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Danner R, Prochniak LM, Pereckas M, Rouse JR, Wahhab A, Hackner LG, Lochhead RB. Identification of Major Histocompatibility Complex Class II Epitopes From Lyme Autoantigen Apolipoprotein B-100 and Borrelia burgdorferi Mcp4 in Murine Lyme Arthritis. J Infect Dis 2024; 230:S27-S39. [PMID: 39140726 PMCID: PMC11322890 DOI: 10.1093/infdis/jiae324] [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] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND During infection with the Lyme arthritis (LA) pathogen Borrelia burgdorferi, T-cell responses to both host and pathogen are dysregulated, resulting in chronic infection and frequent development of autoimmunity. METHODS To assess CD4+ T-cell epitopes presented during development of LA, we used an unbiased, immunopeptidomics approach to characterize the major histocompatibility complex (MHC) class II immunopeptidome in B burgdorferi-infected C57BL/6 (B6) mice, which develop mild, self-limiting LA, and infected B6 Il10-/- mice, which develop severe, persistent LA at 0, 4, and 16 weeks postinfection (22-23 mice per group). RESULTS Peptides derived from proteins involved in adaptive T- and B-cell responses and cholesterol metabolism, including human Lyme autoantigen apolipoprotein B-100 (apoB-100), were enriched in infected Il10-/- mice; whereas peptides derived from proteins involved in neutrophil extracellular net formation were enriched in infected B6 mice. Presentation of apoB-100 peptides showed evidence of epitope expansion during infection. Of several identified B burgdorferi peptides, only 1, a methyl-accepting chemotaxis protein peptide Mcp4442-462, was immunogenic. CONCLUSIONS ApoB-100, a human Lyme autoantigen, undergoes marked epitope expansion during LA development. The paucity of immunogenic B burgdorferi epitopes supports previous findings suggesting CD4+ T-cell responses are suppressed in murine LA.
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Affiliation(s)
- Rebecca Danner
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Lauren M Prochniak
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michaela Pereckas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Joseph R Rouse
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Amanda Wahhab
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Lauren G Hackner
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Robert B Lochhead
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Division of Rheumatology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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2
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Bockenstedt LK, Belperron AA. Insights From Omics in Lyme Disease. J Infect Dis 2024; 230:S18-S26. [PMID: 39140719 DOI: 10.1093/infdis/jiae250] [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] [Indexed: 08/15/2024] Open
Abstract
Lyme disease is a zoonotic infection due to Ixodes tick-transmitted Borrelia burgdorferi sensu lato spirochetes and the most common vector-borne disease in the Northern Hemisphere. Despite nearly 50 years of investigation, the pathogenesis of this infection and its 2 main adverse outcomes-postinfectious Lyme arthritis and posttreatment Lyme disease syndrome-are incompletely understood. Advancement in sequencing and mass spectrometry have led to the rapid expansion of high-throughput omics technologies, including transcriptomics, metabolomics, and proteomics, which are now being applied to human diseases. This review summarizes findings of omics studies conducted on blood and tissue samples of people with acute Lyme disease and its postinfectious outcomes.
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Affiliation(s)
- Linda K Bockenstedt
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Alexia A Belperron
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
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3
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Adkison H, Embers ME. Lyme disease and the pursuit of a clinical cure. Front Med (Lausanne) 2023; 10:1183344. [PMID: 37293310 PMCID: PMC10244525 DOI: 10.3389/fmed.2023.1183344] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
Lyme disease, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne illness in the United States. Many aspects of the disease are still topics of controversy within the scientific and medical communities. One particular point of debate is the etiology behind antibiotic treatment failure of a significant portion (10-30%) of Lyme disease patients. The condition in which patients with Lyme disease continue to experience a variety of symptoms months to years after the recommended antibiotic treatment is most recently referred to in the literature as post treatment Lyme disease syndrome (PTLDS) or just simply post treatment Lyme disease (PTLD). The most commonly proposed mechanisms behind treatment failure include host autoimmune responses, long-term sequelae from the initial Borrelia infection, and persistence of the spirochete. The aims of this review will focus on the in vitro, in vivo, and clinical evidence that either validates or challenges these mechanisms, particularly with regard to the role of the immune response in disease and resolution of the infection. Next generation treatments and research into identifying biomarkers to predict treatment responses and outcomes for Lyme disease patients are also discussed. It is essential that definitions and guidelines for Lyme disease evolve with the research to translate diagnostic and therapeutic advances to patient care.
