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Hepner S, Kuleshov K, Tooming-Kunderud A, Alig N, Gofton A, Casjens S, Rollins RE, Dangel A, Mourkas E, Sheppard SK, Wieser A, Hübner J, Sing A, Fingerle V, Margos G. A high fidelity approach to assembling the complex Borrelia genome. BMC Genomics 2023; 24:401. [PMID: 37460975 DOI: 10.1186/s12864-023-09500-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023] Open
Abstract
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.
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Affiliation(s)
- Sabrina Hepner
- German National Reference Centre for Borrelia, Oberschleissheim, Germany.
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany.
| | | | - Ave Tooming-Kunderud
- Department of Biosciences, Norwegian Sequencing Centre at Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Nikolas Alig
- German National Reference Centre for Borrelia, Oberschleissheim, Germany
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | | | - Sherwood Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Robert E Rollins
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | | | | | - Andreas Wieser
- Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
- Imunology, Infectious Disease and Pandemic Research IIP, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich, Germany
| | - Johannes Hübner
- Dr. Von Hauner Children's Hospital, LMU Munich, Munich, Germany
| | - Andreas Sing
- German National Reference Centre for Borrelia, Oberschleissheim, Germany
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Volker Fingerle
- German National Reference Centre for Borrelia, Oberschleissheim, Germany
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Gabriele Margos
- German National Reference Centre for Borrelia, Oberschleissheim, Germany
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
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2
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Parise CM, Bai Y, Brandt KS, Ford SL, Maes S, Replogle AJ, Kneubehl AR, Lopez JE, Eisen RJ, Hojgaard A. A serological assay to detect and differentiate rodent exposure to soft tick and hard tick relapsing fever infections in the United States. Ticks Tick Borne Dis 2023; 14:102167. [PMID: 36965260 PMCID: PMC10956445 DOI: 10.1016/j.ttbdis.2023.102167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/27/2023]
Abstract
Human cases of relapsing fever (RF) in North America are caused primarily by Borrelia hermsii and Borrelia turicatae, which are spread by argasid (soft) ticks, and by Borrelia miyamotoi, which is transmitted by ixodid (hard) ticks. In some regions of the United States, the ranges of the hard and soft tick RF species are known to overlap; in many areas, recorded ranges of RF spirochetes overlap with Lyme disease (LD) group Borrelia spirochetes. Identification of RF clusters or cases detected in unusual geographic localities might prompt public health agencies to investigate environmental exposures, enabling prevention of additional cases through locally targeted mitigation. However, exposure risks and mitigation strategies differ among hard and soft tick RF, prompting a need for additional diagnostic strategies that differentiate hard tick from soft tick RF. We evaluated the ability of new and previously described recombinant antigens in serological assays to differentiate among prior exposures in mice to LD, soft or hard tick RF spirochetes. We extracted whole-cell protein lysates from RF Borrelia cultures and synthesized six recombinant RF antigens (Borrelia immunogenic protein A (BipA) derived from four species of RF Borrelia, glycerophosphodiester phosphodiesterase (GlpQ), and Borrelia miyamotoi membrane antigen A (BmaA)) to detect reactivity in laboratory derived (Peromyscus sp. and Mus sp.) mouse serum infected with RF and LD Borrelia species. Among 44 Borrelia exposed mouse samples tested, all five mice exposed to LD spirochetes were correctly differentiated from the 39 mice exposed to RF Borrelia using the recombinant targets. Of the 39 mice exposed to RF spirochetes, 28 were accurately categorized to species of exposure (71%). Segregation among soft tick RF species (Borrelia hermsii, Borrelia parkeri and Borrelia turicatae) was inadequate (58%) owing to observed cross-reactivity among recombinant BipA protein targets. However, among the 28 samples accurately separated to species, all were accurately assigned to soft tick or hard tick RF type. Although not adequately specific to accurately categorize exposure to soft tick RF species, the recombinant BipA protein targets from soft and hard tick RF species show utility in accurately discriminating mouse exposures to LD or RF Borrelia, and accurately segregate hard tick from soft tick RF Borrelia exposure.
