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Wilkinson AF, Barra MJ, Novak EN, Bond M, Richards-Kortum R. Point-of-care isothermal nucleic acid amplification tests: progress and bottlenecks for extraction-free sample collection and preparation. Expert Rev Mol Diagn 2024; 24:509-524. [PMID: 38973430 DOI: 10.1080/14737159.2024.2375233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Suitable sample collection and preparation methods are essential to enable nucleic acid amplification testing at the point of care (POC). Strategies that allow direct isothermal nucleic acid amplification testing (iNAAT) of crude sample lysate without the need for nucleic acid extraction minimize time to result as well as the need for operator expertise and costly infrastructure. AREAS COVERED The authors review research to understand how sample matrix and preparation affect the design and performance of POC iNAATs. They focus on approaches where samples are directly combined with liquid reagents for preparation and amplification via iNAAT strategies. They review factors related to the type and method of sample collection, storage buffers, and lysis strategies. Finally, they discuss RNA targets and relevant regulatory considerations. EXPERT OPINION Limitations in sample preparation methods are a significant technical barrier preventing implementation of nucleic acid testing at the POC. The authors propose a framework for co-designing sample preparation and amplification steps for optimal performance with an extraction-free paradigm by considering a sample matrix and lytic strategy prior to an amplification assay and readout. In the next 5 years, the authors anticipate increasing priority on the co-design of sample preparation and iNAATs.
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Affiliation(s)
| | - Maria J Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emilie N Novak
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Meaghan Bond
- Rice360 Institute for Global Health Technologies, Rice University, Houston, TX, USA
| | - Rebecca Richards-Kortum
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice360 Institute for Global Health Technologies, Rice University, Houston, TX, USA
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Lewis JD, Salipante SJ. Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests. J Clin Microbiol 2024; 62:e0024324. [PMID: 38629844 PMCID: PMC11237385 DOI: 10.1128/jcm.00243-24] [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: 02/12/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.
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Affiliation(s)
- Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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Chen Y, Zhao R, Huang Z, Chu C, Xiao Y, Hu X, Wang X. A small-scale external quality assessment for PCR detection of group B streptococcus in China. Clin Chim Acta 2024; 553:117733. [PMID: 38128816 DOI: 10.1016/j.cca.2023.117733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Group B streptococcus (GBS) is considered a leading cause of maternal and infant morbidity and mortality. Molecular diagnosis is a routinely used approach for GBS screening to protect pregnant women and prevent early-onset GBS neonatal disease. The objective of this study was to identify issues and guarantee the dependability of GBS molecular diagnosis by an external quality assessment (EQA) scheme. METHODS The EQA panel comprised eight samples spiked with 10-fold dilutions of GBS suspension (20-2,000,000 copies/mL), and 2 negative control samples. The panels were coded randomly and distributed to participating laboratories for GBS detection. RESULTS In total, 44 participating laboratories submitted results with eight commercial GBS PCR assays and one in-house assay. Among them, 36 obtained an acceptable or higher performance score, while 8 required improvement. Among the 440 results returned, 62 (14.1 %) were incorrect, including 5 false positives and 57 false negatives. CONCLUSIONS Our small-scale EQA showed that most participating laboratories have reliable diagnostic capacities for GBS PCR detection. Nonetheless, further improvements in the detection performance of some laboratories are required, particularly with low-concentration samples. Our survey also reinforces the use of EQA as an essential tool to evaluate the overall proficiency of clinical laboratories.
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Affiliation(s)
- Yingwei Chen
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Ran Zhao
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Zhongqiang Huang
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Chengxiang Chu
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Yanqun Xiao
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Xiaobo Hu
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China.
| | - Xueliang Wang
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China.
