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Akther S, Mongodin EF, Morgan RD, Di L, Yang X, Golovchenko M, Rudenko N, Margos G, Hepner S, Fingerle V, Kawabata H, Norte AC, de Carvalho IL, Núncio MS, Marques A, Schutzer SE, Fraser CM, Luft BJ, Casjens SR, Qiu W. Natural selection and recombination at host-interacting lipoprotein loci drive genome diversification of Lyme disease and related bacteria. mBio 2024; 15:e0174924. [PMID: 39145656 PMCID: PMC11389397 DOI: 10.1128/mbio.01749-24] [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: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 08/16/2024] Open
Abstract
Lyme disease, caused by spirochetes in the Borrelia burgdorferi sensu lato clade within the Borrelia genus, is transmitted by Ixodes ticks and is currently the most prevalent and rapidly expanding tick-borne disease in Europe and North America. We report complete genome sequences of 47 isolates that encompass all established species in this clade while highlighting the diversity of the widespread human pathogenic species B. burgdorferi. A similar set of plasmids has been maintained throughout Borrelia divergence, indicating that they are a key adaptive feature of this genus. Phylogenetic reconstruction of all sequenced Borrelia genomes revealed the original divergence of Eurasian and North American lineages and subsequent dispersals that introduced B. garinii, B. bavariensis, B. lusitaniae, B. valaisiana, and B. afzelii from East Asia to Europe and B. burgdorferi and B. finlandensis from North America to Europe. Molecular phylogenies of the universally present core replicons (chromosome and cp26 and lp54 plasmids) are highly consistent, revealing a strong clonal structure. Nonetheless, numerous inconsistencies between the genome and gene phylogenies indicate species dispersal, genetic exchanges, and rapid sequence evolution at plasmid-borne loci, including key host-interacting lipoprotein genes. While localized recombination occurs uniformly on the main chromosome at a rate comparable to mutation, lipoprotein-encoding loci are recombination hotspots on the plasmids, suggesting adaptive maintenance of recombinant alleles at loci directly interacting with the host. We conclude that within- and between-species recombination facilitates adaptive sequence evolution of host-interacting lipoprotein loci and contributes to human virulence despite a genome-wide clonal structure of its natural populations. IMPORTANCE Lyme disease (also called Lyme borreliosis in Europe), a condition caused by spirochete bacteria of the genus Borrelia, transmitted by hard-bodied Ixodes ticks, is currently the most prevalent and rapidly expanding tick-borne disease in the United States and Europe. Borrelia interspecies and intraspecies genome comparisons of Lyme disease-related bacteria are essential to reconstruct their evolutionary origins, track epidemiological spread, identify molecular mechanisms of human pathogenicity, and design molecular and ecological approaches to disease prevention, diagnosis, and treatment. These Lyme disease-associated bacteria harbor complex genomes that encode many genes that do not have homologs in other organisms and are distributed across multiple linear and circular plasmids. The functional significance of most of the plasmid-borne genes and the multipartite genome organization itself remains unknown. Here we sequenced, assembled, and analyzed whole genomes of 47 Borrelia isolates from around the world, including multiple isolates of the human pathogenic species. Our analysis elucidates the evolutionary origins, historical migration, and sources of genomic variability of these clinically important pathogens. We have developed web-based software tools (BorreliaBase.org) to facilitate dissemination and continued comparative analysis of Borrelia genomes to identify determinants of human pathogenicity.
