Recombination Is a Major Driving Force of Genetic Diversity in the Anaplasmataceae Ehrlichia ruminantium.

Nídia Cangi,Rosalie Aprelon,Karine Huber,Nathalie Vachiéry,Thierry Lefrançois,Valérie Pinarello,Luís Neves,Laure Bournez,Jonathan L Gordon,Damien F Meyer

doi:10.3389/fcimb.2016.00111

Abstract

The disease, Heartwater, caused by the Anaplasmataceae E. ruminantium, represents a major problem for tropical livestock and wild ruminants. Up to now, no effective vaccine has been available due to a limited cross protection of vaccinal strains on field strains and a high genetic diversity of Ehrlichia ruminantium within geographical locations. To address this issue, we inferred the genetic diversity and population structure of 194 E. ruminantium isolates circulating worldwide using Multilocus Sequence Typing based on lipA, lipB, secY, sodB, and sucA genes. Phylogenetic trees and networks were generated using BEAST and SplitsTree, respectively, and recombination between the different genetic groups was tested using the PHI test for recombination. Our study reveals the repeated occurrence of recombination between E. ruminantium strains, suggesting that it may occur frequently in the genome and has likely played an important role in the maintenance of genetic diversity and the evolution of E. ruminantium. Despite the unclear phylogeny and phylogeography, E. ruminantium isolates are clustered into two main groups: Group 1 (West Africa) and a Group 2 (worldwide) which is represented by West, East, and Southern Africa, Indian Ocean, and Caribbean strains. Some sequence types are common between West Africa and Caribbean and between Southern Africa and Indian Ocean strains. These common sequence types highlight two main introduction events due to the movement of cattle: from West Africa to Caribbean and from Southern Africa to the Indian Ocean islands. Due to the long branch lengths between Group 1 and Group 2, and the propensity for recombination between these groups, it seems that the West African clusters of Subgroup 2 arrived there more recently than the original divergence of the two groups, possibly with the original waves of domesticated ruminants that spread across the African continent several thousand years ago.

Highlights

Ehrlichia ruminantium is an intracellular bacterium responsible for heartwater, an important and fatal tropical disease of wild and domestic ruminants (Allsopp, 2009; Moumene and Meyer, 2016)
The prevalent recombination events observed in the current study suggest a complex population structure for E. ruminantium strains and suggests that caution should be taken when reconstructing relationships in closely related species in the Anaplasmataceae, especially if using only a subset of the genome, like in multilocus sequence typing (MLST) analyses
From 194 E. ruminantium isolates, only 97 representing unique sequence types are shown in the phylogenetic network and tree (Figures 1A, 2, Figure S1)

Summary

Introduction

Ehrlichia ruminantium is an intracellular bacterium responsible for heartwater, an important and fatal tropical disease of wild and domestic ruminants (Allsopp, 2009; Moumene and Meyer, 2016). This bacterium is transmitted by Amblyomma hebraeum ticks in southern Africa and by Amblyomma variegatum ticks, the most wide spread vector through sub-Saharan Africa, Indian Ocean islands and the Caribbean (Walker and Olwage, 1987). No efficient single vaccine against heartwater is available due to a limited cross protection between vaccinal and field strains, which is probably caused by the high genetic diversity of E. ruminantium in any given geographical location (Vachiéry et al, 2013). The genetic diversity of E. ruminantium has been elucidated through polymorphic and conserved genes such as map1, 16S rRNA, and some housekeeping genes for a limited number of strains

Methods

Results

Conclusion