Ehrlichia ruminantium is the causal agent of heartwater, a ruminant tropical fatal disease transmitted by Amblyomma ticks. Up to now, no effective vaccine is available due to a limited cross protection of vaccinal strains on field isolates mainly associated to a high genetic diversity of E. ruminantium within geographical locations. Thus, both characterization of E. ruminantium genetic population structure at worldwide and regional scale and estimation of E. ruminantium tick prevalence are important to delimitate better control strategies and improve heartwater monitoring strategies. In Section I, we developed two new qPCR s, pCS20 Sol1 T q M and Sol1 SG, to scree n E. ruminantium in Amblyomma ticks, which are powerful tools for: 1) heartwater epidemiological studies, 2) diagnosis in the context of heartwater clinical cases and 3) follow - up of experimental infections, both in ticks and hosts. The pCS20 Sol1 T q M qPCR was found as sensitive (up to 30 copies/ reaction ) and specific as the gold standard pCS20 nested PCR but less prone to sample contamination and less time - consuming. The whole method including the automated DNA extraction and pCS20 Sol1 T q M qPCR demonstrate d to be sensitive, specific and reproducible. It displayed the same limit of detection of the manual DNA extraction and pCS20 nested PCR, (60 copies/ reaction). Moreover, the development of a high - throughput automated DNA/RNA extraction makes the screen of any tick - borne pathogen in several tick species possible. The development of this new method allowed processing of a high number of tick samples collected in Mozambique that were then typed by Multi Locus Sequence Typing (MLST) and included into a worldwide E. ruminantium strain genetic structure study ( Section II ). Our study reveals the repeated occurrence of recombination between E. ruminantium genotypes and its important role in E. ruminantium genetic div ersity and evolution. Despite the unclear phylogeny and phylogeography due to