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Affiliation(s)
| | - Monica E. Embers
- Division of Immunology, Tulane National Primate Research Center, Tulane University Health Sciences, Covington, LA, United States
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4
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Socarras KM, Haslund-Gourley BS, Cramer NA, Comunale MA, Marconi RT, Ehrlich GD. Large-Scale Sequencing of Borreliaceae for the Construction of Pan-Genomic-Based Diagnostics. Genes (Basel) 2022; 13:1604. [PMID: 36140772 PMCID: PMC9498496 DOI: 10.3390/genes13091604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/03/2022] [Accepted: 09/04/2022] [Indexed: 11/16/2022] Open
Abstract
The acceleration of climate change has been associated with an alarming increase in the prevalence and geographic range of tick-borne diseases (TBD), many of which have severe and long-lasting effects-particularly when treatment is delayed principally due to inadequate diagnostics and lack of physician suspicion. Moreover, there is a paucity of treatment options for many TBDs that are complicated by diagnostic limitations for correctly identifying the offending pathogens. This review will focus on the biology, disease pathology, and detection methodologies used for the Borreliaceae family which includes the Lyme disease agent Borreliella burgdorferi. Previous work revealed that Borreliaceae genomes differ from most bacteria in that they are composed of large numbers of replicons, both linear and circular, with the main chromosome being the linear with telomeric-like termini. While these findings are novel, additional gene-specific analyses of each class of these multiple replicons are needed to better understand their respective roles in metabolism and pathogenesis of these enigmatic spirochetes. Historically, such studies were challenging due to a dearth of both analytic tools and a sufficient number of high-fidelity genomes among the various taxa within this family as a whole to provide for discriminative and functional genomic studies. Recent advances in long-read whole-genome sequencing, comparative genomics, and machine-learning have provided the tools to better understand the fundamental biology and phylogeny of these genomically-complex pathogens while also providing the data for the development of improved diagnostics and therapeutics.
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Affiliation(s)
- Kayla M. Socarras
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Benjamin S. Haslund-Gourley
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Nicholas A. Cramer
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 Health Sciences Research Building, Richmond, VA 23298, USA
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mary Ann Comunale
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 Health Sciences Research Building, Richmond, VA 23298, USA
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Garth D. Ehrlich
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 Health Sciences Research Building, Richmond, VA 23298, USA
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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5
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Paganelli A, Righi V, Tarentini E, Magnoni C. Current Knowledge in Skin Metabolomics: Updates from Literature Review. Int J Mol Sci 2022; 23:ijms23158776. [PMID: 35955911 PMCID: PMC9369191 DOI: 10.3390/ijms23158776] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 11/19/2022] Open
Abstract
Metabolomic profiling is an emerging field consisting of the measurement of metabolites in a biological system. Since metabolites can vary in relation to different stimuli, specific metabolic patterns can be closely related to a pathological process. In the dermatological setting, skin metabolomics can provide useful biomarkers for the diagnosis, prognosis, and therapy of cutaneous disorders. The main goal of the present review is to present a comprehensive overview of the published studies in skin metabolomics. A search for journal articles focused on skin metabolomics was conducted on the MEDLINE, EMBASE, Cochrane, and Scopus electronic databases. Only research articles with electronically available English full text were taken into consideration. Studies specifically focused on cutaneous microbiomes were also excluded from the present search. A total of 97 papers matched all the research criteria and were therefore considered for the present work. Most of the publications were focused on inflammatory dermatoses and immune-mediated cutaneous disorders. Skin oncology also turned out to be a relevant field in metabolomic research. Only a few papers were focused on infectious diseases and rarer genetic disorders. All the major metabolomic alterations published so far in the dermatological setting are described extensively in this review.
