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Shiluli C, Kamath S, N. Kanoi B, Kimani R, Maina M, Waweru H, Kamita M, Ndirangu I, M. Abkallo H, Oduor B, Pamme N, Dupaty J, M. Klapperich C, Raju Lolabattu S, Gitaka J. Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis. OPEN RESEARCH AFRICA 2024; 7:2. [PMID: 38783971 PMCID: PMC11109563 DOI: 10.12688/openresafrica.14316.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Chlamydia trachomatis ( C. trachomatis) is a common sexually transmitted infection (STI). In 2019, the World Health Organization reported about 131 million infections. The majority of infected patients are asymptomatic with cases remaining undetected. It is likely that missed C. trachomatis infections contribute to preventable adverse health outcomes in women and children. Consequently, there is an urgent need of developing efficient diagnostic methods. In this study, genome-mining approaches to identify identical multi-repeat sequences (IMRS) distributed throughout the C. trachomatis genome were used to design a primer pair that would target regions in the genome. Genomic DNA was 10-fold serially diluted (100pg/μL to 1×10 -3pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and products were resolved on agarose gel. The novel assay, C. trachomatis IMRS-PCR, had an analytical sensitivity of 4.31 pg/µL, representing better sensitivity compared with 16S rRNA PCR (9.5 fg/µL). Our experimental data demonstrate the successful development of lateral flow and isothermal assays for detecting C. trachomatis DNA with potential use in field settings. There is a potential to implement this concept in miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for reliable point-of-care testing.
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Affiliation(s)
- Clement Shiluli
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Shwetha Kamath
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, Bangalore, India
| | - Bernard N. Kanoi
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Racheal Kimani
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Michael Maina
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Harrison Waweru
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Moses Kamita
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Ibrahim Ndirangu
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
| | - Hussein M. Abkallo
- Animal and Human Health Program, International Livestock Research Institute, Nairobi, Nairobi County, Kenya
| | - Bernard Oduor
- Animal and Human Health Program, International Livestock Research Institute, Nairobi, Nairobi County, Kenya
| | - Nicole Pamme
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Stockholm County, Sweden
| | - Joshua Dupaty
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | | | | | - Jesse Gitaka
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kiambu County, Kenya
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Favacho JDFR, Leite KK, Jacomasso T, Farias AB, Franco Filho LC, Gomes STM, dos Reis HS, Mota GD, Schluga PHDC, Tassi WS, Rampazzo RDCP, West SK, Gaydos CA, da Cunha AJLA, Costa ADT. Validation of a New Duplex Real-Time Polymerase Chain Reaction for Chlamydia trachomatis DNA Detection in Ocular Swab Samples. Diagnostics (Basel) 2024; 14:892. [PMID: 38732307 PMCID: PMC11083659 DOI: 10.3390/diagnostics14090892] [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: 01/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 05/13/2024] Open
Abstract
Trachoma is the world-leading infectious cause of preventable blindness and is caused by the bacteria Chlamydia trachomatis. In developing countries, diagnosis is usually based on clinical evaluation. Serological-based tests are cheaper than molecular-based ones, but the latter are more sensitive and specific. The present study developed a new duplex qPCR which concomitantly detects the C. trachomatis cryptic plasmid and the human 18S rRNA gene, with an LOD95% for C. trachomatis DNA of 13.04 genome equivalents per reaction. The new qPCR was tested using 50 samples from an endemic area and 12 from a non-endemic area that were previously characterized using direct immunofluorescence assay (DFA) and clinical evaluation. Among the 50 endemic samples, 3 were found to be positive by clinical evaluation (6%), 18 were found to be positive by DFA (36%), and 48 were found to be positive by qPCR (96%). Next, the new duplex qPCR was validated using 50 samples previously characterized by qPCR. Validation was carried out on a benchtop instrument (ABI7500) or on a portable point-of-care instrument (Q3-Plus), showing 95% specificity and 100% sensitivity. The ubiquitous presence of C. trachomatis DNA in samples from the endemic region confirms that constant monitoring is of paramount importance for the effective measurement of the elimination of trachoma. The newly developed duplex qPCR presented in this study, along with its validation in a portable qPCR system, constitutes important tools toward achieving this goal.
