1
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Ye T, Zong Y, Zhao G, Zhou A, Yue B, Zhao H, Li P. Role of Endoscopy in Esophageal Tuberculosis: A Narrative Review. J Clin Med 2022; 11:jcm11237009. [PMID: 36498584 PMCID: PMC9740747 DOI: 10.3390/jcm11237009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
Esophageal tuberculosis (ET) is a rare infectious disease of the gastrointestinal tract. Awareness of ET is deficient due to its low incidence. Unexplained dysphagia and upper gastrointestinal bleeding are the most common symptoms of ET. The prognosis is generally good if patients are diagnosed properly and receive anti-tubercular treatment promptly. However, ET is difficult to differentiate from other diseases. Endoscopic techniques such as esophagogastroduodenoscopy (EGD), endoscopic ultrasonography (EUS), contrast-enhanced harmonic endoscopic ultrasonography (CH-EUS), elastography, and endoscopic ultrasound--guided fine-needle aspiration (EUS-FNA) improve the diagnosis of ET. Thus, the characteristics of ET and other difficult-to-detect diseases according to EGD and EUS were summarized. Intriguingly, there is no literature relevant to the application of CH-EUS and elastography in ET. The authors' research center was first in introducing CH-EUS and elastography into the field of ET. The specific manifestation of ET based on CH-EUS was discovered for the first time. Correlative experience and representative cases were shared. The role of endoscopy in acquiring esophageal specimens and treatment for ET was also established. In this review, we aim to introduce a promising technology for the diagnosis and treatment of ET.
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Affiliation(s)
| | | | | | | | | | | | - Peng Li
- Correspondence: (H.Z.); (P.L.)
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2
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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Guaman-Bautista LP, Moreta-Urbano E, Oña-Arias CG, Torres-Arias M, Kyriakidis NC, Malcı K, Jonguitud-Borrego N, Rios-Solis L, Ramos-Martinez E, López-Cortés A, Barba-Ostria C. Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies. Diagnostics (Basel) 2021; 11:1981. [PMID: 34829328 PMCID: PMC8621220 DOI: 10.3390/diagnostics11111981] [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: 07/14/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19.
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Affiliation(s)
- Linda P. Guaman-Bautista
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Erick Moreta-Urbano
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Claudia G. Oña-Arias
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Marbel Torres-Arias
- Immunology and Virology Laboratory, Department of Life Science and Agriculture, Universidad de las Fuerzas Armadas, Quito 171103, Ecuador;
| | - Nikolaos C. Kyriakidis
- Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas, Quito 170125, Ecuador;
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Espiridion Ramos-Martinez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 4510, Mexico;
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador;
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170901, Ecuador
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4
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Lin CR, Wang HY, Lin TW, Lu JJ, Hsieh JCH, Wu MH. Development of a two-step nucleic acid amplification test for accurate diagnosis of the Mycobacterium tuberculosis complex. Sci Rep 2021; 11:5750. [PMID: 33707640 PMCID: PMC7952592 DOI: 10.1038/s41598-021-85160-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) remains one of the top 10 leading causes of death globally. The early diagnosis of MTBC can reduce mortality and mitigate disease transmission. However, current nucleic acid amplification diagnostic test methods are generally time-consuming and show suboptimal diagnostic performance, especially in extrapulmonary MTBC samples or acid-fast stain (AFS)-negative cases. Thus, development of an accurate assay for the diagnosis of MTBC is necessary, particularly under the above mentioned conditions. In this study, a single-tube nested real-time PCR assay (N-RTP) was developed and compared with a newly in-house-developed high-sensitivity real-time PCR assay (HS-RTP) using 134 clinical specimens (including 73 pulmonary and 61 extrapulmonary specimens). The amplification efficiency of HS-RTP and N-RTP was 99.8% and 100.7%, respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in these specimens were 97.5% (77/79) versus 94.9% (75/79) and 80.0% (44/55) versus 89.1% (49/55), respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in pulmonary specimens were 96.3% (52/54) versus 96.3% (52/54) and 73.7.0% (14/19) versus 89.5% (17/19), respectively; in extrapulmonary specimens, the sensitivity and specificity of HS-RTP and N-RTP were 100% (25/25) versus 92% (23/25) and 83.3% (30/36) versus 88.9% (32/36), respectively. Among the AFS-negative cases, the sensitivity and specificity of HS-RTP and N-RTP were 97.0% (32/33) versus 90.9% (30/33) and 88.0% (44/50) versus 92.0% (46/50), respectively. Overall, the sensitivity of HS-RTP was higher than that of N-RTP, and the performance was not compromised in extrapulmonary specimens and under AFS-negative conditions. In contrast, the specificity of the N-RTP assay was higher than that of the HS-RTP assay in all types of specimens. In conclusion, the HS-RTP assay would be useful for screening patients suspected of exhibiting an MTBC infection due to its higher sensitivity, while the N-RTP assay could be used for confirmation because of its higher specificity. Our results provide a two-step method (screen to confirm) that simultaneously achieves high sensitivity and specificity in the diagnosis of MTBC.