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Chang MM, Ma A, Novak EN, Barra M, Kundrod KA, Montealegre JR, Scheurer ME, Castle PE, Schmeler K, Richards-Kortum R. A novel tailed primer nucleic acid test for detection of HPV 16, 18 and 45 DNA at the point of care. Sci Rep 2023; 13:20397. [PMID: 37989845 PMCID: PMC10663460 DOI: 10.1038/s41598-023-47582-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023] Open
Abstract
Cervical cancer is a leading cause of death for women in low-resource settings despite being preventable through human papillomavirus (HPV) vaccination, early detection, and treatment of precancerous lesions. The World Health Organization recommends high-risk HPV (hrHPV) as the preferred cervical cancer screening strategy, which is difficult to implement in low-resource settings due to high costs, reliance on centralized laboratory infrastructure, and long sample-to-answer times. To help meet the need for rapid, low-cost, and decentralized cervical cancer screening, we developed tailed primer isothermal amplification and lateral flow detection assays for HPV16, HPV18, and HPV45 DNA. We translated these assays into a self-contained cartridge to achieve multiplexed detection of three hrHPV genotypes in a disposable cartridge. The developed test achieves clinically relevant limits of detection of 50-500 copies per reaction with extracted genomic DNA from HPV-positive cells. Finally, we performed sample-to-answer testing with direct lysates of HPV-negative and HPV-positive cell lines and demonstrated consistent detection of HPV16, HPV18, and HPV45 with 5000-50,000 cells/mL in < 35 min. With additional optimization to improve cartridge reliability, incorporation of additional hrHPV types, and validation with clinical samples, the assay could serve as a point-of-care HPV DNA test that improves access to cervical cancer screening in low-resource settings.
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Affiliation(s)
- Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ariel Ma
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jane Richards Montealegre
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael E Scheurer
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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Allan-Blitz LT, Shah P, Adams G, Branda JA, Klausner JD, Goldstein R, Sabeti PC, Lemieux JE. Development of Cas13a-based assays for Neisseria gonorrhoeae detection and gyrase A determination. mSphere 2023; 8:e0041623. [PMID: 37732792 PMCID: PMC10597441 DOI: 10.1128/msphere.00416-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
Neisseria gonorrhoeae is one of the most common bacterial sexually transmitted infections. The emergence of antimicrobial-resistant N. gonorrhoeae is an urgent public health threat. Currently, the diagnosis of N. gonorrhoeae infection requires expensive laboratory infrastructure, while antimicrobial susceptibility determination requires bacterial culture, both of which are infeasible in low-resource areas where the prevalence of infection is highest. Recent advances in molecular diagnostics, such as specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) using CRISPR-Cas13a and isothermal amplification, have the potential to provide low-cost detection of pathogen and antimicrobial resistance. We designed and optimized RNA guides and primer sets for SHERLOCK assays capable of detecting N. gonorrhoeae via the porA gene and of predicting ciprofloxacin susceptibility via a single mutation in the gyrase A (gyrA) gene. We evaluated their performance using both synthetic DNA and purified N. gonorrhoeae isolates. For porA, we created both a fluorescence-based assay and lateral flow assay using a biotinylated fluorescein reporter. Both methods demonstrated sensitive detection of 14 N. gonorrhoeae isolates and no cross-reactivity with 3 non-gonococcal Neisseria isolates. For gyrA, we created a fluorescence-based assay that correctly distinguished between 20 purified N. gonorrhoeae isolates with phenotypic ciprofloxacin resistance and 3 with phenotypic susceptibility. We confirmed the gyrA genotype predictions from the fluorescence-based assay with DNA sequencing, which showed 100% concordance for the isolates studied. We report the development of Cas13a-based SHERLOCK assays that detect N. gonorrhoeae and differentiate ciprofloxacin-resistant isolates from ciprofloxacin-susceptible isolates. IMPORTANCE Neisseria gonorrhoeae, the cause of gonorrhea, disproportionately affects resource-limited settings. Such areas, however, lack the technical capabilities for diagnosing the infection. The consequences of poor or absent diagnostics include increased disease morbidity, which, for gonorrhea, includes an increased risk for HIV infection, infertility, and neonatal blindness, as well as an overuse of antibiotics that contributes to the emergence of antibiotic resistance. We used a novel CRISPR-based technology to develop a rapid test that does not require laboratory infrastructure for both diagnosing gonorrhea and predicting whether ciprofloxacin can be used in its treatment, a one-time oral pill. With further development, that diagnostic test may be of use in low-resource settings.
