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Rodino KG, Simner PJ. Status check: next-generation sequencing for infectious-disease diagnostics. J Clin Invest 2024; 134:e178003. [PMID: 38357923 PMCID: PMC10866643 DOI: 10.1172/jci178003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Next-generation sequencing (NGS) applications for the diagnostics of infectious diseases has demonstrated great potential with three distinct approaches: whole-genome sequencing (WGS), targeted NGS (tNGS), and metagenomic NGS (mNGS, also known as clinical metagenomics). These approaches provide several advantages over traditional microbiologic methods, though challenges still exist.
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Affiliation(s)
- Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Patricia J. Simner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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2
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Bland J, McGowan C, Bush E, Lloyd V. Constructing an ELISA for Detection of Anti-Borrelia in Wildlife and Agricultural Animals. Methods Mol Biol 2024; 2742:47-67. [PMID: 38165614 DOI: 10.1007/978-1-0716-3561-2_4] [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: 01/04/2024]
Abstract
Zoonotic diseases have major impacts on human and animal health, as well as being ecologically significant. Lyme Borreliosis or Lyme disease, caused by infection by pathogenic members of the Borrelia genus, is among these zoonotic diseases. Serology is one of the most accessible means for indirect surveillance of pathogen presence by monitoring the presence, abundance, and type of immune response to the pathogen or pathogen-associated epitopes. Serological surveillance of wild animals is important as wild animals are the primary reservoirs of many zoonotic diseases. Similarly, serological surveillance of agricultural animals is important due to their economic importance, in addition to animal welfare concerns. However, serology in any non-model animal such as wildlife or agricultural animals is difficult because serology necessarily relies on blood samples from the animals being tested. While companion or laboratory animals are generally sufficiently accustomed to humans that blood samples can be obtained, obtaining blood samples from wild or agricultural animals is more challenging. This initial challenge is compounded by the absence of validated serological tools to evaluate antibody titres in the sera. In this chapter, we provide methods for constructing an ELISA for the detection of anti-Borrelia antibodies in non-model animals, using studies on horses and cows as a proof of principle. The methods focus on the problems specific to non-model animals including obtaining sera, options for determining positive and negative controls without the ability to perform controlled infections, and methods for test optimization and validation.
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Affiliation(s)
- Julia Bland
- Department of Biology, Mount Allison University, Sackville, NB, Canada
- Atlantic Veterinary College, Charlottetown, PE, Canada
| | - Caitlin McGowan
- Atlantic Veterinary College, Charlottetown, PE, Canada
- Nova Scotia, Society for Prevention of Cruelty to Animals (SPCA), Dartmouth, NS, Canada
| | - Emma Bush
- Department of Biology, Mount Allison University, Sackville, NB, Canada
- Atlantic Veterinary College, Charlottetown, PE, Canada
| | - Vett Lloyd
- Department of Biology, Mount Allison University, Sackville, NB, Canada.
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3
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Kanaujia R, Sharma V, Biswal M, Singh S, Ray P, Angrup A. Microbial cell-free DNA detection: Minimally invasive diagnosis of infectious diseases. Indian J Med Microbiol 2023; 46:100433. [PMID: 37945127 DOI: 10.1016/j.ijmmb.2023.100433] [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] [Received: 02/15/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Detection of infectious diseases, especially among immunocompromised and patients on prolonged anti-microbial treatment, remains challenging, limited by conventional techniques with low sensitivity and long-turnaround time. Molecular detection by polymerase chain reaction (PCR) also has limited utility as it requires a targeted approach with prior suspicion of the infecting organism. Advancements in sequencing methodologies, specifically next-generation sequencing (NGS), have presented a promising opportunity to identify pathogens in cases where conventional techniques may be inadequate. However, the direct application of these techniques for diagnosing invasive infections is still limited by the need for invasive sampling, highlighting the pressing need to develop and implement non-invasive or minimally invasive approaches to improve the diagnosis of invasive infections. OBJECTIVES The objectives of this article are to explore the notable features, clinical utility, and constraints associated with the detection of microbial circulating cell-free DNA (mcfDNA) as a minimally invasive diagnostic tool for infectious diseases. CONTENT The mcfDNA detection provides an opportunity to identify micro-organisms in the blood of a patient. It is especially beneficial in immunocompromised patients where invasive sampling is not possible or where repeated cultures are negative. This review will discuss the applications and constraints of detecting mcfDNA for diagnosing infections and the various platforms available for its detection.