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Affiliation(s)
- Chien-Ru Lin
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan.,Ph.D. Program in Biomedical Engineering, Chang Gung University, Taoyuan City, Taiwan
| | - Ting-Wei Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Jang-Jih Lu
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City, Taiwan
| | - Jason Chia-Hsun Hsieh
- Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan.,Division of Haematology/Oncology, Department of Internal Medicine, New Taipei Municipal Hospital, New Taipei City, Taiwan
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan. .,Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan. .,Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City, Taiwan.
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5
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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6
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Chu ZJ, Xiao SJ, Yuan MY, Wang LZ, Wang SP, Zhang GM, Zhang ZB. Rapid and sensitive detection of Mycobacterium tuberculosis based on strand displacement amplification and magnetic beads. LUMINESCENCE 2020; 36:66-72. [PMID: 32706457 DOI: 10.1002/bio.3918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022]
Abstract
Tuberculosis is one of the main infectious diseases threatening public health, and the development of simple, rapid, and cost-saving methods for tuberculosis diagnosis is of profound importance for tuberculosis prevention and treatment. The bacterium Mycobacterium tuberculosis (MTB) is the pathogen that causes tuberculosis, and assaying for MTB is the only criterion for tuberculosis diagnosis. A new enzyme-free method based on strand displacement amplification and magnetic beads was developed for simple, rapid, and cost-saving MTB detection. Under optimum conditions, a good linear relationship could be observed between fluorescence and MTB specific DNA concentration ranging from 0.05 to 150 nM with a correlation coefficient of 0.993 (n = 8) and a detection limit of 47 pM (3σ/K). The present method also distinguished a one base mismatch from MTB specific DNA, showing great promise for MTB genome single base polymorphism analysis. MTB specific DNA content in polymerase chain reaction samples was successfully detected using the new method, and recoveries were 97.8-100.8%, indicating that the present method had high accuracy and shows good potential for the early diagnosis of tuberculosis.
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Affiliation(s)
- Zhao Jun Chu
- Fundamental Science on Radioactive Geology and Exploration Technology Laboratory, East China University of Technology, Nanchang, China
| | - Sai Jin Xiao
- Fundamental Science on Radioactive Geology and Exploration Technology Laboratory, East China University of Technology, Nanchang, China.,School of Chemistry, Biology and Material Science, ECUT, Nanchang, China
| | - Ming Yue Yuan
- School of Chemistry, Biology and Material Science, ECUT, Nanchang, China
| | - Li Zhi Wang
- School of Chemistry, Biology and Material Science, ECUT, Nanchang, China
| | - Shan Ping Wang
- School of Chemistry, Biology and Material Science, ECUT, Nanchang, China
| | - Guang Mei Zhang
- School of Chemistry, Biology and Material Science, ECUT, Nanchang, China
| | - Zhi Bin Zhang
- School of Chemistry, Biology and Material Science, ECUT, Nanchang, China
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7
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Tsai TT, Chen CA, Yi-Ju Ho N, Yang S, Chen CF. Fluorescent Double-Stranded DNA-Templated Copper Nanoprobes for Rapid Diagnosis of Tuberculosis. ACS Sens 2019; 4:2885-2892. [PMID: 31576745 DOI: 10.1021/acssensors.9b01163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, we investigate highly sensitive fluorescent Cu nanoparticles for use as rapid and specific nucleic acid amplification nanoprobes (NPs) for the diagnosis of tuberculosis. After applying polymerase chain reaction (PCR) to a tuberculosis (TB) sample, we demonstrate that the presence of the targeted IS6110 DNA sequence of TB can be easily and directly detected through the in situ formation of DNA-templated fluorescent Cu NPs and subsequently quantified using only a smartphone. Compared to traditional DNA analysis, this sensing platform does not require purification steps and eliminates the need for electrophoresis to confirm the PCR results. After optimization, this dsDNA-Cu NP-PCR method has the ability to analyze clinical TB nucleic acid samples at a detection limit of 5 fg/μL, and the fluorescent signal can be distinguished in only ∼3 min after the DNA has been amplified. Moreover, with the combination of smartphone-assisted imaging analysis, we can further reduce the instrument size/cost and enhance the portability. In this manner, we are able to eliminate the need for a fluorescent spectrophotometer to measure the clinical sample. These results demonstrate this platform's practical applicability, combining a smartphone and on-site analysis while retaining the detection performance, making it suitable for clinical DNA applications in resource-limited regions of the world.
