Age of the Association between Helicobacter pylori and Man

When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts. But how long were humans infected by H. pylori prior to the out-of-Africa event? Did this co-evolution predate the emergence of modern humans, spanning the species divide? To answer these questions, we investigated the diversity of H. pylori in Africa, where both humans and H. pylori originated. Three distinct H. pylori populations are native to Africa: hpNEAfrica in Afro-Asiatic and Nilo-Saharan speakers, hpAfrica1 in Niger-Congo speakers and hpAfrica2 in South Africa. Rather than representing a sustained co-evolution over millions of years, we find that the coalescent for all H. pylori plus its closest relative H. acinonychis dates to 88–116 kya. At that time the phylogeny split into two primary super-lineages, one of which is associated with the former hunter-gatherers in southern Africa known as the San. H. acinonychis, which infects large felines, resulted from a later host jump from the San, 43–56 kya. These dating estimates, together with striking phylogenetic and quantitative human-bacterial similarities show that H. pylori is approximately as old as are anatomically modern humans. They also suggest that H. pylori may have been acquired via a single host jump from an unknown, non-human host. We also find evidence for a second Out of Africa migration in the last 52,000 years, because hpEurope is a hybrid population between hpAsia2 and hpNEAfrica, the latter of which arose in northeast Africa 36–52 kya, after the Out of Africa migrations around 60 kya

Neighbor-joining tree of 16SrRNA sequences from gastric and enterohepatic Helicobacter species.

<p>Sequences from gastric Helicobacters (open circles) such as <i>H. pylori</i>, <i>H. cetorum</i> or <i>H. suis</i> form a cluster separate from enterohepatic Helicobacter species (filled circles) such as <i>H. cinaedi</i> or <i>H. macacae</i>. The tree was rooted with the 16SrRNA sequences of the epsilon-proteobacteria <i>Wolinella succinogenes</i> and <i>Campylobacter jejuni</i> (squares). 16SrRNA sequences were obtained from Genbank, accession numbers are provided in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#s4" target="_blank">Materials and Methods</a>.</p

Neighbor-joining population tree of extant populations of <i>H. pylori</i>.

<p>Circle diameters are proportional to the within-population genetic diversity (π). Angles of filled arcs are proportional to the number of isolates. Data are from <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Schwarz1" target="_blank">[2]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Falush2" target="_blank">[6]</a>–<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Moodley1" target="_blank">[8]</a> and the figure is modified from Figure 1 in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Falush2" target="_blank">[6]</a>.</p

Origin of the San samples.

<p>The individuals from the Khwe and !Xun communities in this study had recently migrated to South Africa.</p

Posterior population parameters simulated using an isolation with migration model (IMa) and ClonalFrame for African <i>H. pylori</i> populations.

<p>gen, generation.</p><p>CL 95, 95% confidence limit.</p><p>n, number of haplotypes used in pair-wise IMa simulations.</p><p>kya, kilo years ago.</p><p>hp, <i>Helicobacter</i> population.</p><p>hsp, <i>Helicobacter</i> sub-population.</p><p>hpAfrica2 Southern Group, derived subclade of hpAfrica2, isolated mainly in San and Bantu-speakers of South Africa.</p><p>hpAfrica2 Northern Group, subgroup of hpAfrica2, isolated in San inhabitants of Namibia and Angola.</p><p>TMRCA, time to the most recent common ancestor.</p

A comparison of global <i>H. pylori</i> and human mtDNA phylogenies.

<p>(A) Global phylogeny of <i>H. pylori</i> displayed as the strict consensus of 100 ClonalFrame analyses. After outgroup-rooting with <i>H. cetorum</i>, the time of the basal <i>H. pylori</i> divergence between hpAfrica2 and all other populations was estimated to 102 kya (95% confidence limit, 88–116 kya). Divergence of the other African <i>H. pylori</i> populations, hpAfrica1 and hpNEAfrica, began between 36 and 52 kya. (B) Simplified human mtDNA phylogeny adapted from Behar <i>et al.</i>, 2008 <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Eppinger1" target="_blank">[14]</a> with the permission of <i>AJHG</i>. African lineages are shown on a green background whereas the background for lineages outside Africa is light blue. San clades are purple, non-San clades are orange and <i>H. acinonychis</i> is yellow. San mtDNA lineages in our sample are shown as white lines.</p

Parallel patterns of pair-wise genetic distances between human mtDNA and <i>H. pylori</i> gene sequences.

<p>A Mantel regression (<i>R</i>² = 0.62, P<0.0001) showed that 62% of the pair-wise genetic distances between <i>H. pylori</i> sequences can be accounted for by the pair-wise genetic distances between human mtDNA sequences from analogous geographic locations.</p

The distribution of <i>H. pylori</i> populations in Africa.

<p>(A) The proportions of haplotypes at each sampling location (numbers; <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-t002" target="_blank">Table 2</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693.s001" target="_blank">Table S1</a>) from different bacterial populations are displayed as pie charts whose sizes indicate the numbers of haplotypes. (B) The distribution of the three major subgroups of the San language family in south-central Africa (adapted from <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat.1002693-Guldemann1" target="_blank">[21]</a>). s: Southern Khoisan was spoken on much of the South African plateau and the central Kalahari in Botswana; c: Central Khoisan was distributed in southern and western South Africa, most of Namibia and most of northern Botswana; and n: Northern Khoisan (Ju), was spoken in southern Angola, north-eastern Namibia and north-western Botswana (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002693#ppat-1002693-t001" target="_blank">Table 1</a>). The position of the letters indicates the geographical origin of Northern San (n; !Xun from Angola), Central San (c; Khwe from Namibia) and Southern San (s; Khomani from South Africa). (C) Phylogenetic relationships among hpAfrica2 strains (80% consensus of 100 ClonalFrame analyses). The tree was rooted with <i>H. pylori</i> strains from other populations.</p

Population assignment of unique <i>H. pylori</i> haplotypes from Africa/Mediterranean and human mtDNA haplogroups from Southern Africa.

1<p>mtDNA haplogroups were not determined for samples 1 to 17.</p

Bayesian population assignments using Structure V2.0.

<p>(A) Distruct plot of the assignment of <i>H. pylori</i> haplotypes from Africa, the Middle East and southern Europe as determined by the no admixture model. Each isolate is represented by a thin line that is color coded according to the population assignment. (B) Distruct plot of the proportions of ancestral nucleotides as determined by the linkage model. A thin line for each isolate indicates the estimated amount of ancestry from each of the four ancestral populations as four colored segments. (C) Distruct plot of the population assignment (no admixture model) of <i>H. pylori</i> hpAfrica1 and hpAfrica2 haplotypes from southern Africa and <i>H. acinonychis</i> (Hac).</p