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Affiliation(s)
- Saymon Akther
- Graduate Center and Hunter College, City University of New York, New York, New York, USA
| | | | | | - Lia Di
- Graduate Center and Hunter College, City University of New York, New York, New York, USA
| | - Xiaohua Yang
- Department of Medicine, Renaissance School of Medicine, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Maryna Golovchenko
- Biology Centre Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Natalie Rudenko
- Biology Centre Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Gabriele Margos
- Bavarian Health and Food Safety Authority and German National Reference Centre for Borrelia, Oberschleissheim, Bavaria, Germany
| | - Sabrina Hepner
- Bavarian Health and Food Safety Authority and German National Reference Centre for Borrelia, Oberschleissheim, Bavaria, Germany
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority and German National Reference Centre for Borrelia, Oberschleissheim, Bavaria, Germany
| | | | - Ana Cláudia Norte
- Department of Life Sciences, University of Coimbra, MARE-Marine and Environmental Sciences Centre, Coimbra, Portugal
| | | | - Maria Sofia Núncio
- Centre for Vector and Infectious Diseases Research, Águas de Moura, Portugal
| | - Adriana Marques
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | | | - Claire M Fraser
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Benjamin J Luft
- Department of Medicine, Renaissance School of Medicine, Stony Brook University (SUNY), Stony Brook, New York, USA
| | - Sherwood R Casjens
- University of Utah School of Medicine and School of Biological Sciences, Salt Lake City, Utah, USA
| | - Weigang Qiu
- Graduate Center and Hunter College, City University of New York, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
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Rudolph MJ, Chen Y, Vorauer C, Vance DJ, Piazza CL, Willsey GG, McCarthy K, Muriuki B, Cavacini LA, Guttman M, Mantis NJ. Structure of a human monoclonal antibody in complex with Outer surface protein C (OspC) of the Lyme disease spirochete, Borreliella burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591597. [PMID: 38746285 PMCID: PMC11092446 DOI: 10.1101/2024.04.29.591597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Lyme disease is a tick-borne, multisystem infection caused by the spirochete, Borreliella burgdorferi . Although antibodies have been implicated in the resolution of Lyme disease, the specific B cell epitopes targeted during human infections remain largely unknown. In this study, we characterized and defined the structural epitope of a patient-derived bactericidal monoclonal IgG ("B11") against Outer surface protein C (OspC), a homodimeric lipoprotein necessary for B. burgdorferi tick-mediated transmission and early-stage colonization of vertebrate hosts. High-resolution epitope mapping was accomplished through hydrogen deuterium exchange-mass spectrometry (HDX-MS) and X-ray crystallography. Structural analysis of B11 Fab-OspC A complexes revealed the B11 Fabs associated in a 1:1 stoichiometry with the lateral faces of OspC A homodimers such that the antibodies are essentially positioned perpendicular to the spirochete's outer surface. B11's primary contacts reside within the membrane proximal regions of α-helices 1 and 6 and adjacent loops 5 and 6 in one OspC A monomer. In addition, B11 spans the OspC A dimer interface, engaging opposing α-helix 1', α-helix 2', and loop 2-3' in the second OspC A monomer. The B11-OspC A structure is reminiscent of the recently solved mouse transmission blocking monoclonal IgG B5 in complex with OspC A , indicating a mode of engagement with OspC that is conserved across species. In conclusion, we provide the first detailed insight into the interaction between a functional human antibody and an immunodominant Lyme disease antigen long considered an important vaccine target.
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Shifflett SA, Ferreira FC, González J, Toledo A, Fonseca DM, Ellis VA. Diversity and host specificity of Borrelia burgdorferi's outer surface protein C ( ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections. Infect Immun 2024; 92:e0024423. [PMID: 38099660 PMCID: PMC10790820 DOI: 10.1128/iai.00244-23] [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: 06/23/2023] [Accepted: 11/15/2023] [Indexed: 01/17/2024] Open
Abstract
Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. Borrelia burgdorferi, a bacterium that causes Lyme disease, is typically transmitted among wildlife by Ixodes ticks. Despite the existence of many alleles of B. burgdorferi's sensu stricto outer surface protein C (ospC) gene, most human infections are caused by a small number of ospC alleles ["human infectious alleles" (HIAs)], suggesting variation in host specificity associated with ospC. To characterize the wildlife host association of B. burgdorferi's ospC alleles, we used metagenomics to sequence ospC alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele ("mixed") infections were common. HIAs were most common in mice (Peromyscus spp.) and only one HIA was detected at a site where mice were rarely captured. ospC allele U was exclusively found in chipmunks (Tamias striatus), and although a significant number of different alleles were observed in chipmunks, including HIAs, allele U never co-occurred with other alleles in mixed infections. Our results suggest that allele U may be excluding other alleles, thereby reducing the capacity of chipmunks to act as reservoirs for HIAs.
