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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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Das S, Hammond-McKibben D, Guralski D, Lobo S, Fiedler PN. Development of a sensitive molecular diagnostic assay for detecting Borrelia burgdorferi DNA from the blood of Lyme disease patients by digital PCR. PLoS One 2020; 15:e0235372. [PMID: 33253179 PMCID: PMC7703891 DOI: 10.1371/journal.pone.0235372] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022] Open
Abstract
Lyme disease patients would greatly benefit from a timely, sensitive, and specific molecular diagnostic test that can detect the causal agent Borrelia burgdorferi at the onset of symptoms. Currently available diagnostic methods recommended by the Centers for Disease Control and Prevention for Lyme disease involve indirect serological tests that rely on the detection of a host-antibody response, which often takes more than three weeks to develop. With this process, many positive cases are not detected within a timely manner, preventing a complete cure. In this study, we have developed a digital polymerase chain reaction (PCR) assay that detects Lyme disease on clinical presentation with a sensitivity two-fold higher than that of the currently available diagnostic methods, using a cohort of patient samples collected from the Lyme disease endemic state of Connecticut, USA, in 2016-2018. Digital PCR technology was chosen as it is more advanced and sensitive than other PCR techniques in detecting rare targets. The analytical detection sensitivity of this diagnostic assay is approximately three genome copies of B. burgdorferi. The paucity of spirochetes in the bloodstream of Lyme disease patients has hindered the clinical adoption of PCR-based diagnostic tests. However, this drawback was overcome by using a comparatively larger sample volume, applying pre-analytical processing to the blood samples, and implementing a pre-amplification step to enrich for B. burgdorferi-specific gene targets before the patient samples are analyzed via digital PCR technology. Pre-analytical processing of blood samples from acute patients revealed that the best sample type for Lyme disease detection is platelet-rich plasma rather than whole blood. If detected in a timely manner, Lyme disease can be completely cured, thus limiting antibiotic overuse and associated morbidities.
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Affiliation(s)
- Srirupa Das
- Department of Pathology Research, Nuvance Health, Danbury, CT, United States of America
- Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT, United States of America
- * E-mail:
| | - Denise Hammond-McKibben
- Department of Pathology Research, Nuvance Health, Danbury, CT, United States of America
- Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT, United States of America
| | - Donna Guralski
- Department of Pathology Research, Nuvance Health, Danbury, CT, United States of America
- Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT, United States of America
| | - Sandra Lobo
- Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT, United States of America
| | - Paul N. Fiedler
- Department of Pathology Research, Nuvance Health, Danbury, CT, United States of America
- Rudy L. Ruggles Biomedical Research Institute, Nuvance Health, Danbury, CT, United States of America
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Lohr B, Fingerle V, Norris DE, Hunfeld KP. Laboratory diagnosis of Lyme borreliosis: Current state of the art and future perspectives. Crit Rev Clin Lab Sci 2018; 55:219-245. [PMID: 29606016 DOI: 10.1080/10408363.2018.1450353] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review is directed at physicians and laboratory personnel in private practice and clinics who treat and diagnose Lyme borreliosis (LB) in patients as part of their daily work. A major objective of this paper is to bring together background information on Borrelia (B.) burgdorferi sensu lato (s.l.) and basic clinical knowledge of LB, which is one of the most frequently reported vector-borne diseases in the Northern Hemisphere. The goal is to provide practical guidance for clinicians and for laboratory physicians, and scientists for a better understanding of current achievements and ongoing obstacles in the laboratory diagnosis of LB, an infectious disease that still remains one of the diagnostic chameleons of modern clinical medicine. Moreover, in bringing together current scientific information from guidelines, reviews, and original papers, this review provides recommendations for selecting the appropriate tests in relation to the patient's stage of disease to achieve effective, stage-related application of current direct and indirect laboratory methods for the detection of B. burgdorferi s.l. Additionally, the review aims to discuss the current state of the art concerning the diagnostic potential and limitations of the assays and test methods currently in use to optimize LB patient management and provide insight into the possible future prospects of this rapidly changing area of laboratory medicine.
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Affiliation(s)
- Benedikt Lohr
- a Institute for Laboratory Medicine, Microbiology & Infection Control , Northwest Medical Centre, Medical Faculty, Goethe University , Frankfurt/Main , Germany
| | - Volker Fingerle
- b Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL) , Oberschleissheim , Germany
| | - Douglas E Norris
- c W. Harry Feinstone Department of Molecular Microbiology & Immunology , Bloomberg School of Public Health, Johns Hopkins University , Baltimore , MD , USA
| | - Klaus-Peter Hunfeld
- a Institute for Laboratory Medicine, Microbiology & Infection Control , Northwest Medical Centre, Medical Faculty, Goethe University , Frankfurt/Main , Germany
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Eshoo MW, Carolan HE, Massire C, Chou DM, Crowder CD, Rounds MA, Phillipson CA, Schutzer SE, Ecker DJ. Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species. PLoS One 2015; 10:e0135828. [PMID: 26375033 PMCID: PMC4574436 DOI: 10.1371/journal.pone.0135828] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022] Open
Abstract
Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called ‘Candidatus Cryptoplasma californiense’. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden.
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Affiliation(s)
- Mark W. Eshoo
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
- * E-mail:
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Christian Massire
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Danny M. Chou
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Chris D. Crowder
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | - Megan A. Rounds
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
| | | | - Steven E. Schutzer
- Rutgers New Jersey Medical School, Dept. of Medicine, Newark, New Jersey, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America
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Lindsay LR, Bernat K, Dibernardo A. Laboratory diagnostics for Lyme disease. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2014; 40:209-217. [PMID: 29769843 PMCID: PMC5864437 DOI: 10.14745/ccdr.v40i11a02] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Lyme disease is on the rise in Canada. It is a notifiable disease, and when infection is disseminated, serological testing provides supplemental evidence to confirm a case. OBJECTIVE To describe the current diagnostic tests for Lyme disease, review the recommended approach to laboratory testing for Lyme disease and identify future research priorities for Lyme disease laboratory diagnostics in Canada. METHODS A review of the literature was carried out. We then summarized parameters to consider before Lyme disease testing is conducted, described the current best practice to use a two-tiered diagnostic algorithm for the laboratory confirmation of disseminated Lyme disease, and analyzed the advantages and disadvantages of the supplemental tests for Lyme disease. RESULTS Diagnostic testing is indicated in people who have symptoms of disseminated disease and a history of exposure to vector ticks. To maximize sensitivity and specificity, a two-tiered serological approach is recommended, consisting of an enzyme immunoassay (EIA) screening test followed by confirmation with Western blot (WB) testing. A number of other diagnostic tests are available; however, these are largely for research purposes. CONCLUSION Two-tiered serology is currently the best approach available to assist doctors when they are making a diagnosis of disseminated Lyme disease. The Public Health Agency of Canada (the Agency) will seek to improve on this approach through standardization of the Lyme disease diagnostics used across laboratories in Canada, evaluation of test performance characteristics of current and new diagnostic platforms and development of a process to secure robust serum panels to assist in the development and evaluation of new diagnostic tests for Lyme disease.
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Affiliation(s)
- LR Lindsay
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
| | - K Bernat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
| | - A Dibernardo
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
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