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Affiliation(s)
- Christina M Parise
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Ying Bai
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Kevin S Brandt
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Shelby L Ford
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Sarah Maes
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Adam J Replogle
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Alexander R Kneubehl
- Department of Pediatrics, National School of Tropical Medicine at Baylor College of Medicine One Baylor Plaza, BCM113, Houston, TX 77030, USA
| | - Job E Lopez
- Department of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine at Baylor College of Medicine One Baylor Plaza, BCM113, Houston, TX 77030, USA
| | - Rebecca J Eisen
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA
| | - Andrias Hojgaard
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, USA.
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Rubio LA, Kjemtrup AM, Marx GE, Cronan S, Kilonzo C, Saunders MEM, Choat JL, Dietrich EA, Liebman KA, Park SY. Borrelia miyamotoi Infection in Immunocompromised Man, California, USA, 2021. Emerg Infect Dis 2023; 29:1011-1014. [PMID: 37081591 PMCID: PMC10124667 DOI: 10.3201/eid2905.221638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Infection with Borrelia miyamotoi in California, USA, has been suggested by serologic studies. We diagnosed B. miyamotoi infection in an immunocompromised man in California. Diagnosis was aided by plasma microbial cell-free DNA sequencing. We conclude that the infection was acquired in California.
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Burde J, Bloch EM, Kelly JR, Krause PJ. Human Borrelia miyamotoi Infection in North America. Pathogens 2023; 12:553. [PMID: 37111439 PMCID: PMC10145171 DOI: 10.3390/pathogens12040553] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Borrelia miyamotoi is an emerging pathogen that causes a febrile illness and is transmitted by the same hard-bodied (ixodid) ticks that transmit several other pathogens, including Borrelia species that cause Lyme disease. B. miyamotoi was discovered in 1994 in Ixodes persulcatus ticks in Japan. It was first reported in humans in 2011 in Russia. It has subsequently been reported in North America, Europe, and Asia. B. miyamotoi infection is widespread in Ixodes ticks in the northeastern, northern Midwestern, and far western United States and in Canada. In endemic areas, human B. miyamotoi seroprevalence averages from 1 to 3% of the population, compared with 15 to 20% for B. burgdorferi. The most common clinical manifestations of B. miyamotoi infection are fever, fatigue, headache, chills, myalgia, arthralgia, and nausea. Complications include relapsing fever and rarely, meningoencephalitis. Because clinical manifestations are nonspecific, diagnosis requires laboratory confirmation by PCR or blood smear examination. Antibiotics are effective in clearing infection and are the same as those used for Lyme disease, including doxycycline, tetracycline, erythromycin, penicillin, and ceftriaxone. Preventive measures include avoiding areas where B. miyamotoi-infected ticks are found, landscape management, and personal protective strategies such as protective clothing, use of acaricides, and tick checks with rapid removal of embedded ticks.
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Affiliation(s)
- Jed Burde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Evan M. Bloch
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University, Baltimore, MD 21217, USA
| | - Jill R. Kelly
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA
| | - Peter J. Krause
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
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Lynn GE, Breuner NE, Hojgaard A, Oliver J, Eisen L, Eisen RJ. A comparison of horizontal and transovarial transmission efficiency of Borrelia miyamotoi by Ixodes scapularis. Ticks Tick Borne Dis 2022; 13:102003. [PMID: 35858517 PMCID: PMC10880489 DOI: 10.1016/j.ttbdis.2022.102003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022]
Abstract
Borrelia miyamotoi is a relapsing fever spirochete carried by Ixodes spp. ticks throughout the northern hemisphere. The pathogen is acquired either transovarially (vertically) or horizontally through blood-feeding and passed transtadially across life stages. Despite these complementary modes of transmission, infection prevalence of ticks with B. miyamotoi is typically low (<5%) in natural settings and the relative contributions of the two transmission modes have not been studied extensively. Horizontal transmission of B. miyamotoi (strain CT13-2396 or wild type strain) was initiated using infected Ixodes scapularis larvae or nymphs to expose rodents, which included both the immunocompetent CD-1 laboratory mouse (Mus musculus) and a natural reservoir host, the white-footed mouse (Peromyscus. leucopus), to simulate natural enzootic transmission. Transovarial transmission was evaluated using I. scapularis exposed to B. miyamotoi as either larvae or nymphs feeding on immunocompromised SCID mice (M. musculus) and subsequently fed as females on New Zealand white rabbits. Larvae from infected females were qPCR-tested individually to assess transovarial transmission rates. Tissue tropism of B. miyamotoi in infected ticks was demonstrated using in situ hybridization. Between 1 and 12% of ticks were positive (post-molt) for B. miyamotoi after feeding on groups of CD-1 mice or P. leucopus with evidence of infection, indicating that horizontal transmission was inefficient, regardless of whether infected larvae or nymphs were used to challenge the mice. Transovarial transmission occurred in 7 of 10 egg clutches from infected females. Filial infection prevalence in larvae ranged from 3 to 100% (median 71%). Both larval infection prevalence and spirochete load were highly correlated with maternal spirochete load. Spirochetes were disseminated throughout the tissues of all three stages of unfed ticks, including the salivary glands and female ovarian tissue. The results indicate that while multiple transmission routes contribute to enzootic maintenance of B. miyamotoi, transovarial transmission is likely to be the primary source of infected ticks and therefore risk assessment and tick control strategies should target adult female ticks.