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Affiliation(s)
| | - Vikas Sharma
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Manisha Biswal
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, AIMS, Mohali, India
| | - Pallab Ray
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Archana Angrup
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
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4
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Bell DT. Deciphering the potential of plasma cell-free metagenomic next-generation sequencing using the Karius test. Curr Opin Infect Dis 2023; 36:420-425. [PMID: 37493238 DOI: 10.1097/qco.0000000000000942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
PURPOSE OF REVIEW Plasma cell-free metagenomic next-generation sequencing (cf-mNGS) is increasingly employed for the diagnosis of infection, but a consensus for optimal use has not been established. This minireview focuses on the commercially available Karius Test and is aimed at local leaders seeking to understand the complexities of cf-mNGS to make informed test utilization policies and better interpret results. RECENT FINDINGS Recent retrospective studies have reported how the Karius Test was applied at their institutions and identified areas of potential patient benefit. In addition, substantive studies have reported how this test performs in specific indications, particularly invasive fungal disease, endovascular infection and lower respiratory infection. SUMMARY Successfully integrating plasma cf-mNGS requires careful assessment of performance in the specific applications and patient populations in which it is used. Individual institutions must independently evaluate implementation strategies and determine where diagnostic yields outweigh the potential pitfalls.
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Affiliation(s)
- Drew T Bell
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington, USA
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Lionello FCP, Rotundo S, Bruno G, Marino G, Morrone HL, Fusco P, Costa C, Russo A, Trecarichi EM, Beltrame A, Torti C. Touching Base with Some Mediterranean Diseases of Interest from Paradigmatic Cases at the "Magna Graecia" University Unit of Infectious Diseases: A Didascalic Review. Diagnostics (Basel) 2023; 13:2832. [PMID: 37685370 PMCID: PMC10486464 DOI: 10.3390/diagnostics13172832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Among infectious diseases, zoonoses are increasing in importance worldwide, especially in the Mediterranean region. We report herein some clinical cases from a third-level hospital in Calabria region (Southern Italy) and provide a narrative review of the most relevant features of these diseases from epidemiological and clinical perspectives. Further, the pathogenic mechanisms involved in zoonotic diseases are reviewed, focusing on the mechanisms used by pathogens to elude the immune system of the host. These topics are of particular concern for individuals with primary or acquired immunodeficiency (e.g., people living with HIV, transplant recipients, patients taking immunosuppressive drugs). From the present review, it appears that diagnostic innovations and the availability of more accurate methods, together with better monitoring of the incidence and prevalence of these infections, are urgently needed to improve interventions for better preparedness and response.
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Affiliation(s)
- Ferdinando Carmelo Pio Lionello
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
| | - Salvatore Rotundo
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
| | - Gabriele Bruno
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
| | - Gabriella Marino
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
| | - Helen Linda Morrone
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
| | - Paolo Fusco
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
- Unit of Infectious and Tropical Diseases, “Mater Domini” Teaching Hospital, 88100 Catanzaro, Italy;
| | - Chiara Costa
- Unit of Infectious and Tropical Diseases, “Mater Domini” Teaching Hospital, 88100 Catanzaro, Italy;
| | - Alessandro Russo
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
- Unit of Infectious and Tropical Diseases, “Mater Domini” Teaching Hospital, 88100 Catanzaro, Italy;
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
- Unit of Infectious and Tropical Diseases, “Mater Domini” Teaching Hospital, 88100 Catanzaro, Italy;
| | - Anna Beltrame
- College of Public Health, University of South Florida, Gainesville, FL 33620, USA;
| | - Carlo Torti
- Department of Medical and Surgical Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy; (F.C.P.L.); (S.R.); (G.B.); (G.M.); (H.L.M.); (A.R.); (E.M.T.); (C.T.)
