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Zhu Y, Feng Z, Xu Y, Luo S, Zhang R, Shi X, Wu X, Zhang H. Rapid detection of Mycobacterium tuberculosis based on cyp141 via real-time fluorescence loop-mediated isothermal amplification (cyp141-RealAmp). Front Cell Infect Microbiol 2024; 14:1349063. [PMID: 38938885 PMCID: PMC11208306 DOI: 10.3389/fcimb.2024.1349063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/06/2024] [Indexed: 06/29/2024] Open
Abstract
Background The rapid detection of Mycobacterium tuberculosis (MTB) is essential for controlling tuberculosis. Methods We designed a portable thermocycler-based real-time fluorescence loop-mediated isothermal amplification assay (cyp141-RealAmp) using six oligonucleotide primers derived from cyp141 to detect MTB. A combined number of 213 sputum samples (169 obtained from clinically diagnosed cases of pulmonary TB and 44 from a control group without tuberculosis) underwent Acid-fast bacillus (AFB) smear, culture, Xpert MTB/RIF assays, and cyp141-RealAmp assay. Results By targeting MTB cyp141, this technique could detect as low as 10 copies/reaction within 30 min, and it was successfully rejected by other mycobacteria and other bacterial species tested. Of the 169 patients, there was no statistical difference between the detection rate of cyp141-RealAmp (92.90%, 95% CI: 89.03-96.07) and that of Xpert MTB/RIF (94.67%, 95% CI: 91.28-98.06) (P > 0.05), but both were statistically higher than that of culture (65.68%, 95% CI: 58.52-72.84) (P< 0.05) and AFB (57.40%, 95% CI: 49.94-64.86) (P< 0.05). Both cyp141-RealAmp and Xpert MTB/RIF had a specificity of 100%. Furthermore, a high concordance between cyp141-RealAmp and Xpert MTB/RIF was found (Kappa = 0.89). Conclusion The cyp141-RealAmp assay was shown to be effective, responsive, and accurate in this study. This method offers a prospective strategy for the speedy and precise detection of MTB.
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Affiliation(s)
- Yinyin Zhu
- Department of Microbial Testing, Nanjing Center for Disease Control and Prevention Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zi Feng
- Department of Microbial Testing, Nanjing Center for Disease Control and Prevention Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yinfang Xu
- Department of Infectious Diseases, the Affiliated Zhongda Hospital of Southeast University, Nanjing, Jiangsu, China
| | - Sha Luo
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Ruixian Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xudong Shi
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xuping Wu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Hongying Zhang
- Department of Microbial Testing, Nanjing Center for Disease Control and Prevention Affiliated to Nanjing Medical University, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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Wang Z, Wang Y, Lin L, Wu T, Zhao Z, Ying B, Chang L. A finger-driven disposable micro-platform based on isothermal amplification for the application of multiplexed and point-of-care diagnosis of tuberculosis. Biosens Bioelectron 2022; 195:113663. [PMID: 34610534 DOI: 10.1016/j.bios.2021.113663] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/29/2021] [Accepted: 09/19/2021] [Indexed: 02/08/2023]
Abstract
Tuberculosis (TB) remains the high-risk infectious pathogen that caused global pandemic and high mortality, particularly in the areas lack in health resources. Clinical TB screening and diagnosis are so far mainly conducted on limited types of commercial platforms, which are expensive and require skilled personnel. In this work, we introduced a low-cost and portable finger-driven microfluidic chip (named Fd-MC) based on recombinase polymerase amplification (RPA) for rapid on-site detection of TB. After injection of the pre-treated sample solution, the pre-packaged buffer was driven by the pressure generated by the finger-actuated operation to accomplish sequential processes of diagnosis in a fully isolated microchannel. An in-situ fluorescence strategy based on FAM-probe was implemented for on-chip results read-out though a hand-held UV lamp. Hence, the Fd-MC proved unique advantageous for avoiding the risk of infection or environmental contamination. In addition, the Fd-MC was designed for multiplexed detection, which is able to not only identify TB/non-TB infection, but also differentiate between human Mycobacterium tuberculosis and Mycobacterium bovis. The platform was verified in 37 clinical samples, statistically with 100% specificity and 95.2% sensitivity as compared to commercial real-time RPA. Overall, the proposed platform eliminates the need on external pumps and skilled personnel, holding promise to POC testing in the resource-limited area.