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Affiliation(s)
- Joana da Felicidade Ribeiro Favacho
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Keren Kariene Leite
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Thiago Jacomasso
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Aline Burda Farias
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Luciano Chaves Franco Filho
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Samara Tatielle Monteiro Gomes
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Herald Souza dos Reis
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Gardene Dourado Mota
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | | | - Walleyd Sami Tassi
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | | | - Sheila Kay West
- Dana Center for Preventative Ophthalmology, Johns Hopkins University, Baltimore, MD 21287, USA;
| | - Charlotte Ann Gaydos
- International Sexually Transmitted Disease Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD 21218, USA
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Han Y, An J, Yuan M, Fang J, Zhang J, Liang L, Liu Y. Covalent Coupling Assisted Hydrophilic Perovskite Spheres for Ratiometric Fluorescent Visual Multichannel Immunoassay. Adv Healthc Mater 2024; 13:e2303845. [PMID: 38117032 DOI: 10.1002/adhm.202303845] [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: 11/15/2023] [Revised: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Quantitative fluorescence immunoassay is essential for the construction of biosensing mechanisms and the quantification of trace markers. But the interference problems caused by low fluorescence efficiency and broad fluorescence spectrum of fluorescent probes have hindered the continued development of ratiometric fluorescence sensing in biosensing. Perovskite materials, with ultra-high color purity (FWHM < 30 nm) and photoluminescence quantum yield (PLQY) (close to 100%), are expected to be next-generation fluorescent probes. However, poor water stability and biocompatibility are still non-negligible in biosensor applications. In this work, hyperstatic perovskite fluorescent microspheres prepared by swelling-shrinking method can be used as ratiometric fluorescence signals and biological immunoassay platforms. Meanwhile, inspired by p-aminophenol (AP) controlled synthesis and the catalytic reaction of 4-aminophenol phosphate (APP) triggered by alkaline phosphatase (ALP), a strategy to prepare fluorescent nanoparticles as fluorescence signals for ALP detection is proposed. Most importantly, it is proposed for the first time to combine this enzymatic fluorescence with perovskite materials using covalent linkage to create a novel cascade immunoassay and use it for quantitative and visualization determination of hepatitis B surface antigen (HBsAg) for application verification. These results indicate the biosensing potential of perovskite materials and provide a pathway for high sensitivity enzyme detection and enzyme triggered immune detection.
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Affiliation(s)
- Yaqin Han
- Key Laboratory of Optoelectronic Technology & Systems, Ministry of Education, Chongqing University, Chongqing, 400044, China
- Center for Intelligent Sensing Technology, College of Optoelectronic Engineering, Chongqing University, Chongqing, 400044, China
| | - Jia An
- School of Optoelectronic Engineering, Chongqing university of Posts and Telecommunications, Chongqing, 400065, China
| | - Mengdi Yuan
- Key Laboratory of Optoelectronic Technology & Systems, Ministry of Education, Chongqing University, Chongqing, 400044, China
- Center for Intelligent Sensing Technology, College of Optoelectronic Engineering, Chongqing University, Chongqing, 400044, China
| | - Junan Fang
- Key Laboratory of Optoelectronic Technology & Systems, Ministry of Education, Chongqing University, Chongqing, 400044, China
- Center for Intelligent Sensing Technology, College of Optoelectronic Engineering, Chongqing University, Chongqing, 400044, China
| | - Jiajing Zhang
- Key Laboratory of Optoelectronic Technology & Systems, Ministry of Education, Chongqing University, Chongqing, 400044, China
- Center for Intelligent Sensing Technology, College of Optoelectronic Engineering, Chongqing University, Chongqing, 400044, China
| | - Lanju Liang
- School of Opto-Electronic Engineering, Zaozhuang University, Zaozhuang, 277160, China
| | - Yufei Liu
- Key Laboratory of Optoelectronic Technology & Systems, Ministry of Education, Chongqing University, Chongqing, 400044, China
- Center for Intelligent Sensing Technology, College of Optoelectronic Engineering, Chongqing University, Chongqing, 400044, China
- Faculty of Science and Engineering, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
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Zhong X, Fu Q, Wang Y, Long L, Jiang W, Chen M, Xia H, Zhang P, Tan F. CRISPR-based quantum dot nanobead lateral flow assay for facile detection of varicella-zoster virus. Appl Microbiol Biotechnol 2023; 107:3319-3328. [PMID: 37052634 DOI: 10.1007/s00253-023-12509-0] [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: 01/19/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
Varicella-zoster virus (VZV) infects more than 90% of the population worldwide and has a high incidence of postherpetic neuralgia in elderly patients, seriously affecting their quality of life. Combined with clustered regularly interspaced short palindromic repeats (CRISPR) system, we develop a quantum dot nanobeads (QDNBs) labeled lateral flow assay for VZV detection. Our assay allows the identification of more than 5 copies of VZV genomic DNA in each reaction. The entire process, from sample preparation to obtaining the results, takes less than an hour. In 86 clinical vesicles samples, the test shows 100% concordance with quantitative real-time PCR for VZV detection. Notably, when vesicles are present in specific areas, such as the genitals, our method outperforms clinical diagnosis. Compared to traditional detection methods, only a minute amount of blister fluid is required for accurate detection. Therefore, we anticipate that our method could be translated to clinical applications for specific and rapid VZV detection. KEY POINTS: • CRISPR/Cas12a and quantum dot nanobead-based lateral flow assay achieved 5 copies per reaction for VZV detection • Specific identification of VZV in atypical skin lesions • Results read by the naked eye within one hour.