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Affiliation(s)
- Lao-Tzu Allan-Blitz
- Division of Global Health Equity, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Palak Shah
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gordon Adams
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jeffrey D. Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Robert Goldstein
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
| | - Jacob E. Lemieux
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Kundrod KA, Barra M, Wilkinson A, Smith CA, Natoli ME, Chang MM, Coole JB, Santhanaraj A, Lorenzoni C, Mavume C, Atif H, Montealegre JR, Scheurer ME, Castle PE, Schmeler KM, Richards-Kortum RR. An integrated isothermal nucleic acid amplification test to detect HPV16 and HPV18 DNA in resource-limited settings. Sci Transl Med 2023; 15:eabn4768. [PMID: 37343083 PMCID: PMC10566637 DOI: 10.1126/scitranslmed.abn4768] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
High-risk human papillomavirus (HPV) DNA testing is widely acknowledged as the most sensitive cervical cancer screening method but has limited availability in resource-limited settings, where the burden of cervical cancer is highest. Recently, HPV DNA tests have been developed for use in resource-limited settings, but they remain too costly for widespread use and require instruments that are often limited to centralized laboratories. To help meet the global need for low-cost cervical cancer screening, we developed a prototype, sample-to-answer, point-of-care test for HPV16 and HPV18 DNA. Our test relies on isothermal DNA amplification and lateral flow detection, two technologies that reduce the need for complex instrumentation. We integrated all test components into a low-cost, manufacturable platform, and performance of the integrated test was evaluated with synthetic samples, provider-collected clinical samples in a high-resource setting in the United States, and self-collected clinical samples in a low-resource setting in Mozambique. We demonstrated a clinically relevant limit of detection of 1000 HPV16 or HPV18 DNA copies per test. The test requires six user steps, yields results in 45 min, and can be performed using a benchtop instrument and minicentrifuge by minimally trained personnel. The projected per-test cost is <$5, and the projected instrumentation cost is <$1000. These results show the feasibility of a sample-to-answer, point-of-care HPV DNA test. With the inclusion of other HPV types, this test has the potential to fill a critical gap for decentralized and globally accessible cervical cancer screening.
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Affiliation(s)
- Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mary E Natoli
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jackson B Coole
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Cesaltina Lorenzoni
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Celda Mavume
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Hira Atif
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | | | - Michael E Scheurer
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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8
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Allan-Blitz LT, Shah P, Adams G, Branda JA, Klausner JD, Goldstein R, Sabeti PC, Lemieux JE. Development of Cas13a-based Assays for Neisseria gonorrhoeae Detection and Gyrase A Determination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.21.23290304. [PMID: 37293004 PMCID: PMC10246164 DOI: 10.1101/2023.05.21.23290304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Neisseria gonorrhoeae is one of the most common bacterial sexually transmitted infections. The emergence of antimicrobial-resistant N. gonorrhoeae is an urgent public health threat. Currently, diagnosis of N. gonorrhoeae infection requires expensive laboratory infrastructure, while antimicrobial susceptibility determination requires bacterial culture, both of which are infeasible in low-resource areas where prevalence is highest. Recent advances in molecular diagnostics, such as Specific High-sensitivity Enzymatic Reporter unLOCKing (SHERLOCK) using CRISPR-Cas13a and isothermal amplification, have the potential to provide low-cost detection of pathogen and antimicrobial resistance. Methods and Results We designed and optimized RNA guides and primer-sets for SHERLOCK assays capable of detecting N. gonorrhoeae via the por A gene and of predicting ciprofloxacin susceptibility via a single mutation in the gyrase A ( gyr A) gene. We evaluated their performance using both synthetic DNA and purified N. gonorrhoeae isolates. For por A, we created both a fluorescence-based assay and lateral flow assay using a biotinylated FAM reporter. Both methods demonstrated sensitive detection of 14 N. gonorrhoeae isolates and no cross-reactivity with 3 non-gonococcal Neisseria isolates. For gyr A, we created a fluorescence-based assay that correctly distinguished between 20 purified N. gonorrhoeae isolates with phenotypic ciprofloxacin resistance and 3 with phenotypic susceptibility. We confirmed the gyr A genotype predictions from the fluorescence-based assay with DNA sequencing, which showed 100% concordance for the isolates studied. Conclusion We report the development of Cas13a-based SHERLOCK assays that detect N. gonorrhoeae and differentiate ciprofloxacin-resistant isolates from ciprofloxacin-susceptible isolates.