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Affiliation(s)
- Scarlet A. Shifflett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, USA
| | - Francisco C. Ferreira
- Center for Vector Biology, Department of Entomology, Rutgers University, New Brunswick, New Jersey, USA
| | - Julia González
- Center for Vector Biology, Department of Entomology, Rutgers University, New Brunswick, New Jersey, USA
| | - Alvaro Toledo
- Center for Vector Biology, Department of Entomology, Rutgers University, New Brunswick, New Jersey, USA
| | - Dina M. Fonseca
- Center for Vector Biology, Department of Entomology, Rutgers University, New Brunswick, New Jersey, USA
| | - Vincenzo A. Ellis
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, USA
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Mechai S, Coatsworth H, Ogden NH. Possible effect of mutations on serological detection of Borrelia burgdorferi sensu stricto ospC major groups: An in-silico study. PLoS One 2023; 18:e0292741. [PMID: 37815990 PMCID: PMC10564231 DOI: 10.1371/journal.pone.0292741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
The outer surface protein C (OspC) of the agent of Lyme disease, Borrelia burgdorferi sensu stricto, is a major lipoprotein surface-expressed during early-phase human infections. Antibodies to OspC are used in serological diagnoses. This study explored the hypothesis that serological test sensitivity decreases as genetic similarity of ospC major groups (MGs) of infecting strains, and ospC A (the MG in the strain B31 used to prepare antigen for serodiagnosis assays) decreases. We used a previously published microarray dataset to compare serological reactivity to ospC A (measured as pixel intensity) versus reactivity to 22 other ospC MGs, within a population of 55 patients diagnosed by two-tier serological testing using B. burgdorferi s.s. strain B31 as antigen, in which the ospC MG is OspC A. The difference in reactivity of sera to ospC A and reactivity to each of the other 22 ospC MGs (termed 'reactivity difference') was the outcome variable in regression analysis in which genetic distance of the ospC MGs from ospC A was the explanatory variable. Genetic distance was computed for the whole ospC sequence, and 9 subsections, from Neighbour Joining phylogenetic trees of the 23 ospC MGs. Regression analysis was conducted using genetic distance for the full ospC sequence, and the subsections individually. There was a significant association between the reactivity difference and genetic distance of ospC MGs from ospC A: increased genetic distance reduced reactivity to OspC A. No single ospC subsection sequence fully explained the relationship between genetic distance and reactivity difference. An analysis of single nucleotide polymorphisms supported a biological explanation via specific amino acid modifications likely to change protein binding affinity. This adds support to the hypothesis that genetic diversity of B. burgdorferi s.s. (here specifically OspC) may impact serological diagnostic test performance. Further prospective studies are necessary to explore the clinical implications of these findings.
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Affiliation(s)
- Samir Mechai
- Public Health Risk Sciences, National Microbiology Laboratory Branch, Public Health Agency of Canada, St Hyacinthe, QC, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, St Hyacinthe, QC, Canada
| | - Heather Coatsworth
- One Health Division, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nicholas H. Ogden
- Public Health Risk Sciences, National Microbiology Laboratory Branch, Public Health Agency of Canada, St Hyacinthe, QC, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, St Hyacinthe, QC, Canada
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Shifflett SA, Wiedmeyer T, Kennedy A, Maestas L, Buoni M, Ciloglu A, Ellis VA. Prevalence of Borrelia burgdorferi and diversity of its outer surface protein C (ospC) alleles in blacklegged ticks (Ixodes scapularis) in Delaware. Ticks Tick Borne Dis 2023; 14:102139. [PMID: 36780839 PMCID: PMC10033352 DOI: 10.1016/j.ttbdis.2023.102139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023]
Abstract
Characterizing the diversity of genes associated with virulence and transmission of a pathogen across the pathogen's distribution can inform our understanding of host infection risk. Borrelia burgdorferi is a vector-borne bacterium that causes Lyme disease in humans and is common in the United States. The outer surface protein C (ospC) gene of B. burgdorferi exhibits substantial genetic variation across the pathogen's distribution and plays a critical role in virulence and transmission in vertebrate hosts. In fact, B. burgdorferi infections that disseminate across host tissues in humans are associated with only a subset of ospC alleles. Delaware has a high incidence of Lyme disease, but the diversity of ospC in B. burgdorferi in the state has not been evaluated. We used PCR to amplify ospC in B. burgdorferi-infected blacklegged ticks (Ixodes scapularis) in sites statewide and used short-read sequencing to identify ospC alleles. B. burgdorferi prevalence in blacklegged ticks varied across sites, but not significantly so. We identified 15 previously characterized ospC alleles accounting for nearly all of the expected diversity of alleles across the sites as estimated using the Chao1 index. Nearly 40% of sequenced infections (23/58) had more than one ospC allele present suggesting mixed strain infections and the relative frequencies of alleles in single infections were positively correlated with their relative frequencies in mixed infections. Turnover of ospC alleles was positively related to distance between sites with closer sites having more similar allele compositions than more distant sites. This suggests a degree of B. burgdorferi dispersal limitation or habitat specialization. OspC alleles known to cause disseminated infections in humans were found at the highest frequencies across sites, corresponding to Delaware's high incidence of Lyme disease.
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Affiliation(s)
- Scarlet A Shifflett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Tyler Wiedmeyer
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Ashley Kennedy
- Mosquito Control Section, Division of Fish & Wildlife, Delaware Department of Natural Resources and Environmental Control, DE, USA
| | - Lauren Maestas
- Mosquito Control Section, Division of Fish & Wildlife, Delaware Department of Natural Resources and Environmental Control, DE, USA; Cattle Fever Tick Research Laboratory, USDA, Agricultural Research Service, Edinburg, TX, USA
| | - Michael Buoni
- Delaware Technical Community College, Georgetown, DE, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Arif Ciloglu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Türkiye
| | - Vincenzo A Ellis
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA.