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Affiliation(s)
- Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan 333, Taiwan
| | - Chung-An Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan 333, Taiwan
| | - Shuan Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
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8
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Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
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9
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Li D, Song Y, Zhang CL, Li X, Xia X, Zhang AM. Screening mutations in drug-resistant Mycobacterium tuberculosis strains in Yunnan, China. J Infect Public Health 2017. [DOI: 10.1016/j.jiph.2017.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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10
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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11
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Rodrigues AM, Najafzadeh MJ, de Hoog GS, de Camargo ZP. Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification. Front Microbiol 2015; 6:1385. [PMID: 26696992 PMCID: PMC4672047 DOI: 10.3389/fmicb.2015.01385] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/20/2015] [Indexed: 01/19/2023] Open
Abstract
Sporothrix infections are emerging as an important human and animal threat among otherwise healthy patients, especially in Brazil and China. Correct identification of sporotrichosis agents is beneficial for epidemiological surveillance, enabling implementation of adequate public-health policies and guiding antifungal therapy. In areas of limited resources where sporotrichosis is endemic, high-throughput detection methods that are specific and sensitive are preferred over phenotypic methods that usually result in misidentification of closely related Sporothrix species. We sought to establish rolling circle amplification (RCA) as a low-cost screening tool for species-specific identification of human-pathogenic Sporothrix. We developed six species-specific padlock probes targeting polymorphisms in the gene encoding calmodulin. BLAST-searches revealed candidate probes that were conserved intraspecifically; no significant homology with sequences from humans, mice, plants or microorganisms outside members of Sporothrix were found. The accuracy of our RCA-based assay was demonstrated through the specificity of probe-template binding to 25 S. brasiliensis, 58 S. schenckii, 5 S. globosa, 1 S. luriei, 4 S. mexicana, and 3 S. pallida samples. No cross reactivity between closely related species was evident in vitro, and padlock probes yielded 100% specificity and sensitivity down to 3 × 106 copies of the target sequence. RCA-based speciation matched identifications via phylogenetic analysis of the gene encoding calmodulin and the rDNA operon (kappa 1.0; 95% confidence interval 1.0-1.0), supporting its use as a reliable alternative to DNA sequencing. This method is a powerful tool for rapid identification and specific detection of medically relevant Sporothrix, and due to its robustness has potential for ecological studies.
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Affiliation(s)
- Anderson M Rodrigues
- Cell Biology Division, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo São Paulo, Brazil
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, Ghaem Hospital, School of Medicine, Mashhad University of Medical Sciences Mashhad, Iran
| | - G Sybren de Hoog
- Centraalbureau voor Schimmelcultures, CBS-KNAW Fungal Biodiversity Centre Utrecht, Netherlands
| | - Zoilo P de Camargo
- Cell Biology Division, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo São Paulo, Brazil
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12
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Zhao Y, Li G, Sun C, Li C, Wang X, Liu H, Zhang P, Zhao X, Wang X, Jiang Y, Yang R, Wan K, Zhou L. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis. PLoS One 2015; 10:e0143444. [PMID: 26599667 PMCID: PMC4657947 DOI: 10.1371/journal.pone.0143444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/04/2015] [Indexed: 02/07/2023] Open
Abstract
Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a “probe dropout” manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.
