Plasmid diversity and phylogenetic consistency in the Lyme disease agent Borrelia burgdorferi

Abstract

BackgroundBacteria from the genus Borrelia are known to harbor numerous linear and circular plasmids. We report here a comparative analysis of the nucleotide sequences of 236 plasmids present in fourteen independent isolates of the Lyme disease agent B. burgdorferi.ResultsWe have sequenced the genomes of 14 B. burgdorferi sensu stricto isolates that carry a total of 236 plasmids. These individual isolates carry between seven and 23 plasmids. Their chromosomes, the cp26 and cp32 circular plasmids, as well as the lp54 linear plasmid, are quite evolutionarily stable; however, the remaining plasmids have undergone numerous non-homologous and often duplicative recombination events. We identify 32 different putative plasmid compatibility types among the 236 plasmids, of which 15 are (usually) circular and 17 are linear. Because of past rearrangements, any given gene, even though it might be universally present in these isolates, is often found on different linear plasmid compatibility types in different isolates. For example, the arp gene and the vls cassette region are present on plasmids of four and five different compatibility types, respectively, in different isolates. A majority of the plasmid types have more than one organizationally different subtype, and the number of such variants ranges from one to eight among the 18 linear plasmid types. In spite of this substantial organizational diversity, the plasmids are not so variable that every isolate has a novel version of every plasmid (i.e., there appears to be a limited number of extant plasmid subtypes).ConclusionsAlthough there have been many past recombination events, both homologous and nonhomologous, among the plasmids, particular organizational variants of these plasmids correlate with particular chromosomal genotypes, suggesting that there has not been rapid horizontal transfer of whole linear plasmids among B. burgdorferi lineages. We argue that plasmid rearrangements are essentially non-revertable and are present at a frequency of only about 0.65% that of single nucleotide changes, making rearrangement-derived novel junctions (mosaic boundaries) ideal phylogenetic markers in the study of B. burgdorferi population structure and plasmid evolution and exchange.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3553-5) contains supplementary material, which is available to authorized users.

Direct Diagnostic Tests for Lyme Disease

“…genome is AT-rich (approximately 30%), and nearly half of it consists of linear and circular plasmids. Borrelia burgdorferi isolates an average of 17 such plasmids, with up to 21 for the B31 type strain [33]. Thus, Borrelia genomes are among the most complex and challenging bacterial human-pathogenic genomes to sequence and analyze.…”

Whole genome sequence and comparative analysis ofBorrelia burgdorferiMM1

“…The MM1 lp54 plasmid subtype was identified following the criteria by Casjens et al . [24] . Dot plot analysis was performed to identify large (>400 bp) insertions, inversions or deletions in MM1 lp54 plasmid relative to lp54 subtypes.…”

“…In addition, MM1 carries cp32-5 PFam32 type, which is not encoded by B31 plasmids, but is encoded by the circular plasmids of N40 and present in strains JD1 in fusion with cp32-5 as cp32-1+5 (Table 4) [37] . spielmanii A14S), code N is initially given and later revised to "RS" [24] . Consistently, we designate "RS" as the code for MM1 lp28-8 plasmid.…”

“…MM1 and N40 lp54 plasmids have conserved gene order throughout their length. They do not carry insertions, inversions or deletions larger than 400 bps and inter-plasmid DNA exchanges relative to one another [24] , therefore, MM1 lp54 plasmid appears to be a type II lp54.…”

“…The PFam32 protein from what would eventually be identified as the MM1 lp28-8 plasmid shared only a 60% amino acid sequence identity with PFam32 sequence type from B31 and JD1 cp32-3 plasmids. Meanwhile a protein BLAST against the NCBI non-redundant protein database, revealed it as fully identical to PFam32 type on B. burgdorferi 94a lp28-8 plasmid.The MM1 lp54 plasmid subtype was identified following the criteria by Casjens et al [22]. Dot plot analysis was performed to identify large (>400 bp) insertions, inversions or deletions in MM1 lp54 plasmid relative to lp54 subtypes.…”