Chromosome and Linear Plasmid Sequences of a 2015 Human Isolate of the Tick-Borne Relapsing Fever Spirochete, Borrelia turicatae

Borrelia nietonii sp. nov.: Relapsing Fever Spirochetes Transmitted By the Tick Ornithodoros hermsi Designated Previously as Borrelia hermsii Genomic Group II

Background: The taxonomic status of the relapsing fever spirochete Borrelia hermsii in western North America was established in 1942 and based solely on its specific association with the soft tick vector Ornithodoros hermsi. Multilocus sequence typing (MLST) of the 16S rRNA, flaB, gyrB, glpQ, and 16S-23S rRNA intergenic spacer of B. hermsii isolates collected over many years from various geographic locations and biological sources identified two distinct clades designated previously as B. hermsii Genomic Group I (GGI) and Genomic Group II (GGII). To better assess the taxonomic relationship of these two genomic groups to each other and other species of Borrelia, DNA sequences of the entire linear chromosome were determined. Materials and Methods: Genomic DNA samples were prepared from 11 spirochete isolates grown in Barbour-Stoenner-Kelly-H medium. From these preparations, DNA sequences of the entire linear chromosome of two isolates of B. hermsii belonging to each genomic group and seven additional species were determined. Results: Chromosomal sequences of four isolates of B. hermsii contained 919,212 to 922,307 base pairs. DNA sequence identities between the two genomic groups of B. hermsii were 95.86-95.99%, which were more divergent than chromosomal sequences comparing Borrelia parkeri and Borrelia turicatae (97.13%), Borrelia recurrentis and Borrelia duttonii (97.07%), and Borrelia crocidurae and B. duttonii (97.09%). The 3' end of the chromosome of the two GGII isolates also contained a unique intact oppA gene absent from all other species examined. Conclusion: Previous MLST and the chromosomal sequences presented herein support the division of the B. hermsii species complex into two species, B. hermsii sensu stricto ( = GGI) and Borrelia nietonii sp. nov. ( = GGII). We name this unique relapsing fever spirochete in honor of our late friend and colleague Dr. Nathan Nieto for his outstanding contributions to our understanding of tick-borne relapsing fever.

A high fidelity approach to assembling the complex Borrelia genome

BACKGROUND

Bacteria of the Borrelia burgdorferi sensu lato (s.l.) complex can cause Lyme borreliosis. Different B. burgdorferi s.l. genospecies vary in their host and vector associations and human pathogenicity but the genetic basis for these adaptations is unresolved and requires completed and reliable genomes for comparative analyses. The de novo assembly of a complete Borrelia genome is challenging due to the high levels of complexity, represented by a high number of circular and linear plasmids that are dynamic, showing mosaic structure and sequence homology. Previous work demonstrated that even advanced approaches, such as a combination of short-read and long-read data, might lead to incomplete plasmid reconstruction. Here, using recently developed high-fidelity (HiFi) PacBio sequencing, we explored strategies to obtain gap-free, complete and high quality Borrelia genome assemblies. Optimizing genome assembly, quality control and refinement steps, we critically appraised existing techniques to create a workflow that lead to improved genome reconstruction.

RESULTS

Despite the latest available technologies, stand-alone sequencing and assembly methods are insufficient for the generation of complete and high quality Borrelia genome assemblies. We developed a workflow pipeline for the de novo genome assembly for Borrelia using several types of sequence data and incorporating multiple assemblers to recover the complete genome including both circular and linear plasmid sequences.

CONCLUSION

Our study demonstrates that, with HiFi data and an ensemble reconstruction pipeline with refinement steps, chromosomal and plasmid sequences can be fully resolved, even for complex genomes such as Borrelia. The presented pipeline may be of interest for the assembly of further complex microbial genomes.

First detection of Borrelia and Rickettsia species from Ornithodoros ticks in the Republic of Korea

Ticks are considered important vectors among arthropods and are linked to serious medical and veterinary health problems. In this study, we investigated tick-borne pathogens (TBPs) of Ornithodoros (Carios) sawaii and a newly identified Ornithodoros species from migratory bird nests in the uninhabited islands of the Republic of Korea (ROK). Ticks were collected from seabird nests with soil using a Tullgren funnel. Polymerase chain reaction (PCR) was performed using specific primer sets targeting genes of Borrelia spp., Rickettsia sp., Anaplasma phagocytophilum, Anaplasma bovis, and Bartonella spp. for molecular identification of TBPs, and two pathogens, Borrelia sp. and Rickettsia sp. were detected via PCR. Sequence data were analyzed and a phylogenetic analysis was conducted using the maximum-likelihood method in MEGA v.7. The detection rate of Borrelia sp. in O.(C.) sawaii was 6.8 % (5/74), and that of Rickettsia sp. in O. sawaii and the newly identified Ornithodoros species. was 36.5 % (27/74). Sequencing analysis revealed that the 16S ribosomal (r) RNA and flagellin genes of Borrelia sp., and the citrate synthase (gltA) and 17-kDa antigen gene of Rickettsia sp. were closely phylogenetically related to those of Borrelia turicatae and Rickettsia asembonensis. This is the first report identifying Borrelia sp. and Rickettsia sp. from O. sawaii, and Rickettsia sp. from the newly identified Ornithodoros species in the ROK, and these results imply that soft ticks (O. sawaii, and the newly identified Ornithodoros species) may function as pathogen carriers with important implications for public health throughout their distribution areas in Asia.