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Affiliation(s)
- Lao-Tzu Allan-Blitz
- Division of Global Health Equity: Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Palak Shah
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Gordon Adams
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jeffrey D. Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Robert Goldstein
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
| | - Jacob E. Lemieux
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
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Smith CA, Chang MM, Kundrod KA, Novak EN, Parra SG, López L, Mavume C, Lorenzoni C, Maza M, Salcedo MP, Carns JL, Baker E, Montealegre J, Scheurer M, Castle PE, Schmeler KM, Richards-Kortum RR. A low-cost, paper-based hybrid capture assay to detect high-risk HPV DNA for cervical cancer screening in low-resource settings. LAB ON A CHIP 2023; 23:451-465. [PMID: 36562325 PMCID: PMC9890501 DOI: 10.1039/d2lc00885h] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Cervical cancer is a leading cause of cancer death for women in low-resource settings. The World Health Organization recommends that cervical cancer screening programs incorporate HPV DNA testing, but available tests are expensive, require laboratory infrastructure, and cannot be performed at the point-of-care. We developed a two-dimensional paper network (2DPN), hybrid-capture, signal amplification assay and a point-of-care sample preparation protocol to detect high-risk HPV DNA from exfoliated cervical cells within an hour. The test does not require expensive equipment and has an estimated cost of <$3 per test without the need for batching. We evaluated performance of the paper HPV DNA assay with short synthetic and genomic HPV DNA targets, HPV positive and negative cellular samples, and two sets of clinical samples. The first set of clinical samples consisted of 16 biobanked, provider-collected cervical samples from a study in El Salvador previously tested with careHPV and subsequently tested in a controlled laboratory environment. The paper HPV DNA test correctly identified eight of eight HPV-negative clinical samples and seven of eight HPV-positive clinical samples. We then performed a field evaluation of the paper HPV DNA test in a hospital laboratory in Mozambique. Cellular controls generated expected results throughout field testing with fully lyophilized sample preparation and 2DPN reagents. When evaluated with 16 residual self-collected cervicovaginal samples previously tested by the GeneXpert HPV assay ("Xpert"), the accuracy of the HPV DNA paper test in the field was reduced compared to testing in the controlled laboratory environment, with positive results obtained for all eight HPV-positive samples as well as seven of eight HPV-negative samples. Further evaluation showed reduction in performance was likely due in part to increased concentration of exfoliated cells in the self-collected clinical samples from Mozambique compared with provider-collected samples from El Salvador. Finally, a formal usability assessment was conducted with users in El Salvador and Mozambique; the assay was rated as acceptable to perform after minimal training. With additional optimization for higher cell concentrations and inclusion of an internal cellular control, the paper HPV DNA assay offers promise as a low-cost, point-of-care cervical cancer screening test in low-resource settings.
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Affiliation(s)
- Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | | | - Emilie N Novak
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Sonia G Parra
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Leticia López
- Basic Health International, San Salvador, El Salvador
| | | | - Cesaltina Lorenzoni
- Hospital Central de Maputo, Maputo, Mozambique
- Ministerio da Saude de Moçambique (MISAU), Maputo, Mozambique
| | - Mauricio Maza
- Basic Health International, San Salvador, El Salvador
| | - Mila P Salcedo
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer L Carns
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Ellen Baker
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jane Montealegre
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Michael Scheurer
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Philip E Castle
- Divisions of Cancer Prevention and Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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10
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McCloskey D, Erickson D. Rapid nucleic acid extraction from skin biopsies using a point-of-care device. LAB ON A CHIP 2022; 22:3229-3235. [PMID: 35861177 PMCID: PMC9399003 DOI: 10.1039/d2lc00457g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Sample processing is often the rate-limiting step for point-of-care nucleic acid testing, especially for large, robust tissues such as skin biopsies, which can be used to diagnose a variety of dermatological diseases. Extraction of nucleic acids from these samples often relies on lengthy enzymatic digestions, increasing the time to result and reducing the potential impact of rapid molecular diagnostic approaches. To address this, we have developed BLENDER, a device for rapid nucleic acid extraction from tissue biopsies that combines bead-beating homogenization with simultaneous sample heating for enzymatic lysis. Our device can produce a complete DNA yield from a 3 mm cylindrical skin biopsy with only a 15 minute extraction compared to 4 hours when using a commercially available extraction protocol. Decreasing sample-processing time for tissue biopsies could reduce time-to-result for downstream analysis, enabling faster point-of-care diagnosis of solid cancers in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
