First insights in the variability of Borrelia recurrentis genomes

Abstract

Background
Borrelia recurrentis is the causative agent of louse-borne relapsing fever, endemic to the Horn of Africa. New attention was raised in Europe, with the highest number of cases (n = 45) reported among migrants in 2015 in Germany and sporadically from other European countries. So far only one genome was sequenced, hindering the development of specific molecular diagnostic and typing tools. Here we report on modified culture conditions for B. recurrentis and the intraspecies genome variability of six isolates isolated and cultured in dif- ferent years in order to explore the possibility to identify new targets for typing and examine the molecular epidemiology of the pathogen.
Methodology/Principal findings
Two historical isolates from Ethiopia and four isolates from migrants from Somalia (n = 3) and Ethiopia (n = 1) obtained in 2015 were cultured in MPK-medium supplemented with 50% foetal calf serum. Whole DNA was sequenced using Illumina MiSeq technology and analysed using the CLC Genomics Workbench and SPAdes de novo assembler. Compared to the reference B. recurrentis A1 29–38 SNPs were identified in the genome distributed on the chromosome and plasmids. In addition to that, plasmids of differing length, compared to the available reference genome were identified.
Conclusions/Significance
The observed low genetic variability of B. recurrentis isolates is possibly due to the adapta- tion to a very conserved vector-host (louse-human) cycle, or influenced by the fastidious nature of the pathogen and their resistance to in vitro growth. Nevertheless, isolates obtained in 2015 were bearing the same chromosomal SNPs and could be distinguished from the historical isolates by means of whole genome sequencing, but not hitherto used yping methods. This is the first study examining the molecular epidemiology of B. recurren- tis and provides the necessary background for the development of better diagnostic tools.

Author summary

Louse-borne relapsing fever, as the name suggests, is the only relapsing fever transmitted by lice, and caused by the spirochaete Borrelia recurrentis. Today it is endemic to the Horn of Africa, but due to the cosmopolitan nature of the vector, the pathogen still bears epi- demic potential to spread globally among vulnerable populations. The most recent account of that has been observed among migrants arriving to Europe in 2015. Up to date, only one strain was sequenced, thus hampering the development of species-specific typing tools. We employed state-of-the-art high-throughput sequencing to six B. recurrentis iso- lates obtained at different time-points and currently available in culture. Our aim was to address the question of genome variability of this pathogen at the highest resolution and provide information necessary for the development of specific typing tools. B. recurrentis has highly conserved genomes, differing in 29–38 SNPs compared to the reference genome B. recurrentis A1, all identified outside the loci currently developed and used for relapsing fever Borrelia typing. Therefore, applying these typing methods would render them indistinguishable, while at the SNP level we found a distinction between isolates obtained in 2015 from migrants and the two historical isolates. Our data provide first insights in the genome variability and baseline information necessary for further studies of the molecular epidemiology of the pathogen and for the development of improved diagnostic tools.