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Bartolomeu-Gonçalves G, Souza JMD, Fernandes BT, Spoladori LFA, Correia GF, Castro IMD, Borges PHG, Silva-Rodrigues G, Tavares ER, Yamauchi LM, Pelisson M, Perugini MRE, Yamada-Ogatta SF. Tuberculosis Diagnosis: Current, Ongoing, and Future Approaches. Diseases 2024; 12:202. [PMID: 39329871 PMCID: PMC11430992 DOI: 10.3390/diseases12090202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/31/2024] [Accepted: 08/31/2024] [Indexed: 09/28/2024] Open
Abstract
Tuberculosis (TB) remains an impactful infectious disease, leading to millions of deaths every year. Mycobacterium tuberculosis causes the formation of granulomas, which will determine, through the host-pathogen relationship, if the infection will remain latent or evolve into active disease. Early TB diagnosis is life-saving, especially among immunocompromised individuals, and leads to proper treatment, preventing transmission. This review addresses different approaches to diagnosing TB, from traditional methods such as sputum smear microscopy to more advanced molecular techniques. Integrating these techniques, such as polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP), has significantly improved the sensitivity and specificity of M. tuberculosis identification. Additionally, exploring novel biomarkers and applying artificial intelligence in radiological imaging contribute to more accurate and rapid diagnosis. Furthermore, we discuss the challenges of existing diagnostic methods, including limitations in resource-limited settings and the emergence of drug-resistant strains. While the primary focus of this review is on TB diagnosis, we also briefly explore the challenges and strategies for diagnosing non-tuberculous mycobacteria (NTM). In conclusion, this review provides an overview of the current landscape of TB diagnostics, emphasizing the need for ongoing research and innovation. As the field evolves, it is crucial to ensure that these advancements are accessible and applicable in diverse healthcare settings to effectively combat tuberculosis worldwide.
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Affiliation(s)
- Guilherme Bartolomeu-Gonçalves
- Programa de Pós-Graduação em Fisiopatologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina CEP 86038-350, Paraná, Brazil
| | - Joyce Marinho de Souza
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
- Faculdade de Ciências da Saúde, Biomedicina, Universidade do Oeste Paulista, Presidente Prudente CEP 19050-920, São Paulo, Brazil
| | - Bruna Terci Fernandes
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
- Curso de Farmácia, Faculdade Dom Bosco, Cornélio Procópio CEP 86300-000, Paraná, Brazil
| | | | - Guilherme Ferreira Correia
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
| | - Isabela Madeira de Castro
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
| | | | - Gislaine Silva-Rodrigues
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
| | - Eliandro Reis Tavares
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
- Departamento de Medicina, Pontifícia Universidade Católica do Paraná, Campus Londrina CEP 86067-000, Paraná, Brazil
| | - Lucy Megumi Yamauchi
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
| | - Marsileni Pelisson
- Programa de Pós-Graduação em Fisiopatologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina CEP 86038-350, Paraná, Brazil
| | - Marcia Regina Eches Perugini
- Programa de Pós-Graduação em Fisiopatologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina CEP 86038-350, Paraná, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Programa de Pós-Graduação em Fisiopatologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina CEP 86038-350, Paraná, Brazil
- Programa de Pós-Graduação em Microbiologia, Universidade Estadual de Londrina, Londrina CEP 86057-970, Paraná, Brazil
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Neves YCD, Reis AJ, Rodrigues MA, Chimara E, da Silva Lourenço MC, Fountain J, Ramis IB, von Groll A, Gerasimova Y, Rohde KH, Almeida da Silva PE. Detection of Mtb and NTM: preclinical validation of a new asymmetric PCR-binary deoxyribozyme sensor assay. Microbiol Spectr 2024; 12:e0350623. [PMID: 38651877 PMCID: PMC11237447 DOI: 10.1128/spectrum.03506-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
