Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi

Abstract

Borrelia burgdorferi is a causative agent of Lyme disease in North America and Eurasia. The first complete genome sequence of B. burgdorferi strain 31, available for more than a decade, has assisted research on the pathogenesis of Lyme disease. Because a single genome sequence is not sufficient to understand the relationship between genotypic and geographic variation and disease phenotype, we determined the whole-genome sequences of 13 additional B. burgdorferi isolates that span the range of natural variation. These sequences should allow improved understanding of pathogenesis and provide a foundation for novel detection, diagnosis, and prevention strategies.Lyme disease is the most frequent tick-borne disease in North America and Europe (3,16,17). There are multiple variants of B. burgdorferi (1,7,15,20,21), the causative agent, but questions remain about how their variation correlates with different clinical manifestations. Whole-genome sequencing (WGS) can orient approaches to diagnostics and vaccines and help avoid potential host cross-reactivity. Improved diagnostics are needed because the best clinical sign, the erythema migrans skin rash, does not always occur. Diagnostic assays and vaccines (18) have been less than satisfactory. However, these were developed before WGS of microbes and the human genome. This project was stimulated by the initial finding of genotypes of B. burgdorferi associated with invasiveness/dissemination (15). This has been substantiated (7, 21).The sequencing of strain B31 (6, 8) has accelerated progress in Lyme disease research. We sequenced 13 additional isolates, chosen to cover a large fraction of the genetic and geographic diversity and obtained from humans and other natural hosts (Table 1).These genomes were sequenced by the random shotgun method as described previously, using Sanger DNA sequencing to an estimated 8-fold coverage (12). Approximately 10,000 and 6,000 successful reads for the small and medium insert plasmid libraries, respectively, were sequenced, representing a total of about 14 Mbp of sequencing data for each. All plasmids were sequenced to closure unless noted otherwise (see Table S1 in the supplemental material). Genome annotation was performed using the JCVI Prokaryotic Annotation Pipeline (www.jcvi.org/cms /research/projects/prokaryotic-annotation-pipeline/overview/).The B31 sequence showed that B. burgdorferi has many more replicons (DNA molecules) than other bacteria. Besides its 910-kbp linear chromosome, strain B31 has been shown to have 12 linear and 10 circular plasmids (5), expanding observations (2, 10) indicating that Borrelia bacteria universally harbor numerous plasmids, many essential for survival of the bacteria in mice and/or ticks (4). The newly sequenced genomes contain a total of 17,084,900 bp, averaging 1,314,223 bp/genome. Each strain carried between 13 and 21 plasmids (239 plasmids were sequenced, about half predicted to be linear replicons). At least 9 new plasmid types not in B31 were identified. Many plasmids underwent substantial r...

Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme Disease Bacterium

“…genomes and focused on the comparison of 14 conspecific genomes of the genospecies B. burgdorferi sensu stricto (B. burgdorferi s.s.) (Table 1) (Fraser et al 1997;Casjens et al 2000Casjens et al , 2011aCasjens et al , 2011bGlockner et al 2004Glockner et al , 2006Schutzer et al 2011). Ten of the B. burgdorferi s.s. genomes were from sympatric isolates from the northeastern United States (Table 1).…”

Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates

“…nov. are also frequent causes of this disease (9). To date, whole-genome sequences have been reported from 14 B. burgdorferi sensu stricto isolates (2,5,13) and one unnamed sensu lato species (3), and the chromosome and incomplete plasmid sequences have been reported for one B. afzelii and one B. bavariensis sp. nov. isolate (6,7).…”

BB0844, an RpoS-Regulated Protein, Is Dispensable for Borrelia burgdorferi Infectivity and Maintenance in the Mouse-Tick Infectious Cycle

“…The results indicated that bb0844 is located on a smaller replicon, most likely on a linear plasmid of 25 to 28 kbp, rather than on the chromosome (data not shown). Genomic sequences of several B. burgdorferi strains have recently been reported (40). BLAST analysis revealed a sequence with Ͼ99% identity to bb0844 on plasmid lp28-1 of strain WI91-23.…”

“…OspC types A, B, C, and K have the largest chromosomes, as indicated in the current study by the presence of bb0852. B31, a typical OspC type A strain, contains an extra 8.5 kbp at the right chromosomal end; Sh-2-82 and JD1, OspC types K and C, respectively, have chromosomes which are approximately 12 kbp longer than that of B31 (40). The chromosomes of Sh-2-82 and JD1 have not been sequenced, and thus, the precise nature of the right chromosomal ends in these strains beyond that of B31 is not currently known.…”

“…A majority of the chromosomal sequence and gene order is conserved among B. burgdorferi strains; however, the chromosomes vary in length. These differences were shown to be the result of variability in the right telomeric region (10,11) and have been confirmed by sequencing of additional B. burgdorferi genomes (40). It has been proposed that linear plasmid fragments were added to the right chromosomal telomere by means of nonhomologous recombination, after which portions of the transposed plasmid sequences underwent mutational decay (12,13,25).…”