The bacteria that cause human Lyme disease belong to a group of at least 15 species, referred to as Borrelia burgdorferi
sensu lato, or the Lyme disease agent bacterial group (20
). Among these, B. burgdorferi
sensu stricto causes Lyme disease in North America, while in Europe and eastern Asia Borrelia afzelii
, Borrelia garinii
, and Borrelia bavariensis
sp. nov. are the best-known causes (reference 15
and references therein); however, more recently, Borrelia bissettii
, Borrelia lusitaniae
, Borrelia spielmanii
, and Borrelia valaisiana
have been isolated from Lyme disease patients (5
). Other species in this bacterial group, such as Borrelia japonica
and Borrelia sincia
in Asia, have not been associated with human disease. To date, genome sequences have been reported for 14 B. burgdorferi
), 2 B. afzelii
), 2 B. garinii
), 1 B. bavariensis
sp. nov. isolate (10
), and 1 isolate of unassigned species (2
We report here the complete genome sequences for three additional Borrelia
species: B. valaisiana
isolate VS116 (from an Ixodes rinicus
tick [Switzerland]) (14
), B. bissettii
isolate DN127 clone 9 (Ixodes pacificus
tick [northern California]) (12
), and B. spielmanii
isolate A14S (human skin [The Netherlands]) (21
). DNA samples from low-passage isolates were sequenced to minimize plasmid loss, and genomes were sequenced to about 8-fold coverage as previously described (13
). Genome annotation was performed using the JCVI Prokaryotic Annotation Pipeline (www.jcvi.org/cms/research/projects/annotation-service/overview/
). The DN127 chromosome and 35 of 39 plasmid sequence contigs were closed, but in order to maximize the use of available funds, the sequences of a few replicons were not closed and some gaps remained in these sequences (two chromosomes and one cp9 and three cp32 plasmids, because they are much less variable than the other plasmids).
These three genome sequences include 3,914,891 bp in total (1,258,865, 1,403,466, and 1,252,560 bp for strains VS116, DN127, and A14S, respectively), with an average of 1,304,497 bp/genome. Like the sequences of other Borrelia
species, they include numerous linear plasmids (6, 7, and 7, respectively) and circular plasmids (2, 2, and 2, respectively). Plasmid numbers in these three strains range from 11 in VS116 and 12 in A14S to 16 in DN127. Plasmids that are very similar to B. burgdorferi
sensu stricto cp26, cp32 (7 in DN127, versus 3 in the other two strains analyzed), and lp54 plasmids are present in each of these isolates, and DN127 also contains an unusual fusion of four partial cp32 plasmids. Plasmids with predicted lp17 compatibility (3
) are also present in all three genomes, making it the only other plasmid type, in addition to cp26 and lp54, to be found in all 23 B. burgdorferi
sensu lato sequenced genomes. However, the gene contents of the lp17s are much more variable than the other universally present plasmids.
The detailed analyses of these genome sequences will be a major step forward in attaining a complete understanding of B. burgdorferi sensu lato diversity. They will contribute to the development of species- and group-specific vaccines and diagnostic tools, as well as inform us whether these species are in genetic contact with the more-common Lyme disease-associated agents. These foundational sequencing efforts can now be further developed with the use of evolving deep sequencing methods.
Nucleotide sequence accession numbers.
The nucleotide sequences for these three strains and relevant replicons have been deposited in the GenBank database, and their accession numbers are listed in .
B. valaisiana, B. bissettii, and B. spielmanii sequence accession numbers