Comparative Genomic Analysis of Three Strains of Ehrlichia ruminantium Reveals an Active Process of Genome Size Plasticity

Abstract

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...

The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes

“…Indeed, the duplicationloss model suggests that the background frequency of tandem duplications is high, but that the copy number is normally kept in balance by an equally rapid collapse unless there is selection for more than one copy (36,37). Speaking against such a scenario is that the tra clusters are not situated in tandem, that there are few tandem gene repeats inside the clusters, and that the sizes of the repeated clusters is Ͼ10-fold longer than normally found for tandem repeats, such as for example in E. ruminantium (38,39). Furthermore, subsequent intragenomic recombination events must be invoked to explain the current distribution of the tra clusters across the genome.…”

Identification of a Glycosylated Ehrlichia canis 19-Kilodalton Major Immunoreactive Protein with a Species-Specific Serine-Rich Glycopeptide Epitope

“…Interestingly, the VLPT ortholog that we identified in E. canis in this study lacks the tandem repeats found in the E. chaffeensis VLPT gene, but it has a Ser/Thr/Glu-rich patch that is similar in size and composition to that of a single VLPT repeat unit. The addition and deletion of tandem repeats are considered a major source of change and instability in ehrlichial genomes (11). The fact that the E. canis gp19 protein lacks tandem repeats while the E. chaffeensis VLPT protein has variable numbers is indicative of these genes being affected by this process.…”

“…The genomes of E. canis and other organisms in the genus, including Ehrlichia chaffeensis and Ehrlichia ruminantium, exhibit a high degree of genomic synteny, paralogous protein families, a large proportion of proteins with transmembrane helices and/or signal sequences, tandem repeats and ankyrin domains in proteins associated with host-pathogen interactions, and a unique serine-threonine bias associated with a potential for O glycosylation and phosphorylation (6,10,11,18). A small subset of the approximately 1,000 proteins (including hypothetical proteins) encoded by each of these genomes is recognized by antibody (8,20,25,32).…”

“…Extensive variability in the number and/or sequence of tandem repeats in the E. chaffeensis immunoreactive proteins (gp120, gp47, and VLPT) as well as E. canis gp36 is well documented (5,7,8,32). The presence of tandem repeats in both coding and noncoding regions of the genome has been linked to an active process of expansion and reduction of ehrlichial genomes (11) and is considered a major source of genomic change and instability (4).…”

Advances in the genomics of ticks and tick-borne pathogens

“…However, differences also emerge relating to host pathology, the presence or absence of transovarial transmission and adaptation to a haematophagous vector [3], as well as the expansion of families of immunodominant outer membrane proteins, facilitating antigenic variation. The generation of multiple E. ruminantium genome sequences has enabled a third series of comparative approaches [4,5] (Frutos et al, this issue) to understanding the active process of genome evolution.…”