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Affiliation(s)
- Alessia Paganelli
- Clinical and Experimental Medicine Ph.D. Program, University of Modena and Reggio Emilia, 41124 Modena, Italy
- Regenerative and Oncological Dermatological Surgery Unit, Modena University Hospital, 41124 Modena, Italy
- Correspondence: ; Tel.: +39-059-4222347
| | - Valeria Righi
- Department for Life Quality Studies, University of Bologna, 47921 Rimini, Italy
| | - Elisabetta Tarentini
- Servizio Formazione, Ricerca e Innovazione, Modena University Hospital, 41124 Modena, Italy
| | - Cristina Magnoni
- Regenerative and Oncological Dermatological Surgery Unit, Modena University Hospital, 41124 Modena, Italy
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6
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Groth M, Skrzydlewska E, Dobrzyńska M, Pancewicz S, Moniuszko-Malinowska A. Redox Imbalance and Its Metabolic Consequences in Tick-Borne Diseases. Front Cell Infect Microbiol 2022; 12:870398. [PMID: 35937690 PMCID: PMC9353526 DOI: 10.3389/fcimb.2022.870398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
One of the growing global health problems are vector-borne diseases, including tick-borne diseases. The most common tick-borne diseases include Lyme disease, tick-borne encephalitis, human granulocytic anaplasmosis, and babesiosis. Taking into account the metabolic effects in the patient’s body, tick-borne diseases are a significant problem from an epidemiological and clinical point of view. Inflammation and oxidative stress are key elements in the pathogenesis of infectious diseases, including tick-borne diseases. In consequence, this leads to oxidative modifications of the structure and function of phospholipids and proteins and results in qualitative and quantitative changes at the level of lipid mediators arising in both reactive oxygen species (ROS) and ROS enzyme–dependent reactions. These types of metabolic modifications affect the functioning of the cells and the host organism. Therefore, links between the severity of the disease state and redox imbalance and the level of phospholipid metabolites are being searched, hoping to find unambiguous diagnostic biomarkers. Assessment of molecular effects of oxidative stress may also enable the monitoring of the disease process and treatment efficacy.
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Affiliation(s)
- Monika Groth
- Department of Infectious Diseases and Neuroinfections, Medical University of Bialystok, Bialystok, Poland
- *Correspondence: Monika Groth,
| | - Elżbieta Skrzydlewska
- Department of Inorganic and Analytical Chemistry, Medical University of Bialystok, Bialystok, Poland
| | - Marta Dobrzyńska
- Department of Inorganic and Analytical Chemistry, Medical University of Bialystok, Bialystok, Poland
| | - Sławomir Pancewicz
- Department of Infectious Diseases and Neuroinfections, Medical University of Bialystok, Bialystok, Poland
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Bialystok, Bialystok, Poland
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7
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Barupal DK, Mahajan P, Fakouri-Baygi S, Wright RO, Arora M, Teitelbaum SL. CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets. ENVIRONMENT INTERNATIONAL 2022; 164:107240. [PMID: 35461097 PMCID: PMC9195052 DOI: 10.1016/j.envint.2022.107240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 05/18/2023]
Abstract
Inter-chemical correlations in metabolomics and exposomics datasets provide valuable information for studying relationships among chemicals reported for human specimens. With an increase in the number of compounds for these datasets, a network graph analysis and visualization of the correlation structure is difficult to interpret. We have developed the Chemical Correlation Database (CCDB), as a systematic catalogue of inter-chemical correlation in publicly available metabolomics and exposomics studies. The database has been provided via an online interface to create single compound-centric views. We have demonstrated various applications of the database to explore: 1) the chemicals from a chemical class such as Per- and Polyfluoroalkyl Substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalates and tobacco smoke related metabolites; 2) xenobiotic metabolites such as caffeine and acetaminophen; 3) endogenous metabolites (acyl-carnitines); and 4) unannotated peaks for PFAS. The database has a rich collection of 35 human studies, including the National Health and Nutrition Examination Survey (NHANES) and high-quality untargeted metabolomics datasets. CCDB is supported by a simple, interactive and user-friendly web-interface to retrieve and visualize the inter-chemical correlation data. The CCDB has the potential to be a key computational resource in metabolomics and exposomics facilitating the expansion of our understanding about biological and chemical relationships among metabolites and chemical exposures in the human body. The database is available at www.ccdb.idsl.me site.