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Affiliation(s)
- Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Long Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Tao Wu
- Department of Laboratory Medicine, Med+X Center for Manufacturing, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Clinical Laboratory Medicine, People's Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest Minzu University), Yinchuan 750002, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, Med+X Center for Manufacturing, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, Med+X Center for Manufacturing, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China; School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei 230032, China.
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Rapid detection of multidrug-resistant tuberculosis based on allele-specific recombinase polymerase amplification and colorimetric detection. PLoS One 2021; 16:e0253235. [PMID: 34115793 PMCID: PMC8195408 DOI: 10.1371/journal.pone.0253235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) poses a serious threat to TB control. Early diagnosis and proper treatment are essential factors to limit the spread of the disease. The existing molecular tests for MDR-TB usually require specific instruments, steady power supply, and routine maintenance, which might be obstacles for low-resource settings. This study aimed to develop allele-specific isothermal recombinase polymerase amplification (allele-specific RPA) to simultaneously detect the most common mutations in the rpoB gene at codons 516, 526, and 531, which are associated with rifampicin resistance, and in the katG gene at codon 315, which is related to isoniazid resistance. Allele-specific primers targeting four major mutations, rpoB516, rpoB526, rpoB531, and katG315, were constructed and used in individual RPA reactions. The RPA amplicons were endpoints detected by the naked eye immediately after applying SYBR Green I. The optimised RPA assay was evaluated with the Mycobacterium tuberculosis wild-type strain H37Rv and 141 clinical M. tuberculosis isolates. The results revealed that allele-specific RPA combined with SYBR Green I detection (AS-RPA/SYBR) detected these four major mutations with 100% sensitivity and specificity relative to DNA sequencing. The limits of detection for these particular mutations with AS-RPA/SYBR were 5 ng. As a result of the outstanding performance of AS-RPA/SYBR, including its easy setup, speed, lack of a specific instrument requirement, and lack of cross-reaction with other bacteria, this technique may be integrated for the molecular diagnosis of MDR-TB, especially in low-resource settings.
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Xu Y, Wu P, Zhang H, Li J. Rapid detection of Mycobacterium tuberculosis based on antigen 85B via real-time recombinase polymerase amplification. Lett Appl Microbiol 2020; 72:106-112. [PMID: 32726877 DOI: 10.1111/lam.13364] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB), as a common infectious disease, still remains a severe challenge to public health. Due to the unsatisfied clinical needs of currently available diagnostic vehicles, it is desired to establish a new approach for universally detecting Mycobacterium tuberculosis. Herein, we designed a real-time recombinase polymerase amplification (RPA) technology for identifying M. tuberculosis within 20 min at 39°C via custom-designed oligonucleotide primers and probe, which could specifically target antigen 85B (Ag85B). Particularly, the primers F4-R4 produced the fastest fluorescence signal with the probe among four pairs of designed primers in the RPA assays. The optimal primers/probe combination could effectively identify M. tuberculosis with the detection limit of 4·0 copies per μl, as it could not show a positive signal for the genomic DNA from other mycobacteria or pathogens. The Ag85B-based RPA could determine the genomic DNA extracted from M. tuberculosis with high reliability (100%, 22/22). More importantly, when testing clinical sputum samples, the real-time RPA displayed an admirable sensitivity (90%, 95% CI: 80·0-96·0%) and specificity (98%, 95% CI: 89·0-100·0%) compared to traditional smear microscopy, which was similar to the assay of Xpert MTB/RIF. This real-time RPA based Ag85B provides a promising strategy for the rapid and universal diagnosis of TB.
