa, USA—USA, Col—Colombia, Thailand—Thailand, Vietnam—Vietnam, Alas—Alaska, and Hongkong—Hongkong, Shi—Shi; Bar indicates 2 nucleotide substitutions per site. vacAm2 sequences were compared with the following sequences with accession numbers (AB057325.1 AB057323.1, AB057328.1, AB057327.1, AB057326.1, AB057334.1, AB057301.1, AB057290.1, AB057295.1, AB057302.1, AB057292.1, AB057307.1, AB057277.1, AB057276.1, AB057284.1, AB057286.1, AB057280.1, AB057281.1, AB057279.1, AB057282.1, GU064493.1, GU064499.1, GU064498.1, GU064495.1, GU064496.1, GU064497.1) derived from the gene bank.