Isolation of Borrelia miyamotoi and other Borreliae using a modified BSK medium

Borrelia spirochetes are the causative agents of Lyme borreliosis (LB) and relapsing fever (RF). Despite the steady rise in infections and the identification of new species causing human illness over the last decade, isolation of borreliae in culture has become increasingly rare. A modified Barbour-Stoenner-Kelly (BSK) media formulation, BSK-R, was developed for isolation of the emerging RF pathogen, Borrelia miyamotoi. BSK-R is a diluted BSK-II derivative supplemented with Lebovitz’s L-15, mouse and fetal calf serum. Decreasing the concentration of CMRL 1066 and other components was essential for growth of North American B. miyamotoi. Sixteen B. miyamotoi isolates, originating from Ixodes scapularis ticks, rodent and human blood collected in the eastern and upper midwestern United States, were isolated and propagated to densities > 10⁸ spirochetes/mL. Growth of five other RF and ten different LB borreliae readily occurred in BSK-R. Additionally, primary culture recovery of 20 isolates of Borrelia hermsii, Borrelia turicatae, Borrelia burgdorferi and Borrelia mayonii was achieved in BSK-R using whole blood from infected patients. These data indicate this broadly encompassing borreliae media can aid in in vitro culture recovery of RF and LB spirochetes, including the direct isolation of new and emerging human pathogens.

Transgenic functional complementation with a transmission -associated protein restores spirochete infectivity by tick bite

The relapsing fever spirochete Borrelia hermsii and the Lyme disease spirochete Borrelia burgdorferi sensu stricto each produces an abundant, orthologous, outer membrane protein, Vtp and OspC, respectively, when transmitted by tick bite. Gene inactivation studies have shown that both proteins are essential for spirochete infectivity when transmitted by their respective tick vectors. Therefore, we transformed a vtp-minus mutant of B. hermsii with ospC from B. burgdorferi and examined the behavior of this transgenic spirochete in its soft tick vector Ornithodoros hermsi. IFA staining indicated up to 97.8 % of the transgenic B. hermsii upregulated OspC in the ticks' salivary glands compared to no more than 12.8 % in the midgut, similar to our previous findings with wild-type B. hermsii producing Vtp. Transformation with ospC also restored B. hermsii infectivity to mice when fed upon by infected ticks. Previous sequence analysis of Vtp for 79 isolates and DNA samples of B. hermsii in our laboratory showed this protein is highly polymorphic with 9 divergent amino acid types, yet strikingly the signal peptide is identical among all samples and the same for all OspC signal peptides for B. burgdorferi and related species examined to date. Searches in multiple genome sequences for other species of relapsing fever spirochetes failed to find the same signal peptide sequence to help identify potential transmission-associated proteins. However, some candidate signal peptides with highly similar sequences were found and worthy of future efforts with other species. While OspC of B. burgdorferi restored infectivity to a Vtp-minus mutant of B. hermsii, the functions of these proteins are not known. Our results should stimulate investigators to search for orthologous transmission-associated proteins in other tick-borne spirochetes to better understand how this group of pathogens has coevolved with diverse tick vectors.

Anaplasmataceae, Borrelia and Hepatozoon agents in ticks (Acari: Argasidae, Ixodidae) from Chile

Microorganisms harbored by Chilean autochthonous ticks have been scarcely studied and current knowledge is restricted to three species of hard ticks only. The current study aimed to assess the presence of Anaplasmataceae, Borrelia and Hepatozoon agents in ticks collected directly from the environment, on reptiles, birds and mammals in twelve localities from northern, central and southern regions of the country and Antarctica. Ticks were identified by means of a morphological and molecular approach. PCR detections point the occurrence of an Anaplasma-like agent and a relapsing fever Borrelia sp. in Ornithodoros spheniscus; an Ehrlichia sp. and a Hepatozoon sp. in Ornithodoros atacamensis; "Candidatus Neoehrlichia chilensis", Borrelia burgdorferi sensu lato (s. l.), and Hepatozoon in Ixodes ticks morphologically related to the Ixodes sigelos group; and B. burgdorferi s. l. in Ixodes auritulus. Supported by phylogenetic analyses of characterized microorganisms, this study introduces putative vector roles and initial evidence on possible new agents detected in Chilean ticks.