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11
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Narahari T, Dahmer J, Sklavounos A, Kim T, Satkauskas M, Clotea I, Ho M, Lamanna J, Dixon C, Rackus DG, Silva SJRD, Pena L, Pardee K, Wheeler AR. Portable sample processing for molecular assays: application to Zika virus diagnostics. LAB ON A CHIP 2022; 22:1748-1763. [PMID: 35357372 DOI: 10.1039/d1lc01068a] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper introduces a digital microfluidic (DMF) platform for portable, automated, and integrated Zika viral RNA extraction and amplification. The platform features reconfigurable DMF cartridges offering a closed, humidified environment for sample processing at elevated temperatures, as well as programmable control instrumentation with a novel thermal cycling unit regulated using a proportional integral derivative (PID) feedback loop. The system operates on 12 V DC power, which can be supplied by rechargeable battery packs for remote testing. The DMF system was optimized for an RNA processing pipeline consisting of the following steps: 1) magnetic-bead based RNA extraction from lysed plasma samples, 2) RNA clean-up, and 3) integrated, isothermal amplification of Zika RNA. The DMF pipeline was coupled to a paper-based, colorimetric cell-free protein expression assay for amplified Zika RNA mediated by toehold switch-based sensors. Blinded laboratory evaluation of Zika RNA spiked in human plasma yielded a sensitivity and specificity of 100% and 75% respectively. The platform was then transported to Recife, Brazil for evaluation with infectious Zika viruses, which were detected at the 100 PFU mL-1 level from a 5 μL sample (equivalent to an RT-qPCR cycle threshold value of 32.0), demonstrating its potential as a sample processing platform for miniaturized diagnostic testing.
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Affiliation(s)
- Tanya Narahari
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Joshua Dahmer
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Alexandros Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Taehyeong Kim
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Monika Satkauskas
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Ioana Clotea
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Man Ho
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Julian Lamanna
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Christopher Dixon
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Darius G Rackus
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3M2, Canada
| | - Severino Jefferson Ribeiro da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Institute (FIOCRUZ Pernambuco), Av. Professor Moraes Rego, s/n - Cidade Universitária, Recife, PE, CEP 50.740-465, Brazil
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Institute (FIOCRUZ Pernambuco), Av. Professor Moraes Rego, s/n - Cidade Universitária, Recife, PE, CEP 50.740-465, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, M5S 3G8 Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
- Institute for Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
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12
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Karlikow M, da Silva SJR, Guo Y, Cicek S, Krokovsky L, Homme P, Xiong Y, Xu T, Calderón-Peláez MA, Camacho-Ortega S, Ma D, de Magalhães JJF, Souza BNRF, de Albuquerque Cabral DG, Jaenes K, Sutyrina P, Ferrante T, Benitez AD, Nipaz V, Ponce P, Rackus DG, Collins JJ, Paiva M, Castellanos JE, Cevallos V, Green AA, Ayres C, Pena L, Pardee K. Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples. Nat Biomed Eng 2022; 6:246-256. [PMID: 35256758 PMCID: PMC8940623 DOI: 10.1038/s41551-022-00850-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
AbstractIn low-resource settings, resilience to infectious disease outbreaks can be hindered by limited access to diagnostic tests. Here we report the results of double-blinded studies of the performance of paper-based diagnostic tests for the Zika and chikungunya viruses in a field setting in Latin America. The tests involved a cell-free expression system relying on isothermal amplification and toehold-switch reactions, a purpose-built portable reader and onboard software for computer vision-enabled image analysis. In patients suspected of infection, the accuracies and sensitivities of the tests for the Zika and chikungunya viruses were, respectively, 98.5% (95% confidence interval, 96.2–99.6%, 268 serum samples) and 98.5% (95% confidence interval, 91.7–100%, 65 serum samples) and approximately 2 aM and 5 fM (both concentrations are within clinically relevant ranges). The analytical specificities and sensitivities of the tests for cultured samples of the viruses were equivalent to those of the real-time quantitative PCR. Cell-free synthetic biology tools and companion hardware can provide de-centralized, high-capacity and low-cost diagnostics for use in low-resource settings.