- Unit of Infectious and Tropical Diseases, “Mater Domini” Teaching Hospital, 88100 Catanzaro, Italy;
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McCormick DW, Brown CM, Bjork J, Cervantes K, Esponda-Morrison B, Garrett J, Kwit N, Mathewson A, McGinnis C, Notarangelo M, Osborn R, Schiffman E, Sohail H, Schwartz AM, Hinckley AF, Kugeler KJ. Characteristics of Hard Tick Relapsing Fever Caused by Borrelia miyamotoi, United States, 2013-2019. Emerg Infect Dis 2023; 29. [PMID: 37610298 PMCID: PMC10461660 DOI: 10.3201/eid2909.221912] [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: 08/24/2023] Open
Abstract
Borrelia miyamotoi, transmitted by Ixodes spp. ticks, was recognized as an agent of hard tick relapsing fever in the United States in 2013. Nine state health departments in the Northeast and Midwest have conducted public health surveillance for this emerging condition by using a shared, working surveillance case definition. During 2013-2019, a total of 300 cases were identified through surveillance; 166 (55%) were classified as confirmed and 134 (45%) as possible. Median age of case-patients was 52 years (range 1-86 years); 52% were male. Most cases (70%) occurred during June-September, with a peak in August. Fever and headache were common symptoms; 28% of case-patients reported recurring fevers, 55% had arthralgia, and 16% had a rash. Thirteen percent of patients were hospitalized, and no deaths were reported. Ongoing surveillance will improve understanding of the incidence and clinical severity of this emerging disease.
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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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Pratt GW, Platt M, Velez A, Rao LV. Utility of Whole Blood Real-Time PCR Testing for the Diagnosis of Early Lyme Disease. Am J Clin Pathol 2022; 158:327-330. [PMID: 35723600 DOI: 10.1093/ajcp/aqac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/04/2022] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVES Whole blood real-time polymerase chain reaction (WB-RTPCR) detection of Borrelia burgdorferi is not currently recommended for diagnosing Lyme disease. This study aims to elucidate the utility of WB-RTPCR as a diagnostic aid for early Lyme disease (ELD), defined as either positive PCR or positive immunoglobulin M with negative immunoglobulin G immunoblot. METHODS A retrospective analysis was performed on 33,199 blood specimens evaluated concurrently by WB-RTPCR and antibody-capture serology (ACEIA) methods (group A). Fifty-six pairs of specimens from a separate data set were retrospectively identified and analyzed at initial and follow-up time points to monitor for seroconversion (group B). Also, a separate data set of 2,526 specimens concurrently assessed by molecular and modified two-tiered enzyme-linked immunosorbent assay serology methods was analyzed (group C). RESULTS Group A yielded 1,379 specimens consistent with ELD when tested by ACEIA and WB-RTPCR. In total, 131 (9.5% of positive results) were identified by WB-RTPCR, with negative serology. Group C identified 358 samples compatible with ELD, with 31 (8.7% of positive results) identified by RTPCR alone. CONCLUSIONS When used concurrently with serologic testing, WB-RTPCR testing increases diagnostic sensitivity in cases of ELD.
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Affiliation(s)
| | - Mihae Platt
- Quest Diagnostics, North Region, Marlborough, MA, USA.,Athena Diagnostics, Marlborough, MA, USA
| | - Ana Velez
- Quest Diagnostics, North Region, Marlborough, MA, USA
| | - Lokinendi V Rao
- Quest Diagnostics, North Region, Marlborough, MA, USA.,UMass Chan Medical School, Worcester, MA, USA
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Pietikäinen A, Glader O, Kortela E, Kanerva M, Oksi J, Hytönen J. Borrelia burgdorferi specific serum and cerebrospinal fluid antibodies in Lyme neuroborreliosis. Diagn Microbiol Infect Dis 2022; 104:115782. [DOI: 10.1016/j.diagmicrobio.2022.115782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/06/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
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10
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Sfeir MM, Meece JK, Theel ES, Granger D, Fritsche TR, Steere AC, Branda JA. Multicenter Clinical Evaluation of Modified Two-Tiered Testing Algorithms for Lyme Disease Using Zeus Scientific Commercial Assays. J Clin Microbiol 2022; 60:e0252821. [PMID: 35418241 PMCID: PMC9116174 DOI: 10.1128/jcm.02528-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/28/2022] [Indexed: 11/20/2022] Open
Abstract