Tuberculosis (TB) and infectious diseases caused by non-tuberculous mycobacteria (NTM) are global concerns. The development of a rapid and accurate diagnostic method, capable of detecting and identifying different mycobacteria species, is crucial. We propose a molecular approach, the BiDz-TB/NTM, based on the use of binary deoxyribozyme (BiDz) sensors for the detection of Mycobacterium tuberculosis (Mtb) and NTM of clinical interest. A panel of DNA samples was used to evaluate Mtb-BiDz, Mycobacterium abscessus/Mycobacterium chelonae-BiDz, Mycobacterium avium-BiDz, Mycobacterium intracellulare/Mycobacterium chimaera-BiDz, and Mycobacterium kansasii-BiDz sensors in terms of specificity, sensitivity, accuracy, and limit of detection. The BiDz sensors were designed to hybridize specifically with the genetic signatures of the target species. To obtain the BiDz sensor targets, amplification of a fragment containing the hypervariable region 2 of the 16S rRNA was performed, under asymmetric PCR conditions using the reverse primer designed based on linear-after-the-exponential principles. The BiDz-TB/NTM was able to correctly identify 99.6% of the samples, with 100% sensitivity and 0.99 accuracy. The individual values of specificity, sensitivity, and accuracy, obtained for each BiDz sensor, satisfied the recommendations for new diagnostic methods, with sensitivity of 100%, specificity and accuracy ranging from 98% to 100% and from 0.98 to 1.0, respectively. The limit of detection of BiDz sensors ranged from 12 genome copies (Mtb-BiDz) to 2,110 genome copies (Mkan-BiDz). The BiDz-TB/NTM platform would be able to generate results rapidly, allowing the implementation of the appropriate therapeutic regimen and, consequently, the reduction of morbidity and mortality of patients.IMPORTANCEThis article describes the development and evaluation of a new molecular platform for accurate, sensitive, and specific detection and identification of Mycobacterium tuberculosis and other mycobacteria of clinical importance. Based on BiDz sensor technology, this assay prototype is amenable to implementation at the point of care. Our data demonstrate the feasibility of combining the species specificity of BiDz sensors with the sensitivity afforded by asymmetric PCR amplification of target sequences. Preclinical validation of this assay on a large panel of clinical samples supports the further development of this diagnostic tool for the molecular detection of pathogenic mycobacteria.
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Affiliation(s)
- Yasmin Castillos das Neves
- Laboratory of Mycobacteria, Núcleo de Pesquisa em Microbiologia Médica, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Ana Julia Reis
- Laboratory of Mycobacteria, Núcleo de Pesquisa em Microbiologia Médica, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Marcos Alaniz Rodrigues
- Laboratory of Mycobacteria, Núcleo de Pesquisa em Microbiologia Médica, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Erica Chimara
- Rede Brasileira de Pesquisa em Tuberculose (REDE-TB), Rio Grande, Rio Grande do Sul, Brazil
- Instituto Adolfo Lutz, São Paulo, Brazil
| | - Maria Cristina da Silva Lourenço
- Rede Brasileira de Pesquisa em Tuberculose (REDE-TB), Rio Grande, Rio Grande do Sul, Brazil
- Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Jacques Fountain
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, Orlando, USA
| | - Ivy Bastos Ramis
- Laboratory of Mycobacteria, Núcleo de Pesquisa em Microbiologia Médica, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
- Rede Brasileira de Pesquisa em Tuberculose (REDE-TB), Rio Grande, Rio Grande do Sul, Brazil
| | - Andrea von Groll
- Laboratory of Mycobacteria, Núcleo de Pesquisa em Microbiologia Médica, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
- Rede Brasileira de Pesquisa em Tuberculose (REDE-TB), Rio Grande, Rio Grande do Sul, Brazil
| | - Yulia Gerasimova
- Department of Chemistry, College of Sciences, University of Central Florida, Orlando, Florida, Orlando, USA
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, Orlando, USA
| | - Pedro Eduardo Almeida da Silva
- Laboratory of Mycobacteria, Núcleo de Pesquisa em Microbiologia Médica, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
- Rede Brasileira de Pesquisa em Tuberculose (REDE-TB), Rio Grande, Rio Grande do Sul, Brazil
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RNA-cleaving DNAzymes as a diagnostic and therapeutic agent against antimicrobial resistant bacteria. Curr Genet 2021; 68:27-38. [PMID: 34505182 DOI: 10.1007/s00294-021-01212-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The development of nucleic-acid-based antimicrobials such as RNA-cleaving DNAzyme (RCD), a short catalytically active nucleic acid, is a promising alternative to the current antibiotics. The current rapid spread of antimicrobial resistance (AMR) in bacteria renders some antibiotics useless against bacterial infection, thus creating the need for alternative antimicrobials such as DNAzymes. This review summarizes recent advances in the use of RCD as a diagnostic and therapeutic agent against AMR. Firstly, the recent diagnostic application of RCD for the detection of bacterial cells and the associated resistant gene(s) is discussed. The next section summarises the therapeutic application of RCD in AMR bacterial infections which includes direct targeting of the resistant genes and indirect targeting of AMR-associated genes. Finally, this review extends the discussion to challenges of utilizing RCD in real-life applications, and the potential of combining both diagnostic and therapeutic applications of RCD into a single agent as a theranostic agent.
