pylori isolates, including 27 Chinese, 16 Malay and 35 find more Indian isolates. MLST data of 423 isolates comprising of isolates from two studies by Achtman’s group [2, 12] available at the time of analysis were extracted from the H. pylori MLST database http://​pubmlst.​org/​helicobacter/​ and included in the analysis with data AS1842856 chemical structure from this study. The level of nucleotide diversity between populations and between genes is shown in Table 1. The most diverse

gene was trpC in all except the Malaysian Chinese population with the highest diversity at nearly 7.6% while the least diverse gene was atpA at 2.6%. The three ethnic populations showed different levels of diversity with the Chinese population the lowest while the Indian and Malay populations were similar. All ethnic groups had lower level of variation than the global population as a whole. Table 1 Sequence variation Gene Size (bp) Diversity (%) Population segregation sites     Chinese (27) Indian (35) Malay (16) Global (492) hspEAsia vs hspMaori hspEAsia vs hspAmerind hspIndia vs hspEAsia hspIndia vs hspLadakh atpA 566 1.77

1.61 2.22 2.62 5 4 5 4 efp 350 1.95 2.38 3.13 3.34 4 1 6 3 mutY 361 3.62 4.85 4.49 6.5 8 7 9 7 ppa 338 1.76 2.24 2.16 3.22 1 1 1 0 trpC 396 3.35 6.78 6.91 7.6 9 16 16 16 ureI 525 2.08 2.39 2.66 3.21 9 9 8 5 yphC 450 2.34 3.79 3.87 4.84 10 4 8 6 All seven 2,980 2.37 3.35 3.55 4.33 39 32 48 27 STRUCTURE analysis To determine the relationship of the Malaysian H. pylori isolates and check details the global isolates, we analysed our MLST data together with the global data using the Bayesian statistics tool, STRUCTURE [25], which was previously used to divide global H. pylori isolates into six Fludarabine order ancestral populations, designated as hpAfrica1, hpAfrica2, hpNEAfrica, hpEurope, hpEastAsia and hpAsia2 [2, 12]. The Malaysian H. pylori isolates were found to fall into four of the six known populations

(Fig. 1A). Twenty three Indian and nine Malay isolates were grouped with hpAsia2; 26 Chinese, four Indian and two Malay isolates grouped with hpEastAsia; one Chinese, eight Indian and four Malay isolates grouped with hpEurope; and one Malay isolate grouped with hpAfrica1 (Fig. 1A). Phylogenetic analysis using the Neighbour joining algorithm as shown in Figure 1B divided the isolates into three clusters, consistent with the STRUCTURE analysis. Figure 1 Population and phylogenetic structure of the Malaysian isolates. A) Ancestral populations and population assignment of the Malaysian isolates. The division into populations and subpopulations according to Falush et al. [12] and Linz et al. [2] with the new subpopulation identified in this study in bold. The number of isolates from this study falling into each subpopulation or population is shown in brackets. B) Neighbour joining tree of the Malaysian isolates. Since some populations can be further divided into subpopulations (Fig.