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Affiliation(s)
- Geoffrey E Lynn
- Division of Vector-borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, United States; AgriLife Texas A&M University, 1619 Garner Field Road, Uvalde, TX 78801, United States.
| | - Nicole E Breuner
- Division of Vector-borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, United States; Current address: College of Public Health and Human Sciences, Oregon State University, 160 SW 26th St. Corvallis, OR 97331, United States
| | - Andrias Hojgaard
- Division of Vector-borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, United States
| | - Jonathan Oliver
- School of Public Health, University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Lars Eisen
- Division of Vector-borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, United States
| | - Rebecca J Eisen
- Division of Vector-borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO 80521, United States
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Hojgaard A, Osikowicz LM, Maes S, Eisen L, Eisen RJ. Detection of Genetic Variability in Borrelia miyamotoi (Spirochaetales: Spirochaetaceae) Between and Within the Eastern and Western United States. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:2154-2160. [PMID: 33956124 DOI: 10.1093/jme/tjab075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Borrelia miyamotoi is a hard tick-associated relapsing fever spirochete that is geographically widespread in Ixodes spp. (Acari: Ixodidae) ticks, but typically occurs at low prevalence. Genetic variability has been described among strains derived from Asia, Europe, and North America, and among tick species that carry the infection, but little variability has been described within foci or tick species. Capitalizing on access to B. miyamotoi nucleic acid extracted from host-seeking Ixodes scapularis Say or Ixodes pacificus Cooley & Kohls from 16 states, we explored genetic variability based on sequence analysis of four amplicons described herein. Consistent with previous studies, we detected significant genetic differences between strains derived from I. scapularis (eastern United States) and I. pacificus (western United States) and identified two distinct sequences in the western United States (Am-West-1 and Am-West-2). Unique to this study, we identified two distinct sequences in the eastern United States (Am-East-1 and Am-East-2). Based on the 161 samples we analyzed, Am-East-1 was the only type represented in 50 B. miyamotoi-infected ticks collected from the Northeast (Vermont, Maine, New York, Connecticut, and Rhode Island), whereas ticks collected from the North-Central and Mid-Atlantic states harbored B. miyamotoi comprised of both Am-East-1 and Am-East-2. Further studies are needed to better characterize the phylogeography of B. miyamotoi and to discern if there are biologically meaningful differences among sequence types. To facilitate further exploration, we developed a polymerase chain reaction (PCR) assay designed to differentiate Am-East-1, Am-East-2, and Am-West sequence types without having to sequence the amplicon.
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Affiliation(s)
- Andrias Hojgaard
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Lynn M Osikowicz
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Sarah Maes
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Lars Eisen
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Rebecca J Eisen
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
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7
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Replogle AJ, Sexton C, Young J, Kingry LC, Schriefer ME, Dolan M, Johnson TL, Connally NP, Padgett KA, Petersen JM. Isolation of Borrelia miyamotoi and other Borreliae using a modified BSK medium. Sci Rep 2021; 11:1926. [PMID: 33479281 PMCID: PMC7820315 DOI: 10.1038/s41598-021-81252-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/16/2020] [Indexed: 12/28/2022] Open
Abstract
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.