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Cozma I, McConnell EM, Brennan JD, Li Y. DNAzymes as key components of biosensing systems for the detection of biological targets. Biosens Bioelectron 2021; 177:112972. [DOI: 10.1016/j.bios.2021.112972] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/01/2021] [Accepted: 01/02/2021] [Indexed: 12/11/2022]
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Dhar BC, Reed AJ, Mitra S, Rodriguez Sanchez P, Nedorezova DD, Connelly RP, Rohde KH, Gerasimova YV. Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis. Biosens Bioelectron 2020; 165:112385. [PMID: 32729510 DOI: 10.1016/j.bios.2020.112385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 02/01/2023]
Abstract
A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.
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Affiliation(s)
- Bidhan C Dhar
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Adam J Reed
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Suvra Mitra
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | | | - Daria D Nedorezova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Ryan P Connelly
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA.
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Abstract
Hybridization probes are RNA or DNA oligonucleotides or their analogs that bind to specific nucleotide sequences in targeted nucleic acids (analytes) via Watson-Crick base pairs to form probe-analyte hybrids. Formation of a stable hybrid would indicate the presence of a DNA or RNA fragment complementary to the known probe sequence. Some of the well-known technologies that rely on nucleic acid hybridization are TaqMan and molecular beacon (MB) probes, fluorescent in situ hybridization (FISH), polymerase chain reaction (PCR), antisense, siRNA, and CRISPR/cas9, among others. Although invaluable tools for DNA and RNA recognition, hybridization probes suffer from several common disadvantages including low selectivity under physiological conditions, low affinity to folded single-stranded RNA and double-stranded DNA, and high cost of dye-labeled and chemically modified probes. Hybridization probes are evolving into multifunctional molecular devices (dubbed here "multicomponent probes", "DNA machines", and "DNA robots") to satisfy complex and often contradictory requirements of modern biomedical applications. In the definition used here, "multicomponent probes" are DNA probes that use more than one oligonucleotide complementary to an analyzed sequence. A "DNA machine" is an association of a discrete number of DNA strands that undergoes structural rearrangements in response to the presence of a specific analyte. Unlike multicomponent probes, DNA machines unify several functional components in a single association even in the absence of a target. DNA robots are DNA machines equipped with computational (analytic) capabilities. This Account is devoted to an overview of the ongoing evolution of hybridization probes to DNA machines and robots. The Account starts with a brief excursion to historically significant and currently used instantaneous probes. The majority of the text is devoted to the design of (i) multicomponent probes and (ii) DNA machines for nucleic acid recognition and analysis. The fundamental advantage of both designs is their ability to simultaneously address multiple problems of RNA/DNA analysis. This is achieved by modular design, in which several specialized functional components are used simultaneously for recognition of RNA or DNA analytes. The Account is concluded with the analysis of perspectives for further evolution of DNA machines into DNA robots.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences
255, Orlando, Florida 32816-2366, United States
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