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Affiliation(s)
- Yong Zhao
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
| | - Guilian Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Chongyun Sun
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- Department of Clinical Laboratory, Chinese People’s Liberation Army General Hospital, Beijing 100853, P. R. China
| | - Chao Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Xiaochen Wang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, P. R. China
| | - Haican Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Pingping Zhang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Xinrui Wang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- Institute for Plague Prevention and Control of Hebei Province, Zhangjiakou 075000, P. R. China
| | - Yi Jiang
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Ruifu Yang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
| | - Kanglin Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
- * E-mail: (LZ); (KW)
| | - Lei Zhou
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- * E-mail: (LZ); (KW)
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Khalid FA, Hamid ZA, Mukhtar MM. Tuberculosis drug resistance isolates from pulmonary tuberculosis patients, Kassala State, Sudan. Int J Mycobacteriol 2015; 4:44-7. [PMID: 26655197 DOI: 10.1016/j.ijmyco.2014.11.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 11/30/2014] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND This study was conducted in Kassala Teaching Hospital, Kassala State, Sudan (January 2006-June 2008) to determine the rate of mycobacterium drug resistance to anti-tuberculous treatment and to explore the genotype of Mycobacterium tuberculosis resistant isolates using rpoB gene. METHODS 53 isolates of mycobacterium isolated from pulmonary tuberculosis (PTB) patients from Kassala State were subjected to drug susceptibility testing (DST) to anti-tuberculous drugs; 10 M.tuberculosis complex (MTBC) resistant isolates were subjected to polymerase chain reaction (PCR), and commercially the amplified DNA was sequenced. RESULTS DST detected resistance in 23/53 (43.39%) isolates, among which rifampicin had a high number of resistant isolates (13/23), followed by streptomycin (11/23), and multi-drug resistance was detected in 5 isolates. DNA sequence analysis of 10 MTBC-resistant isolates detected variations within and outside the rifampicin resistant determining region (RRDR). Variation within RRDR was detected at positions 512 (AGC/ATC, Ser/Ile), and 528 (CGC/CTC, Arg/Leu). Outside the RRDR region variations were detected at positions 498 (GTG/GGG, Val/gly), 488 (ACA/ACC, Thr/Thr), which is a silent mutation. Insertions were observed at positions 484, 496 (GTG/GTGA, CGG/CAGG, respectively). Deletion was observed at position 487 (ATC/_TC). DISCUSSION AND CONCLUSION This study revealed that high resistance to rifampicin was associated with various point mutations in and out of the RRDR of the rpoB gene. Molecular methods are needed for early detection of TB disease and drug resistance.
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Affiliation(s)
| | - Zuhal A Hamid
- National Institute of Cancer, University of Gezira, Sudan
| | - M M Mukhtar
- Institute of Endemic Diseases, University of Khartoum, Sudan.
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Rapid identification of black grain eumycetoma causative agents using rolling circle amplification. PLoS Negl Trop Dis 2014; 8:e3368. [PMID: 25474355 PMCID: PMC4256478 DOI: 10.1371/journal.pntd.0003368] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022] Open
Abstract
Accurate identification of mycetoma causative agent is a priority for treatment. However, current identification tools are far from being satisfactory for both reliable diagnosis and epidemiological investigations. A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling Circle Amplification (RCA) uses species-specific padlock probes and isothermal DNA amplification. The tests were based on ITS sequences and developed for Falciformispora senegalensis, F. tompkinsii, Madurella fahalii, M. mycetomatis, M. pseudomycetomatis, M. tropicana, Medicopsis romeroi, and Trematosphaeria grisea. With the isothermal RCA assay, 62 isolates were successfully identified with 100% specificity and no cross reactivity or false results. The main advantage of this technique is the low-cost, high specificity, and simplicity. In addition, it is highly reproducible and can be performed within a single day. Treatment of eumycetoma largely depends on the causative pathogen. Identification of mycetoma agent with phenotypic features is too limited, and physiological and biochemical techniques are laborious, time-consuming and nonspecific, whereas the currently available molecular methods based on DNA sequencing are specific but extremely expensive. We describe rolling circle amplification method for identification of black grain eumycetoma using species-specific padlock probes. Eight probes were designed and successfully used for species identification and the results were easily visualized in 1% agarose gel. RCA provides a simple, reproducible, and cost-effective method for rapid identification of mycetoma agent that can be used in low-resource clinical settings.
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Wang X, Yu X, Wang X, Suzuki M, Asanuma H, Dong P, Wu W, Liang X. Highly specific DNA detection from massive background nucleic acids based on rolling circle amplification of target dsDNA. RSC Adv 2014. [DOI: 10.1039/c4ra05642f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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