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Affiliation(s)
- Adam J Replogle
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Christopher Sexton
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - John Young
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Luke C Kingry
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Martin E Schriefer
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Marc Dolan
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA
| | - Tammi L Johnson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA.,Texas A&M AgriLife Research, Uvalde, TX, 78801, USA
| | - Neeta P Connally
- Department of Biological and Environmental Sciences, Western Connecticut State University, Danbury, CT, 06810, USA
| | - Kerry A Padgett
- California Department of Public Health, Infectious Diseases Branch/Vector-Borne Disease Section, Marina Bay Parkway, Richmond, CA, 94804, USA
| | - Jeannine M Petersen
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, 80521, USA.
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Borrelia miyamotoi-An Emerging Human Tick-Borne Pathogen in Europe. Microorganisms 2021; 9:microorganisms9010154. [PMID: 33445492 PMCID: PMC7827671 DOI: 10.3390/microorganisms9010154] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/18/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Borrelia miyamotoi is classified as a relapsing fever spirochete. Although B. miyamotoi is genetically and ecologically distinct from Borrelia burgdorferi sensu lato, both microorganisms are transmitted by the same Ixodes tick species. B. miyamotoi was detected in I. persulcatus ticks in 1994 in Japan. A phylogenetic analysis based on selected sequences of B. miyamotoi genome revealed genetic differences between isolates from Asia, North America, and Europe, which are clearly separated into three genotypes. Symptomatic human cases of Borrelia miyamotoi disease (BMD) were first reported in 2011 in Russia and then in North America, Europe, and Asia. The most common clinical manifestation of BMD is fever with flu-like symptoms. Several differences in rare symptoms (thrombocytopenia, monocytosis, cerebrospinal fluid pleocytosis, or symptoms related to the central nervous system) have been noted among cases caused by Asian, European, and American types of B. miyamotoi. BMD should be considered in the diagnosis of patients after tick bites, particularly with meningoencephalitis, without anti-Borrelia antibodies in the cerebrospinal fluid. This review describes the biology, ecology, and potential of B. miyamotoi as a tick-borne pathogen of public health concern, with particular emphasis on Europe.
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Abstract
Relapsing fever (RF) is caused by several species of Borrelia; all, except two species, are transmitted to humans by soft (argasid) ticks. The species B. recurrentis is transmitted from one human to another by the body louse, while B. miyamotoi is vectored by hard-bodied ixodid tick species. RF Borrelia have several pathogenic features that facilitate invasion and dissemination in the infected host. In this article we discuss the dynamics of vector acquisition and subsequent transmission of RF Borrelia to their vertebrate hosts. We also review taxonomic challenges for RF Borrelia as new species have been isolated throughout the globe. Moreover, aspects of pathogenesis including symptomology, neurotropism, erythrocyte and platelet adhesion are discussed. We expound on RF Borrelia evasion strategies for innate and adaptive immunity, focusing on the most fundamental pathogenetic attributes, multiphasic antigenic variation. Lastly, we review new and emerging species of RF Borrelia and discuss future directions for this global disease.
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Affiliation(s)
- Job Lopez
- Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston TX, USA
| | - Joppe W Hovius
- Center for Experimental and Molecular Medicine, Amsterdam Medical centers, location Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Sven Bergström
- Department of Molecular Biology, Umeå Center for Microbial Research, Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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Janeček J, Nováková M, Oppelt J, Pospíšilová P, Cunha A, Silva AC, Dantong L, Šmajs D. Complete Chromosomal Sequences of Two Borrelia miyamotoi Samples Obtained from Ixodes ricinus Eggs in Czechia. Microbiol Resour Announc 2020; 9:e01504-19. [PMID: 32241866 PMCID: PMC7118192 DOI: 10.1128/mra.01504-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/11/2020] [Indexed: 11/20/2022] Open
Abstract
Here, we present complete chromosome sequences of Borrelia miyamotoi samples CZ-F1E and CZ-F190E, which were obtained from Ixodes ricinus eggs from Czechia. The chromosome sequences, assembled from Illumina and Sanger sequencing data, had average coverage values of 647× and 3,216×, respectively. They belong to the European genotype, distinct from the Asian and American strains.