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Affiliation(s)
- Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA.
| | - Priyanka Mahajan
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Sadjad Fakouri-Baygi
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
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8
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Mantle D, Turton N, Hargreaves IP. Lyme Disease: A Role for Coenzyme Q10 Supplementation? Antioxidants (Basel) 2022; 11:667. [PMID: 35453352 PMCID: PMC9027459 DOI: 10.3390/antiox11040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Lyme disease results from a bacterial infection following a bite from an infected tick. Patients are initially treated with antibiotics; however, in cases where antibiotic treatment is delayed, or when patients do not respond to antibiotic treatment, fatigue may develop alongside problems affecting the nervous system, cardiovascular system, and joints. It is thought that most of the damage to these tissues results from the excessive inflammatory response of the host, involving a self-reinforcing cycle of mitochondrial dysfunction, oxidative stress and inflammation. In this article, we review the potential role of supplementary coenzyme Q10 (CoQ10) in mediating the pathogenic mechanism underlying Lyme disease, on the basis of its role in mitochondrial function, as well as its anti-inflammatory and antioxidant actions.
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Affiliation(s)
| | - Nadia Turton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
| | - Iain P. Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK;
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9
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Drecktrah D, Hall LS, Crouse B, Schwarz B, Richards C, Bohrnsen E, Wulf M, Long B, Bailey J, Gherardini F, Bosio CM, Lybecker MC, Samuels DS. The glycerol-3-phosphate dehydrogenases GpsA and GlpD constitute the oxidoreductive metabolic linchpin for Lyme disease spirochete host infectivity and persistence in the tick. PLoS Pathog 2022; 18:e1010385. [PMID: 35255112 PMCID: PMC8929704 DOI: 10.1371/journal.ppat.1010385] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/17/2022] [Accepted: 02/18/2022] [Indexed: 12/18/2022] Open
Abstract
We have identified GpsA, a predicted glycerol-3-phosphate dehydrogenase, as a virulence factor in the Lyme disease spirochete Borrelia (Borreliella) burgdorferi: GpsA is essential for murine infection and crucial for persistence of the spirochete in the tick. B. burgdorferi has a limited biosynthetic and metabolic capacity; the linchpin connecting central carbohydrate and lipid metabolism is at the interconversion of glycerol-3-phosphate and dihydroxyacetone phosphate, catalyzed by GpsA and another glycerol-3-phosphate dehydrogenase, GlpD. Using a broad metabolomics approach, we found that GpsA serves as a dominant regulator of NADH and glycerol-3-phosphate levels in vitro, metabolic intermediates that reflect the cellular redox potential and serve as a precursor for lipid and lipoprotein biosynthesis, respectively. Additionally, GpsA was required for survival under nutrient stress, regulated overall reductase activity and controlled B. burgdorferi morphology in vitro. Furthermore, during in vitro nutrient stress, both glycerol and N-acetylglucosamine were bactericidal to B. burgdorferi in a GlpD-dependent manner. This study is also the first to identify a suppressor mutation in B. burgdorferi: a glpD deletion restored the wild-type phenotype to the pleiotropic gpsA mutant, including murine infectivity by needle inoculation at high doses, survival under nutrient stress, morphological changes and the metabolic imbalance of NADH and glycerol-3-phosphate. These results illustrate how basic metabolic functions that are dispensable for in vitro growth can be essential for in vivo infectivity of B. burgdorferi and may serve as attractive therapeutic targets. Lyme disease (borreliosis) is the most common tick-borne disease in the Northern hemisphere and its prevalence is increasing. Borrelia burgdorferi, the etiological agent of Lyme disease, is an enzootic pathogen that alternates between a tick vector and vertebrate host. Humans are considered an incidental host after transmission of B. burgdorferi following the bite of an infected tick. The mechanisms by which B. burgdorferi persists in the Ixodid tick, transmits to a vertebrate host and establishes infection are not well understood. Therefore, identifying virulence factors and uncovering the pathogenic strategies in the spirochete remain important to address the public health concerns of Lyme disease. In this study, we identify an enzyme involved in three-carbon metabolism, GpsA, as a new virulence factor with an effect on persistence in ticks. GpsA and GlpD, another enzyme, constitute a bidirectional metabolic node connecting lipid biosynthesis and glycolysis, which serves as the linchpin for regulating carbon utilization for B. burgdorferi throughout its enzootic cycle. Disruption of this node causes a lethal metabolic imbalance revealing a potential therapeutic target for the treatment of Lyme disease.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- * E-mail: (DD); (DSS)