Modified two-tiered testing (MTTT) algorithms for Lyme disease (LD), which involve the sequential use of orthogonal enzyme immunoassays (EIAs) without immunoblotting, are acceptable alternatives to standard two-tiered testing (STTT; EIA followed by immunoblots) provided the EIAs have been FDA-cleared for this intended use. We evaluated four Zeus Scientific LD EIAs used in two distinct MTTT algorithms for FDA review. MTTT 1 used a VlsE1/pepC10 polyvalent EIA followed by a whole-cell sonicate (WCS) polyvalent EIA. MTTT 2 used the same first-tier EIA followed by separate IgM and IgG WCS EIAs. In a retrospective phase, we compared each MTTT algorithm to STTT using archived samples from LD patients or control subjects. In a prospective phase, we used the same algorithms to analyze consecutive excess samples submitted for routine LD serology to three clinical laboratories. For the retrospective phase, MTTTs 1 and 2 were more sensitive (56% and 74%) than STTT (41%; P ≤ 0.03) among 61 patients with acute erythema migrans (EM). In LD patients with neuroborreliosis, carditis, or arthritis (n = 75), sensitivity was comparable between algorithms (96 to 100%; P = 1.0). Among 190 control subjects without past LD, all algorithms were highly and comparably specific (≥99%, P = 0.48). For the prospective phase, (n = 2,932), positive percent-agreement (PPA), negative percent-agreement (NPA), and overall agreement of MTTT 1 with STTT were 93%, 97.7% and 97.4% (kappa 0.80). MTTT 2 yielded higher PPA (98%) but lower NPA (96.1%) and overall agreement (96.2%, kappa 0.74; all P < 0.05). Compared with STTT, both MTTT algorithms provided increased sensitivity in EM patients, comparable sensitivity in later disease and non-inferior specificity.
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Affiliation(s)
| | | | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Dane Granger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Allen C. Steere
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - John A. Branda
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Fida M, Wolf MJ, Hamdi A, Vijayvargiya P, Esquer Garrigos Z, Khalil S, Greenwood-Quaintance KE, Thoendel MJ, Patel R. Detection of Pathogenic Bacteria From Septic Patients Using 16S Ribosomal RNA Gene-Targeted Metagenomic Sequencing. Clin Infect Dis 2021; 73:1165-1172. [PMID: 33893492 PMCID: PMC8492209 DOI: 10.1093/cid/ciab349] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Conventional blood cultures were compared to plasma cell-free DNA-based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR)/next-generation sequencing (NGS) for detection and identification of potential pathogens in patients with sepsis. METHODS Plasma was prospectively collected from 60 adult patients with sepsis presenting to the Mayo Clinic (Minnesota) Emergency Department from March through August 2019. Results of routine clinical blood cultures were compared to those of 16S rRNA gene NGS. RESULTS Nineteen (32%) subjects had positive blood cultures, of which 13 yielded gram-negative bacilli, 5 gram-positive cocci, and 1 both gram-negative bacilli and gram-positive cocci. 16S rRNA gene NGS findings were concordant in 11. For the remaining 8, 16S rRNA gene NGS results yielded discordant detections (n = 5) or were negative (n = 3). Interestingly, Clostridium species were additionally detected by 16S rRNA gene NGS in 3 of the 6 subjects with gastrointestinal sources of gram-negative bacteremia and none of the 3 subjects with urinary sources of gram-negative bacteremia. In the 41 remaining subjects, 16S rRNA gene NGS detected at least 1 potentially pathogenic organism in 17. In 15, the detected microorganism clinically correlated with the patient's syndrome. In 17 subjects with a clinically defined infectious syndrome, neither test was positive; in the remaining 7 subjects, a noninfectious cause of clinical presentation was identified. CONCLUSIONS 16S rRNA gene NGS may be useful for detecting bacteria in plasma of septic patients. In some cases of gram-negative sepsis, it may be possible to pinpoint a gastrointestinal or urinary source of sepsis based on the profile of bacteria detected in plasma.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ahmed Hamdi
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Prakhar Vijayvargiya
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, USA
| | - Zerelda Esquer Garrigos
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, USA
| | - Sarwat Khalil
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Matthew J Thoendel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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Pritt BS. Unbiased Metagenomics-A New Tool for Detecting Early Lyme Disease? Clin Infect Dis 2021; 73:e2362-e2363. [PMID: 32585015 DOI: 10.1093/cid/ciaa854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bobbi S Pritt
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, 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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Pollock NR, MacIntyre AT, Blauwkamp TA, Blair L, Ho C, Calderon R, Franke MF. Detection of Mycobacterium tuberculosis cell-free DNA to diagnose TB in pediatric and adult patients. Int J Tuberc Lung Dis 2021; 25:403-405. [PMID: 33977910 DOI: 10.5588/ijtld.21.0055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- N R Pollock
