Ehrlichia ruminantium is the causative agent of heartwater, a major tick-borne disease of livestock in Africa that has been introduced in the Caribbean and is threatening to emerge and spread on the American mainland. We sequenced the complete genomes of two strains of E. ruminantium of differing phenotypes, strains Gardel (Erga; 1,499,920 bp), from the island of Guadeloupe, and Welgevonden (Erwe; 1,512,977 bp), originating in South Africa and maintained in Guadeloupe in a different cell environment. Comparative genomic analysis of these two strains was performed with the recently published parent strain of Erwe (Erwo) and other Rickettsiales (Anaplasma, Wolbachia, and Rickettsia spp.). Gene order is highly conserved between the E. ruminantium strains and with A. marginale. In contrast, there is very little conservation of gene order with members of the Rickettsiaceae. However, gene order may be locally conserved, as illustrated by the tuf operons. Eighteen truncated protein-encoding sequences (CDSs) differentiate Erga from Erwe/Erwo, whereas four other truncated CDSs differentiate Erwe from Erwo. Moreover, E. ruminantium displays the lowest coding ratio observed among bacteria due to unusually long intergenic regions. This is related to an active process of genome expansion/contraction targeted at tandem repeats in noncoding regions and based on the addition or removal of ca. 150-bp tandem units. This process seems to be specific to E. ruminantium and is not observed in the other Rickettsiales.Ehrlichia ruminantium is the causative agent of cowdriosis, or heartwater, in domestic and wild ruminants in sub-Saharan Africa; African islands, including Madagascar; and some of the lesser Caribbean islands (56). This tick-borne member of the Rickettsiales, an ␣-proteobacterium, is a small, gram-negative, aerobic, obligate intracellular pathogen of endothelial cells that can cause up to 90% mortality in susceptible animals. Heartwater is responsible for great economic losses in Africa (48) but also represents a threat to the American mainland owing to the presence of potentially transmitting ticks (8,17). The control strategy is based on vector eradication and immunization, a strategy possible only on islands, where the incoming flow of ticks is highly limited (53). Vaccine development therefore remains critical. The only available commercial vaccine relies on the risky and inappropriate infection of animals with infected blood followed by treatment with antibiotics (12). Attenuated and DNA vaccines were developed (20, 21, 33, 71), but they induce long-lasting protection only against homologous virulent strains while conferring limited protection against heterologous strains in the field. The main difficulty in developing efficient vaccines is the simultaneous field occurrence of various genotypes in limited geographical areas (39). Similarly, serodiagnosis of heartwater has long been hampered by a lack of specificity and sensitivity (45), although these have been greatly improved recently (34,36,65). Additional diagnos...