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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 (Table11).
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 rearrangements in different lineages. The linear chromosomes are very stable, with little variation among isolates. With the exception of a few differences at their right ends, the gene content of the chromosomes is essentially identical. Contrary to previous assumptions that genetic changes occurred only by slower point mutations, our initial WGS comparison of 4 strains showed that closely related B. burgdorferi strains frequently and more rapidly than by point mutation undergo horizontal exchange of genetic information (14). Evidence of this is also found in the newer genomes sequenced in this work.
The genetic diversity of B. burgdorferi appears to be maintained in part by neutral and adaptive processes, such as resistance to host immune defense mechanisms and host preferences (4, 9). Key questions remain on the genomic basis of these intra- and interspecific variations, particularly those associated with host resistance, high-frequency proliferation in wildlife populations, and invasiveness in humans.
Our long-range objectives are to develop a pangenomic picture of B. burgdorferi diversity (13) and to understand how the variations influence pathogenicity. We believe solutions for many of the problems associated with Lyme disease will come from scientific information, beginning with comparative genomics of this organism. Sequencing is a superb discovery tool whose greatest impact is realized when additional biology can implemented. Information from WGS of these well-characterized strains should provide a foundation for new hypotheses on the pathogenesis of Lyme disease and rational diagnostics and vaccines.
These sequences have been deposited in GenBank, and their Genome Project ID numbers and accession numbers are listed in Table Table11 and in Table S1 in the supplemental material, respectively.
This research was supported by the following grants from the National Institutes of Health: AI49003, AI37256, AI30071, GM083722, and RR03037. Additional funding was provided by the Lyme Disease Association and the Tami Fund.
Published ahead of print on 8 October 2010.
†Supplemental material for this article may be found at http://jb.asm.org/.