African relapsing Fever borreliae genomospecies revealed by comparative genomics

Abstract

Background: Relapsing fever borreliae are vector-borne bacteria responsible for febrile infection in humans in North America, Africa, Asia, and in the Iberian Peninsula in Europe. Relapsing fever borreliae are phylogenetically closely related, yet they differ in pathogenicity and vectors. Their long-term taxonomy, based on geography and vector grouping, needs to be re-apprised in a genomic context. We therefore embarked into genomic analyses of relapsing fever borreliae, focusing on species found in Africa.

Results: Genome-wide phylogenetic analyses group Old World Borrelia crocidurae, Borrelia hispanica, B. duttonii, and B. recurrentis in one clade, and New World Borrelia turicatae and Borrelia hermsii in a second clade. Accordingly, average nucleotide identity is 99% among B. duttonii, B. recurrentis, and B. crocidurae and 96% between latter borreliae and B. hispanica while the similarity is 86% between Old World and New World borreliae. Comparative genomics indicates that the Old World relapsing fever B. duttonii, B. recurrentis, B. crocidurae, and B. hispanica have a 2,514-gene pan genome and a 933-gene core genome that includes 788 chromosomal and 145 plasmidic genes. Analyzing the role that natural selection has played in the evolution of Old World borreliae species revealed that 55 loci were under positive diversifying selection, including loci coding for membrane, flagellar, and chemotaxis proteins, three categories associated with adaption to specific niches.

Conclusion: Genomic analyses led to a reappraisal of the taxonomy of relapsing fever borreliae in Africa. These analyses suggest that B. crocidurae, B. duttonii, and B. recurrentis are ecotypes of a unique genomospecies, while B. hispanica is a distinct species.

Keywords: Borrelia; genomics; phylogeny; relapsing fever; speciation.

Figure 1

Phylogenetic tree based on the Borrelia telomere resolvase gene sequence, separating the Lyme disease group from the recurrent fever group; and separating the Old World from the New World recurrent fever Borrelia. Only bootstrap values >80% are indicated at nodes. The bar indicates a 0.5% divergence in nucleotidic sequences.

Figure 2

Functional classification of the genes encoded by five recurrent fever Borrelia (chromosomal genes). The protein-coding sequences are classified according to categories determined in the cluster of orthologous group (COG) database, as indicated in the left-hand table.

Figure 3

Functional classification of plasmidic genes according to COG categories showing gene categories, which are missing in B. duttonii (dark blue symbol) and B. crocidurae (light blue symbol), compared to B. recurrentis (green symbol). Red arrows indicate known functions missing in B. recurrentis.

Figure 4

Primary concordance analysis. The tree shows the topology of Borrelia sp., grouped into the Lyme disease and relapsing fever group. Concordance factor values are indicated at nodes.