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Bethany Crouse
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Crystal Richards
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Michael Wulf
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Bonnie Long
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Jessica Bailey
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Frank Gherardini
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Catharine M. Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Meghan C. Lybecker
- Department of Biology, University of Colorado, Colorado Springs, Colorado, United States of America
| | - D. Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana, United States of America
- * E-mail: (DD); (DSS)
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10
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Kehoe ER, Fitzgerald BL, Graham B, Islam MN, Sharma K, Wormser GP, Belisle JT, Kirby MJ. Biomarker selection and a prospective metabolite-based machine learning diagnostic for lyme disease. Sci Rep 2022; 12:1478. [PMID: 35087163 PMCID: PMC8795431 DOI: 10.1038/s41598-022-05451-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
We provide a pipeline for data preprocessing, biomarker selection, and classification of liquid chromatography–mass spectrometry (LCMS) serum samples to generate a prospective diagnostic test for Lyme disease. We utilize tools of machine learning (ML), e.g., sparse support vector machines (SSVM), iterative feature removal (IFR), and k-fold feature ranking to select several biomarkers and build a discriminant model for Lyme disease. We report a 98.13% test balanced success rate (BSR) of our model based on a sequestered test set of LCMS serum samples. The methodology employed is general and can be readily adapted to other LCMS, or metabolomics, data sets.
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Affiliation(s)
- Eric R Kehoe
- Department of Mathematics, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Bryna L Fitzgerald
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Barbara Graham
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - M Nurul Islam
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kartikay Sharma
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gary P Wormser
- Department of Medicine, New York Medical College, Valhalla, NY, 10595, USA
| | - John T Belisle
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael J Kirby
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, USA.,Department of Mathematics, Colorado State University, Fort Collins, CO, 80523, USA
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11
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Tkáčová Z, Bhide K, Mochnáčová E, Petroušková P, Hruškovicová J, Kulkarni A, Bhide M. Comprehensive Mapping of the Cell Response to Borrelia bavariensis in the Brain Microvascular Endothelial Cells in vitro Using RNA-Seq. Front Microbiol 2021; 12:760627. [PMID: 34819924 PMCID: PMC8606740 DOI: 10.3389/fmicb.2021.760627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/11/2021] [Indexed: 12/01/2022] Open
Abstract
Borrelia bavariensis can invade the central nervous system (CNS) by crossing the blood-brain barrier (BBB). It is predicted that B. bavariensis evokes numerous signaling cascades in the human brain microvascular endothelial cells (hBMECs) and exploits them to traverse across the BBB. The complete picture of signaling events in hBMECs induced by B. bavariensis remains uncovered. Using RNA sequencing, we mapped 11,398 genes and identified 295 differentially expressed genes (DEGs, 251 upregulated genes and 44 downregulated genes) in B. bavariensis challenged hBMECs. The results obtained from RNA-seq were validated with qPCR. Gene ontology analysis revealed the participation of DEGs in a number of biological processes like cell communication, organization of the extracellular matrix, vesicle-mediated transport, cell response triggered by pattern recognition receptors, antigen processing via MHC class I, cellular stress, metabolism, signal transduction, etc. The expression of several non-protein coding genes was also evoked. In this manuscript, we discuss in detail the correlation between several signaling cascades elicited and the translocation of BBB by B. bavariensis. The data revealed here may contribute to a better understanding of the mechanisms employed by B. bavariensis to cross the BBB.