Detection of Tickborne Relapsing Fever Spirochete, Austin, Texas, USA

In March 2017, a patient became febrile within 4 days after visiting a rustic conference center in Austin, Texas, USA, where Austin Public Health suspected an outbreak of tickborne relapsing fever a month earlier. Evaluation of a patient blood smear and molecular diagnostic assays identified Borrelia turicatae as the causative agent. We could not gain access to the property to collect ticks. Thus, we focused efforts at a nearby public park, <1 mile from the suspected exposure site. We trapped Ornithodoros turicata ticks from 2 locations in the park, and laboratory evaluation resulted in cultivation of 3 B. turicatae isolates. Multilocus sequencing of 3 chromosomal loci (flaB, rrs, and gyrB) indicated that the isolates were identical to those of B. turicatae 91E135 (a tick isolate) and BTE5EL (a human isolate). We identified the endemicity of O. turicata ticks and likely emergence of B. turicatae in this city.

Primordial origin and diversification of plasmids in Lyme disease agent bacteria

Background

With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparative analysis of plasmids in eleven Borreliella (also known as Borrelia burgdorferi sensu lato) species.

Results

We sequenced the complete genomes of two B. afzelii, two B. garinii, and individual B. spielmanii, B. bissettiae, B. valaisiana and B. finlandensis isolates. These individual isolates carry between seven and sixteen plasmids, and together harbor 99 plasmids. We report here a comparative analysis of these plasmids, along with 70 additional Borreliella plasmids available in the public sequence databases. We identify only one new putative plasmid compatibility type (the 30th) among these 169 plasmid sequences, suggesting that all or nearly all such types have now been discovered. We find that the linear plasmids in the non-B. burgdorferi species have undergone the same kinds of apparently random, chaotic rearrangements mediated by non-homologous recombination that we previously discovered in B. burgdorferi. These rearrangements occurred independently in the different species lineages, and they, along with an expanded chromosomal phylogeny reported here, allow the identification of several whole plasmid transfer events among these species. Phylogenetic analyses of the plasmid partition genes show that a majority of the plasmid compatibility types arose early, most likely before separation of the Lyme agent Borreliella and relapsing fever Borrelia clades, and this, with occasional cross species plasmid transfers, has resulted in few if any species-specific or geographic region-specific Borreliella plasmid types.

Conclusions

The primordial origin and persistent maintenance of the Borreliella plasmid types support their functional indispensability as well as evolutionary roles in facilitating genome diversity. The improved resolution of Borreliella plasmid phylogeny based on conserved partition-gene clusters will lead to better determination of gene orthology which is essential for prediction of biological function, and it will provide a basis for inferring detailed evolutionary mechanisms of Borreliella genomic variability including homologous gene and plasmid exchanges as well as non-homologous rearrangements.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4597-x) contains supplementary material, which is available to authorized users.

Isolation and molecular characterization of a relapsing fever Borrelia recovered from Ornithodoros rudis in Brazil

In South America, early reports from more than 50 years ago incriminated Ornithodoros rudis as vector of Borrelia venezuelensis, an agent of tick-borne relapsing fever (TBRF). Herein we report the rediscovery of O. rudis by means of morphological, biological and molecular analyses, which also comprise the first report of this tick species in Brazil. Phylogenetic analysis using partial fragments of mitochondrial 16S rRNA gene suggested that O. rudis forms a monophyletic group with Ornithodoros erraticus. By using laboratory rodents as hosts, we isolated a relapsing fever Borrelia from an infected O. rudis female. Phylogenetic analysis inferred from the rrs, flaB, and glpQ genes of Borrelia spp. placed the spirochete harbored by O. rudis closely related to Borrelia turicatae. Until further genetic evidence is not obtained we are referring to this O. rudis spirochete as B. venezuelensis. This is the first in vitro isolation of a TBRF Borrelia from South America. The presence of O. rudis in Brazil should not be overlooked, since this tick has been historically implicated in human cases of TBRF in Colombia, Panama, and Venezuela. This study provides new reports of O. rudis and B. venezuelensis after decades of scientific silence on these agents.

Chromosome and Large Linear Plasmid Sequences of a Borrelia miyamotoi Strain Isolated from Ixodes pacificus Ticks from California

Borrelia miyamotoi, a relapsing fever group spirochete, is an emerging tick-borne pathogen. It has been identified in ixodid ticks across the Northern Hemisphere, including the West Coast of the United States. We describe the chromosome and large linear plasmid sequence of a B. miyamotoi isolate cultured from a California field-collected Ixodes pacificus tick.

Diagnosis and Management of Borrelia turicatae Infection in Febrile Soldier, Texas, USA

In August 2015, a soldier returned from field exercises in Texas, USA, with nonspecific febrile illness. Culture and sequencing of spirochetes from peripheral blood diagnosed Borrelia turicatae infection. The patient recovered after receiving doxycycline. No illness occurred in asymptomatic soldiers potentially exposed to the vector tick and prophylactically given treatment.

Toward a Complete North American Borrelia miyamotoi Genome

Borrelia miyamotoi, of the relapsing-fever spirochete group, is an emerging tick-borne pathogen causing human illness in the northern hemisphere. Here, we present the chromosome, eight extrachromosomal linear plasmids, and a draft sequence for five circular and one linear plasmid of a Borrelia miyamotoi strain isolated from an Ixodes sp. tick from Connecticut, USA.