Genome Sequence of Borrelia crocidurae Strain 03-02, a Clinical Isolate from Senegal.

The draft genome sequence of Borrelia crocidurae strain 03-02, a blood isolate from a febrile Senegalese patient, comprises a 920,021-bp linear chromosome (27.7% G+C content), 32 tRNAs, 818 open reading frames, and one cluster of regularly interspaced short palindromic repeats. Its genotype differs from that of the Achema reference strain.

GENOME ANNOUNCEMENT

Borrelia crocidurae is a spirochete responsible for tick-borne relapsing fever in West Africa (1). It is maintained in a triangle that involves humans, Ornithodoros sonrai soft ticks, and rodents (2, 3). Here, we report the draft genome of an isolate from a febrile patient with relapsing fever in rural Senegal (3). For isolation, blood was inoculated in Barbour-Stoenner-Kelly-H (BSK-H) medium (Sigma, Saint-Quentin-Fallavier, France) supplemented with 10% heat-inactivated rabbit serum (Eurobio, Courtaboeuf, France) at 32°C (4).

B. crocidurae strain 03-02 (deposited in the Collection de Souches de l’Unité des Rickettsies, CSUR P235) genome was sequenced by combining paired-end libraries and a bar code strategy in order to be mixed with 11 other genomic projects constructed according to the Nextera XT library kit using high-throughput MiSeq Technology (Illumina, San Diego, CA). Genomic DNA extracted using a phenol-chloroform protocol was quantified by a Qubit assay at 100 ng/µl, and 1 ng was used as input. The “tagmentation” step generated inserts in the range of 700 bp to 1 kb, validated on a Caliper Lab Chip (PerkinElmer). Lab chip PCR amplification completed the tag adapters and introduced dual-index bar codes. After purification on Ampere beads, the library was normalized on specific beads, according to the Nextera XT protocol. The pooled single-strand library was loaded onto the reagent cartridge and then onto the MiSeq instrument, along with the flow cell. Automated cluster generation and paired-end sequencing with dual-index reads was performed in a single 39-h 2 × 250 bp run. The total run information of 7.64 Gb was obtained from a 524,000/mm2 cluster density, with a cluster passing quality control filters of 96.10% (12,380,000 clusters). Within this run, the index representation for B. crocidurae strain Achema was determined to 2.97%. A total of 367,964 paired-end reads were mapped to B. crocidurae strain Achema (4) using the CLC Genomics Workbench software package 6.0.1 (CLC bio, Denmark) and generated one scaffold. A preliminary open reading frame (ORF) prediction was conducted by automated annotation with Prokka (http://www.vicbioinformatics.com/software.prokka.shtml) and RAST (5). Clusters of regularly interspaced short palindromic repeats (CRISPRs) were detected using the CRISPR finder (http://crispr.u-psud.fr/Server/).

The 920,021-bp linear chromosome of B. crocidurae strain 03-02 is 0.6% larger than that of strain Achema (919,477 bp) (4), yet it contains 818 ORFs (85.26% of the proteins it encodes are listed in the COG database) compared to 865 ORFs for strain Achema (79% of the proteins it encodes are listed in the COG database) and 32 tRNAs. Its G+C content is 27.70%. Accordingly, the nucleotide similarity at the genome level between B. crocidurae strains Achema and 03-02 is 98.88%. In silico multispacer sequence typing of B. crocidurae 03-02 strain found sequence type 6 (ST6), a genotype previously found in patients with relapsing fever in rural Senegal. It differed in the five spacer sequences used from the type strain Achema, isolated from an Ornithodoros tick from Mauritania (6). No antibiotic resistance genes were found in the genome using the ResFinder tool.

Nucleotide sequence accession number.

The genome sequence from B. crocidurae strain 03-02 has been deposited in EMBL-EBI under the accession no. CCXD00000000.