- Department of Laboratory Medicine, Boston Children´s Hospital and Harvard Medical School, Boston, MA
| | | | | | - L Blair
- Karius Inc, Redwood City, CA, USA
| | - C Ho
- Karius Inc, Redwood City, CA, USA
| | - R Calderon
- Socios En Salud Sucursal Peru, Lima, Peru, Programa Acadêmico de Tuberculose, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - M F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
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15
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Abstract
Lyme borreliosis is caused by a growing list of related, yet distinct, spirochetes with complex biology and sophisticated immune evasion mechanisms. It may result in a range of clinical manifestations involving different organ systems, and can lead to persistent sequelae in a subset of cases. The pathogenesis of Lyme borreliosis is incompletely understood, and laboratory diagnosis, the focus of this review, requires considerable understanding to interpret the results correctly. Direct detection of the infectious agent is usually not possible or practical, necessitating a continued reliance on serologic testing. Still, some important advances have been made in the area of diagnostics, and there are many promising ideas for future assay development. This review summarizes the state of the art in laboratory diagnostics for Lyme borreliosis, provides guidance in test selection and interpretation, and highlights future directions.
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16
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Sanderson VP, Mainprize IL, Verzijlenberg L, Khursigara CM, Wills MKB. The Platelet Fraction Is a Novel Reservoir to Detect Lyme Borrelia in Blood. BIOLOGY 2020; 9:biology9110366. [PMID: 33137967 PMCID: PMC7694117 DOI: 10.3390/biology9110366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022]
Abstract
Simple Summary To diagnose Lyme disease, a patient’s blood is tested for antibodies that develop as part of the immune response. This can lead to cases being missed or inadequately treated. An ideal test would directly detect the Lyme disease bacteria, Borrelia, to provide better clinical guidance. In this study, we aimed to improve the methods currently used to find Borrelia in human blood, and identified two opportunities for optimization. We demonstrate that the container most commonly used to collect blood (EDTA) decreases Borrelia’s ability to grow, and we identify a superior alternative (citrate). Additionally, using experimentally infected blood, we show that Borrelia is highly concentrated in the platelet fraction, making it an ideal candidate for direct detection. These results lay the foundation for diagnostic test development, which could improve patient outcomes in Lyme disease. Abstract Serological diagnosis of Lyme disease suffers from considerable limitations. Yet, the technique cannot currently be replaced by direct detection methods, such as bacterial culture or molecular analysis, due to their inadequate sensitivity. The low bacterial burden in vasculature and lack of consensus around blood-based isolation of the causative pathogen, Borrelia burgdorferi, are central to this challenge. We therefore addressed methodological optimization of Borrelia recovery from blood, first by analyzing existing protocols, and then by using experimentally infected human blood to identify the processing conditions and fractions that increase Borrelia yield. In this proof-of-concept study, we now report two opportunities to improve recovery and detection of Borrelia from clinical samples. To enhance pathogen viability and cultivability during whole blood collection, citrate anticoagulant is superior to more commonly used EDTA. Despite the widespread reliance on serum and plasma as analytes, we found that the platelet fraction of blood concentrates Borrelia, providing an enriched resource for direct pathogen detection by microscopy, laboratory culture, Western blot, and PCR. The potential for platelets to serve as a reservoir for Borrelia and its diagnostic targets may transform direct clinical detection of this pathogen.
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Affiliation(s)
- Victoria P. Sanderson
- G. Magnotta Lyme Disease Research Lab, Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.P.S.); (I.L.M.); (L.V.)
| | - Iain L. Mainprize
- G. Magnotta Lyme Disease Research Lab, Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.P.S.); (I.L.M.); (L.V.)
| | - Lisette Verzijlenberg
- G. Magnotta Lyme Disease Research Lab, Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.P.S.); (I.L.M.); (L.V.)
| | - Cezar M. Khursigara
- Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Melanie K. B. Wills
- G. Magnotta Lyme Disease Research Lab, Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.P.S.); (I.L.M.); (L.V.)
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 54062); Fax: +1-519-837-1802
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