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Affiliation(s)
- Zuzana Tkáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Evelina Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Patrícia Petroušková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Jana Hruškovicová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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12
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Fitzgerald BL, Graham B, Delorey MJ, Pegalajar-Jurado A, Islam MN, Wormser GP, Aucott JN, Rebman AW, Soloski MJ, Belisle JT, Molins CR. Metabolic Response in Patients With Post-treatment Lyme Disease Symptoms/Syndrome. Clin Infect Dis 2021; 73:e2342-e2349. [PMID: 32975577 PMCID: PMC8492154 DOI: 10.1093/cid/ciaa1455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Post-treatment Lyme disease symptoms/syndrome (PTLDS) occurs in approximately 10% of patients with Lyme disease following antibiotic treatment. Biomarkers or specific clinical symptoms to identify patients with PTLDS do not currently exist and the PTLDS classification is based on the report of persistent, subjective symptoms for ≥6 months following antibiotic treatment for Lyme disease. METHODS Untargeted liquid chromatography-mass spectrometry metabolomics was used to determine longitudinal metabolic responses and biosignatures in PTLDS and clinically cured non-PTLDS Lyme patients. Evaluation of biosignatures included (1) defining altered classes of metabolites, (2) elastic net regularization to define metabolites that most strongly defined PTLDS and non-PTLDS patients at different time points, (3) changes in the longitudinal abundance of metabolites, and (4) linear discriminant analysis to evaluate robustness in a second patient cohort. RESULTS This study determined that observable metabolic differences exist between PTLDS and non-PTLDS patients at multiple time points. The metabolites with differential abundance included those from glycerophospholipid, bile acid, and acylcarnitine metabolism. Distinct longitudinal patterns of metabolite abundance indicated a greater metabolic variability in PTLDS versus non-PTLDS patients. Small numbers of metabolites (6 to 40) could be used to define PTLDS versus non-PTLDS patients at defined time points, and the findings were validated in a second cohort of PTLDS and non-PTLDS patients. CONCLUSIONS These data provide evidence that an objective metabolite-based measurement can distinguish patients with PTLDS and help understand the underlying biochemistry of PTLDS.
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Affiliation(s)
| | - Barbara Graham
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Mark J Delorey
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | | | - M Nurul Islam
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Gary P Wormser
- Division of Infectious Diseases, New York Medical College, Valhalla, New York, USA
| | - John N Aucott
- The Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Lutherville, Maryland, USA
| | - Alison W Rebman
- The Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Lutherville, Maryland, USA
| | - Mark J Soloski
- The Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Lutherville, Maryland, USA
| | - John T Belisle
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Claudia R Molins
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
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13
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Bobe JR, Jutras BL, Horn EJ, Embers ME, Bailey A, Moritz RL, Zhang Y, Soloski MJ, Ostfeld RS, Marconi RT, Aucott J, Ma'ayan A, Keesing F, Lewis K, Ben Mamoun C, Rebman AW, McClune ME, Breitschwerdt EB, Reddy PJ, Maggi R, Yang F, Nemser B, Ozcan A, Garner O, Di Carlo D, Ballard Z, Joung HA, Garcia-Romeu A, Griffiths RR, Baumgarth N, Fallon BA. Recent Progress in Lyme Disease and Remaining Challenges. Front Med (Lausanne) 2021; 8:666554. [PMID: 34485323 PMCID: PMC8416313 DOI: 10.3389/fmed.2021.666554] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Lyme disease (also known as Lyme borreliosis) is the most common vector-borne disease in the United States with an estimated 476,000 cases per year. While historically, the long-term impact of Lyme disease on patients has been controversial, mounting evidence supports the idea that a substantial number of patients experience persistent symptoms following treatment. The research community has largely lacked the necessary funding to properly advance the scientific and clinical understanding of the disease, or to develop and evaluate innovative approaches for prevention, diagnosis, and treatment. Given the many outstanding questions raised into the diagnosis, clinical presentation and treatment of Lyme disease, and the underlying molecular mechanisms that trigger persistent disease, there is an urgent need for more support. This review article summarizes progress over the past 5 years in our understanding of Lyme and tick-borne diseases in the United States and highlights remaining challenges.