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Affiliation(s)
- Y Xu
- Department of Infectious Diseases, the First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China.,Department of Infectious Diseases, the Affiliated Zhongda Hospital of Southeast University, Nanjing, PR China
| | - P Wu
- Department of Infectious Diseases, the Affiliated Zhongda Hospital of Southeast University, Nanjing, PR China
| | - H Zhang
- Department of Microbial Inspection, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, PR China
| | - J Li
- Department of Infectious Diseases, the First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China
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Waema MW, Misinzo G, Kagira JM, Agola EL, Ngowi HA. DNA-Detection Based Diagnostics for Taenia solium Cysticercosis in Porcine. J Parasitol Res 2020; 2020:5706981. [PMID: 32395335 PMCID: PMC7199576 DOI: 10.1155/2020/5706981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/02/2019] [Indexed: 11/17/2022] Open
Abstract
Porcine cysticercosis is a neglected and underestimated disease caused by metacestode stage of the tapeworm, Taenia solium (T. solium). Pigs are the intermediate hosts of T. solium while human are the only known definitive host. The disease has an economic consequence because the affected farmers lose 50-100 percent of the value of pigs if they are infected. Lack of affordable, easy to use, sensitive, and specific molecular diagnostic tools for detection of infections at the farm level hinders the control of porcine cysticercosis in endemic areas. A number of DNA based diagnostic assays for the detection of T. solium infections in pigs have been developed and evaluated but none is applicable at low-resource areas where this disease is an endemic. This review focuses mainly on DNA based diagnostic methods, their sensitivity, specificity, and utilization at low-resource areas. We summarized data from 65 studies on the current DNA-detection based diagnostic techniques for T. solium cysticercosis in porcine, published in English between the years 2000-2018, identified through PubMed search engine. Of the different polymerase chain reaction (PCR) assays developed for identification of T. solium, the most sensitive (97-100%) and specific (100%) one is nested PCR. One study utilized loop-mediated isothermal amplification (LAMP) as a diagnostic tool for the detection of T. solium infections though its field use was never determined. Recombinase polymerase amplification (RPA) has been evaluated as a diagnostic tool for a variety of diseases, but has never been exploited for the diagnosis of cysticercosis/taeniasis. In conclusion, several molecular methods have been developed and evaluated in lab settings. However, there is need to validate these methods as a diagnostic tool to diagnose porcine cysticercosis in low-resource areas.
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Affiliation(s)
- Maxwell W. Waema
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, P.O Box 3297, Chuo Kikuu, Morogoro, Tanzania
| | - Gerald Misinzo
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, P.O Box 3297, Chuo Kikuu, Morogoro, Tanzania
| | - John M. Kagira
- Department of Animal Health and Production, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000-00200, Nairobi, Kenya
| | - Eric L. Agola
- Centre of Biotechnology Research and Development, Kenya Medical Research Institute, P.O Box 3297, Nairobi, Kenya
| | - Helena A. Ngowi
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, P.O Box 3021, Chuo Kikuu, Morogoro, Tanzania
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Nelson MM, Waldron CL, Bracht JR. Rapid molecular detection of macrolide resistance. BMC Infect Dis 2019; 19:144. [PMID: 30755177 PMCID: PMC6373131 DOI: 10.1186/s12879-019-3762-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emerging antimicrobial resistance is a significant threat to human health. However, methods for rapidly diagnosing antimicrobial resistance generally require multi-day culture-based assays. Macrolide efflux gene A, mef(A), provides resistance against erythromycin and azithromycin and is known to be laterally transferred among a wide range of bacterial species. METHODS We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. To validate these results we performed broth dilution assays to assess antimicrobial resistance to erythromycin and ampicillin (a negative control). RESULTS We validate the detection of mef(A) in raw lysates of Streptococcus pyogenes, S. pneumoniae, S. salivarius, and Enterococcus faecium bacterial lysates within 7-10 min of assay time. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. The assay was unaffected by single-nucleotide polymorphisms within divergent mef(A) gene sequences, strengthening its utility as a robust diagnostic tool. CONCLUSIONS This finding opens the door to implementation of rapid genomic diagnostics in a clinical setting, while providing researchers a rapid, cost-effective tool to track antibiotic resistance in both pathogens and commensal strains.
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Affiliation(s)
- Megan M. Nelson
- Department of Biology, American University, Washington, DC 20016 USA
| | | | - John R. Bracht
- Department of Biology, American University, Washington, DC 20016 USA
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