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Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. Pathogens 2023; 12:pathogens12030388. [PMID: 36986310 PMCID: PMC10053453 DOI: 10.3390/pathogens12030388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/12/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Driven by host–pathogen coevolution, cell surface antigens are often the fastest evolving parts of a microbial pathogen. The persistent evolutionary impetus for novel antigen variants suggests the utility of novelty-seeking algorithms in predicting antigen diversification in microbial pathogens. In contrast to traditional genetic algorithms maximizing variant fitness, novelty-seeking algorithms optimize variant novelty. Here, we designed and implemented three evolutionary algorithms (fitness-seeking, novelty-seeking, and hybrid) and evaluated their performances in 10 simulated and 2 empirically derived antigen fitness landscapes. The hybrid walks combining fitness- and novelty-seeking strategies overcame the limitations of each algorithm alone, and consistently reached global fitness peaks. Thus, hybrid walks provide a model for microbial pathogens escaping host immunity without compromising variant fitness. Biological processes facilitating novelty-seeking evolution in natural pathogen populations include hypermutability, recombination, wide dispersal, and immune-compromised hosts. The high efficiency of the hybrid algorithm improves the evolutionary predictability of novel antigen variants. We propose the design of escape-proof vaccines based on high-fitness variants covering a majority of the basins of attraction on the fitness landscape representing all potential variants of a microbial antigen.
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Li L, Di L, Akther S, Zeglis BM, Qiu W. Evolution of the vls Antigenic Variability Locus of the Lyme Disease Pathogen and Development of Recombinant Monoclonal Antibodies Targeting Conserved VlsE Epitopes. Microbiol Spectr 2022; 10:e0174322. [PMID: 36150043 PMCID: PMC9604149 DOI: 10.1128/spectrum.01743-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/02/2022] [Indexed: 01/12/2023] Open
Abstract
VlsE (variable major protein-like sequence, expressed) is an outer surface protein of the Lyme disease pathogen (Borreliella species) responsible for its within-host antigenic variation and a key diagnostic biomarker of Lyme disease. However, the high sequence variability of VlsE poses a challenge to the development of consistent VlsE-based diagnostics and therapeutics. In addition, the standard diagnostic protocols detect immunoglobins elicited by the Lyme pathogen, not the presence of the pathogen or its derived antigens. Here, we described the development of recombinant monoclonal antibodies (rMAbs) that bound specifically to conserved epitopes on VlsE. We first quantified amino-acid sequence variability encoded by the vls genes from 13 B. burgdorferi genomes by evolutionary analyses. We showed broad inconsistencies of the sequence phylogeny with the genome phylogeny, indicating rapid gene duplications, losses, and recombination at the vls locus. To identify conserved epitopes, we synthesized peptides representing five long conserved invariant regions (IRs) on VlsE. We tested the antigenicity of these five IR peptides using sera from three mammalian host species including human patients, the natural reservoir white-footed mouse (Peromyscus leucopus), and VlsE-immunized New Zealand rabbits (Oryctolagus cuniculus). The IR4 and IR6 peptides emerged as the most antigenic and reacted strongly with both the human and rabbit sera, while all IR peptides reacted poorly with sera from natural hosts. Four rMAbs binding specifically to the IR4 and IR6 peptides were identified, cloned, and purified. Given their specific recognition of the conserved epitopes on VlsE, these IR-specific rMAbs are potential novel diagnostic and research agents for direct detection of Lyme disease pathogens regardless of strain heterogeneity. IMPORTANCE Current diagnostic protocols of Lyme disease indirectly detect the presence of antibodies produced by the patient upon infection by the bacterial pathogen, not the pathogen itself. These diagnostic tests tend to underestimate early-stage bacterial infections before the patients develop robust immune responses. Further, the indirect tests do not distinguish between active or past infections by the Lyme disease bacteria in a patient sample. Here, we described novel monoclonal antibodies that have the potential to become the basis of direct and definitive diagnostic detection of the Lyme disease pathogen, regardless of its genetic heterogeneity.
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Affiliation(s)
- Li Li
- Graduate Center, City University of New York, New York, New York, USA
| | - Lia Di
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York, USA
| | - Saymon Akther
- Graduate Center, City University of New York, New York, New York, USA
| | - Brian M. Zeglis
- Graduate Center, City University of New York, New York, New York, USA
- Department of Chemistry, Hunter College, City University of New York, New York, New York, USA
- Department of Radiology, Weill Cornell Medical College, New York, New York, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Weigang Qiu
- Graduate Center, City University of New York, New York, New York, USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
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