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Affiliation(s)
- Jan Janeček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Anita Cunha
- Faculty of Medicine, University of Porto, Porto, Portugal
| | | | - Li Dantong
- Southern Medical University, Guangzhou, China
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Kuleshov KV, Margos G, Fingerle V, Koetsveld J, Goptar IA, Markelov ML, Kolyasnikova NM, Sarksyan DS, Kirdyashkina NP, Shipulin GA, Hovius JW, Platonov AE. Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome. BMC Genomics 2020; 21:16. [PMID: 31906865 PMCID: PMC6945570 DOI: 10.1186/s12864-019-6388-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The genus Borrelia comprises spirochaetal bacteria maintained in natural transmission cycles by tick vectors and vertebrate reservoir hosts. The main groups are represented by a species complex including the causative agents of Lyme borreliosis and relapsing fever group Borrelia. Borrelia miyamotoi belongs to the relapsing fever group of spirochetes and forms distinct populations in North America, Asia, and Europe. As all Borrelia species B. miyamotoi possess an unusual and complex genome consisting of a linear chromosome and a number of linear and circular plasmids. The species is considered an emerging human pathogen and an increasing number of human cases are being described in the Northern hemisphere. The aim of this study was to produce a high quality reference genome that will facilitate future studies into genetic differences between different populations and the genome plasticity of B. miyamotoi. RESULTS We used multiple available sequencing methods, including Pacific Bioscience single-molecule real-time technology (SMRT) and Oxford Nanopore technology (ONT) supplemented with highly accurate Illumina sequences, to explore the suitability for whole genome assembly of the Russian B. miyamotoi isolate, Izh-4. Plasmids were typed according to their potential plasmid partitioning genes (PF32, 49, 50, 57/62). Comparing and combining results of both long-read (SMRT and ONT) and short-read methods (Illumina), we determined that the genome of the isolate Izh-4 consisted of one linear chromosome, 12 linear and two circular plasmids. Whilst the majority of plasmids had corresponding contigs in the Asian B. miyamotoi isolate FR64b, there were only four that matched plasmids of the North American isolate CT13-2396, indicating differences between B. miyamotoi populations. Several plasmids, e.g. lp41, lp29, lp23, and lp24, were found to carry variable major proteins. Amongst those were variable large proteins (Vlp) subtype Vlp-α, Vlp-γ, Vlp-δ and also Vlp-β. Phylogenetic analysis of common plasmids types showed the uniqueness in Russian/Asian isolates of B. miyamotoi compared to other isolates. CONCLUSIONS We here describe the genome of a Russian B. miyamotoi clinical isolate, providing a solid basis for future comparative genomics of B. miyamotoi isolates. This will be a great impetus for further basic, molecular and epidemiological research on this emerging tick-borne pathogen.
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Affiliation(s)
- Konstantin V Kuleshov
- Central Research Institute of Epidemiology, Moscow, 111123, Russia. .,Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia.
| | - Gabriele Margos
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764, Oberschleissheim, Germany.
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764, Oberschleissheim, Germany
| | - Joris Koetsveld
- Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Irina A Goptar
- Izmerov Research Institute of Occupational Health, Moscow, Russia
| | | | - Nadezhda M Kolyasnikova
- Central Research Institute of Epidemiology, Moscow, 111123, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and- Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - Denis S Sarksyan
- Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Izhevsk State Medical Academy, Izhevsk, Russia
| | | | - German A Shipulin
- Center of Strategical Planning and Management of Biomedical Health Risks of the Ministry of Health, Moscow, Russia
| | - Joppe W Hovius
- Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia. GENOME ANNOUNCEMENTS 2018; 6:6/1/e01424-17. [PMID: 29301891 PMCID: PMC5754500 DOI: 10.1128/genomea.01424-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the whole-genome sequence of six clinical Borrelia miyamotoi isolates from the Russian Federation. Using two independent next-generation sequencing platforms, we determined the complete sequence of the chromosome and several plasmids. All strains have an Asian genotype with 99.8% chromosome nucleotide similarity with B. miyamotoi strain FR64b.
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