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Affiliation(s)
- Jason R. Bobe
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Brandon L. Jutras
- Department of Biochemistry, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States
| | | | - Monica E. Embers
- Tulane University Health Sciences, New Orleans, LA, United States
| | - Allison Bailey
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mark J. Soloski
- Division of Rheumatology, Department of Medicine, Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - John Aucott
- Division of Rheumatology, Department of Medicine, Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Avi Ma'ayan
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, United States
| | | | - Alison W. Rebman
- Division of Rheumatology, Department of Medicine, Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mecaila E. McClune
- Department of Biochemistry, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States
| | - Edward B. Breitschwerdt
- Department of Clinical Sciences, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | | | - Ricardo Maggi
- Department of Clinical Sciences, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bennett Nemser
- Steven & Alexandra Cohen Foundation, Stamford, CT, United States
| | - Aydogan Ozcan
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Omai Garner
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Dino Di Carlo
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Zachary Ballard
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Hyou-Arm Joung
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Albert Garcia-Romeu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Roland R. Griffiths
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nicole Baumgarth
- Center for Immunology and Infectious Diseases and the Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Brian A. Fallon
- Columbia University Irving Medical Center, New York, NY, United States
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14
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An rfuABCD-like operon and its relationship to riboflavin utilization and mammalian. Infect Immun 2021; 89:e0030721. [PMID: 34310888 DOI: 10.1128/iai.00307-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Riboflavin is an essential micronutrient, but its transport and utilization has remained largely understudied among pathogenic spirochetes. Here we show that Borrelia burgdorferi, the zoonotic spirochete that causes Lyme disease, is able to import riboflavin via products of its rfuABCD-like operon as well as synthesize flavin mononucleotide and flavin adenine dinucleotide despite lacking canonical genes for their synthesis. Additionally, a mutant deficient in the rfuABCD-like operon is resistant to the antimicrobial effect of roseoflavin, a natural riboflavin analog, and is attenuated in a murine model of Lyme borreliosis. Our combined results indicate that not only are riboflavin and the maintenance of flavin pools essential for B. burgdorferi growth, but that flavin utilization and its downstream products (e.g., flavoproteins) may play a more prominent role in B. burgdorferi pathogenesis than previously appreciated.
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15
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Tokarz R, Lipkin WI. Discovery and Surveillance of Tick-Borne Pathogens. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1525-1535. [PMID: 33313662 PMCID: PMC8285023 DOI: 10.1093/jme/tjaa269] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Within the past 30 yr molecular assays have largely supplanted classical methods for detection of tick-borne agents. Enhancements provided by molecular assays, including speed, throughput, sensitivity, and specificity, have resulted in a rapid increase in the number of newly characterized tick-borne agents. The use of unbiased high throughput sequencing has enabled the prompt identification of new pathogens and the examination of tick microbiomes. These efforts have led to the identification of hundreds of new tick-borne agents in the last decade alone. However, little is currently known about the majority of these agents beyond their phylogenetic classification. Our article outlines the primary methods involved in tick-borne agent discovery and the current status of our understanding of tick-borne agent diversity.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
- Corresponding author, e-mail:
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
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16
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Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens. Sci Rep 2021; 11:12384. [PMID: 34117323 PMCID: PMC8196166 DOI: 10.1038/s41598-021-91956-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
Inadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.
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17
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O'Neal AJ, Butler LR, Rolandelli A, Gilk SD, Pedra JH. Lipid hijacking: a unifying theme in vector-borne diseases. eLife 2020; 9:61675. [PMID: 33118933 PMCID: PMC7595734 DOI: 10.7554/elife.61675] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
Vector-borne illnesses comprise a significant portion of human maladies, representing 17% of global infections. Transmission of vector-borne pathogens to mammals primarily occurs by hematophagous arthropods. It is speculated that blood may provide a unique environment that aids in the replication and pathogenesis of these microbes. Lipids and their derivatives are one component enriched in blood and are essential for microbial survival. For instance, the malarial parasite Plasmodium falciparum and the Lyme disease spirochete Borrelia burgdorferi, among others, have been shown to scavenge and manipulate host lipids for structural support, metabolism, replication, immune evasion, and disease severity. In this Review, we will explore the importance of lipid hijacking for the growth and persistence of these microbes in both mammalian hosts and arthropod vectors.
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Affiliation(s)
- Anya J O'Neal
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States
| | - L Rainer Butler
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States
| | - Agustin Rolandelli
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States
| | - Stacey D Gilk
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, United States
| | - Joao Hf Pedra
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States
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