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Affiliation(s)
- Xiaoqin Zhong
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Qiaoting Fu
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Yaoqun Wang
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Lan Long
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, 518172, China
| | - Wencheng Jiang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - Meiyu Chen
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China
| | - Hui Xia
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - Pengfei Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.
| | - Fei Tan
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, Shanghai Skin Disease Hospital, Shanghai, 200443, China.
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.
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Chen X, Zhou Q, Yuan W, Shi Y, Dong S, Luo X. Visual and rapid identification of Chlamydia trachomatis and Neisseria gonorrhoeae using multiplex loop-mediated isothermal amplification and a gold nanoparticle-based lateral flow biosensor. Front Cell Infect Microbiol 2023; 13:1067554. [PMID: 36926514 PMCID: PMC10011439 DOI: 10.3389/fcimb.2023.1067554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
Sexually transmitted chlamydia and gonorrhea infections caused by the bacteria Chlamydia trachomatis and Neisseria gonorrhoeae remain a major public health concern worldwide, particularly in less developed nations. It is crucial to use a point of care (POC) diagnostic method that is quick, specific, sensitive, and user-friendly to treat and control these infections effectively. Here, a novel molecular diagnostic assay, combining multiplex loop-mediated isothermal amplification (mLAMP) with a visual gold nanoparticles-based lateral flow biosensor (AuNPs-LFB) was devised and used for highly specific, sensitive, rapid, visual, and easy identification of C. trachomatis and N. gonorrhoeae. Two unique independent primer pairs were successful designed against the ompA and orf1 genes of C. trachomatis and N. gonorrhoeae, respectively. The optimal mLAMP-AuNPs-LFB reaction conditions were determined to be 67°C for 35 min. The detection procedure, involving crude genomic DNA extraction (~5 min), LAMP amplification (35 min), and visual results interpretation (<2 min), can be completed within 45 min. Our assay has a detection limit of 50 copies per test, and we did not observe any cross-reactivity with any other bacteria in our testing. Hence, our mLAMP-AuNPs-LFB assay can potentially be used for POC testing to detect C. trachomatis and N. gonorrhoeae in clinical settings, particularly in underdeveloped regions.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- *Correspondence: Xinhua Luo, ; Shilei Dong, ; Xu Chen,
| | - Qingxue Zhou
- Clinical Laboratory, Hangzhou Women’s Hospital, Hangzhou, Zhejiang, China
| | - Wei Yuan
- Department of Quality Control, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Yuanfang Shi
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
- *Correspondence: Xinhua Luo, ; Shilei Dong, ; Xu Chen,
| | - Xinhua Luo
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- *Correspondence: Xinhua Luo, ; Shilei Dong, ; Xu Chen,
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Charlermroj R, Makornwattana M, Phuengwas S, Karoonuthaisiri N. A rapid colorimetric lateral flow test strip for detection of live Salmonella Enteritidis using whole phage as a specific binder. Front Microbiol 2022; 13:1008817. [PMID: 36246228 PMCID: PMC9556839 DOI: 10.3389/fmicb.2022.1008817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Specific antibodies are essential components of immunoassay, which can be applied for the detection of pathogens. However, producing an antibody specific to live bacterial pathogens by the classical method of immunizing animals with live pathogens can be impractical. Phage display technology is an effective alternative method to obtain antibodies with the desired specificity against selected antigenic molecules. In this study, we demonstrated the power of a microarray-based technique for obtaining specific phage-derived antibody fragments against Salmonella, an important foodborne pathogen. The selected phage-displayed antibody fragments were subsequently employed to develop a lateral flow test strip assay for the detection of live Salmonella. The test strips showed specificity to Salmonella Enteritidis without cross-reactivity to eight serovars of Salmonella or other bacteria strains. The test strip assay requires 15 min, whereas the conventional biochemical and serological confirmation test requires at least 24 h. The microarray screening technique for specific phage-based binders and the test strip method can be further applied to other foodborne pathogens.
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Affiliation(s)
- Ratthaphol Charlermroj
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
- *Correspondence: Ratthaphol Charlermroj,
| | - Manlika Makornwattana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sudtida Phuengwas
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
- International Joint Research Center on Food Security, Pathum Thani, Thailand
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
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