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Borrelia mayonii , a  Borrelia burgdorferi sensu lato  (Bbsl) genospecies, was recently identified as a cause of Lyme borreliosis (LB) among patients from the upper midwestern United States. By microscopy and PCR, spirochete/genome loads in infected patients were estimated at 10 5  to 10 6  per milliliter of blood. Here, we present the full chromosome and plasmid sequences of two  B .  mayonii  isolates, MN14-1420 and MN14-1539, cultured from blood of two of these patients. Whole genome sequencing and assembly was conducted using PacBio long read sequencing (Pacific Biosciences RSII instrument) followed by hierarchical genome-assembly process (HGAP). The  B .  mayonii  genome is ~1.31 Mbp in size (26.9% average GC content) and is comprised of a linear chromosome, 8 linear and 7 circular plasmids. Consistent with its taxonomic designation as a new Bbsl genospecies, the  B .  mayonii  linear chromosome shares only 93.83% average nucleotide identity with other genospecies. Both  B .  mayonii  genomes contain plasmids similar to  B .  burgdorferi sensu stricto  lp54, lp36, lp28-3, lp28-4, lp25, lp17, lp5, 5 cp32s, cp26, and cp9. The  vls  locus present on lp28-10 of  B .  mayonii  MN14-1420 is remarkably long, being comprised of 24 silent  vls  cassettes. Genetic differences between the two  B .  mayonii  genomes are limited and include 15 single nucleotide variations as well as 7 fewer silent  vls  cassettes and a lack of the lp5 plasmid in MN14-1539. Notably, 68 homologs to proteins present in  B .  burgdorferi sensu stricto  appear to be lacking from the  B .  mayonii  genomes. These include the complement inhibitor, CspZ (BB_H06), the fibronectin binding protein, BB_K32, as well as multiple lipoproteins and proteins of unknown function. This study shows the utility of long read sequencing for full genome assembly of Bbsl genomes, identifies putative genome regions of  B .  mayonii  that may be linked to clinical manifestation or tissue tropism, and provides a valuable resource for pathogenicity, diagnostic and vaccine studies.

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii