Whole-Genome Sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii

Abstract

It has been known for decades that human Lyme disease is caused by the three spirochete species Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii. Recently, Borrelia valaisiana, Borrelia spielmanii, and Borrelia bissettii have been associated with Lyme disease. We report the complete genome sequences of B. valaisiana VS116, B. spielmanii A14S, and B. bissettii DN127.

GENOME ANNOUNCEMENT

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 (5–8, 16, 17). 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 isolates (1, 9, 19), 2 B. afzelii isolates (4, 11), 2 B. garinii isolates (4, 11), 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, 18), 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 Table 1.

Table 1.

B. valaisiana, B. bissettii, and B. spielmanii sequence accession numbers

Replicon namea	Accession no. for strain (GPID)b
	B. valaisiana VS116 (19843)	B. bissettii DN127 (29363)	B. spielmanii A14S (28635)
Chromosome	ABCY02000001c	CP002746	ABKB02000001 to -13c
lp17	CP001439	CP002756	CP001468
lp25	CP001437	CP002757
lp28-2
lp28-3	CP001440	CP002758	CP001471
lp28-4		CP002759	CP001470
lp28-7		CP002760
lp28-8	CP001442		CP001465
lp36	CP001436		CP001466
lp38			CP001464
lp54	CP001433	CP002761	CP001469
lp56		CP002762
cp9	CP001438e	CP002755	ABKB02000016,cABKB02000020c,e
cp26	CP001432	CP002747	CP001467
cp32-3		CP002749	ABKB02000026c
cp32-4		CP002750
cp32-5	CP001441	CP002751	ABKB02000031c
cp32-6		CP002752
cp32-7	CP001434	CP002753
cp32-quad (cp32-9)f		CP002754
cp32-10	CP001435
cp32-11		CP002748
cp32-12		Fused to cp32-quad	ABKB02000021c
cp32-13		Fused to cp32-quad
Unidentified plasmid contigs			ABKB02000014, -15, -17 to -19, -22 to -25, -27 to -30, -32 to -41c,d

^aPlasmids are named according to their PFam32 partition/replication protein (see Casjens et al. [3]).

^bGenome project ID number.

^cDraft sequence; contigs not joined.

^dAll but ABKC02000036 are cp32-like.

^eUnlike other cp9 plasmids in B. burgdorferi, VS116 cp9 (and probably a very similar sequence in A14S) carries a parA-type gene in the partition gene cluster.

^fThe DN127 plasmid that carries cp32-9, cp32-12, and cp32-13 type partition genes (i.e., is a fusion between these three plasmids and a fourth whose partition genes are deleted) was named cp32-quad.