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13
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Chondrogiannis G, Khaliliazar S, Toldrà A, Réu P, Hamedi MM. Nitrocellulose-bound achromopeptidase for point-of-care nucleic acid tests. Sci Rep 2021; 11:6140. [PMID: 33731748 PMCID: PMC7969615 DOI: 10.1038/s41598-021-85481-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/24/2021] [Indexed: 11/23/2022] Open
Abstract
Enzymes are the cornerstone of modern biotechnology. Achromopeptidase (ACP) is a well-known enzyme that hydrolyzes a number of proteins, notably proteins on the surface of Gram-positive bacteria. It is therefore used for sample preparation in nucleic acid tests. However, ACP inhibits DNA amplification which makes its integration difficult. Heat is commonly used to inactivate ACP, but it can be challenging to integrate heating into point-of-care devices. Here, we use recombinase polymerase amplification (RPA) together with ACP, and show that when ACP is immobilized on nitrocellulose paper, it retains its enzymatic function and can easily and rapidly be activated using agitation. The nitrocellulose-bound ACP does, however, not leak into the solution, preventing the need for deactivation through heat or by other means. Nitrocellulose-bound ACP thus opens new possibilities for paper-based Point-of-Care (POC) devices.
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Affiliation(s)
- Georgios Chondrogiannis
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Shirin Khaliliazar
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Toldrà
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Mahiar M Hamedi
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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14
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Perebikovsky A, Liu Y, Hwu A, Kido H, Shamloo E, Song D, Monti G, Shoval O, Gussin D, Madou M. Rapid sample preparation for detection of antibiotic resistance on a microfluidic disc platform. LAB ON A CHIP 2021; 21:534-545. [PMID: 33393956 DOI: 10.1039/d0lc00838a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rapid, point-of-care (PoC) diagnostics for antibiotic susceptibility testing (AST) are critical in combating the antimicrobial resistance epidemic. While new, alternative technologies are capable of rapidly identifying antibiotic resistance, traditional AST methods, where a patient sample is incubated with different antibiotics, remain the most reliable and practical in determining antibiotic effectiveness. Here, we demonstrate a novel sample incubation technique on a microfluidic centrifugal disc (CD) as a proof of concept automated sample processing platform for AST. By using ribosomal RNA (rRNA) as a marker for cell growth, we demonstrated that incubation on the microfluidic CD was enhanced (>1.6 fold) for 11 out of 14 clinically relevant isolates of Escherichia coli compared to traditional shaker incubators. Finally, we utilize the system to identify antibiotic resistance of 11 E. coli isolates incubated with 5 different antibiotics in under 2 hours.
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Affiliation(s)
- Alexandra Perebikovsky
- Department of Physics and Astronomy, University of California, 4129 Frederick Reines Hall, Irvine, CA 92697, USA.
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15
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Nunez-Bajo E, Silva Pinto Collins A, Kasimatis M, Cotur Y, Asfour T, Tanriverdi U, Grell M, Kaisti M, Senesi G, Stevenson K, Güder F. Disposable silicon-based all-in-one micro-qPCR for rapid on-site detection of pathogens. Nat Commun 2020; 11:6176. [PMID: 33268779 PMCID: PMC7710731 DOI: 10.1038/s41467-020-19911-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022] Open
Abstract
Rapid screening and low-cost diagnosis play a crucial role in choosing the correct course of intervention when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2, and shows no or similar symptoms to other common infections. Here, we report a disposable silicon-based integrated Point-of-Need transducer (TriSilix) for real-time quantitative detection of pathogen-specific sequences of nucleic acids. TriSilix can be produced at wafer-scale in a standard laboratory (37 chips of 10 × 10 × 0.65 mm in size can be produced in 7 h, costing ~0.35 USD per device). We are able to quantitatively detect a 563 bp fragment of genomic DNA of Mycobacterium avium subspecies paratuberculosis through real-time PCR with a limit-of-detection of 20 fg, equivalent to a single bacterium, at the 35th cycle. Using TriSilix, we also detect the cDNA from SARS-CoV-2 (1 pg) with high specificity against SARS-CoV (2003).
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Affiliation(s)
| | | | - Michael Kasimatis
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Yasin Cotur
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tarek Asfour
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Ugur Tanriverdi
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Max Grell
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Matti Kaisti
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Department of Future Technologies, University of Turku, 20500, Turku, Finland
| | - Guglielmo Senesi
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Karen Stevenson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Scotland, EH26 0PZ, UK
| | - Firat Güder
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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16
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Everitt ML, Tillery A, David MG, Singh N, Borison A, White IM. A critical review of point-of-care diagnostic technologies to combat viral pandemics. Anal Chim Acta 2020; 1146:184-199. [PMID: 33461715 PMCID: PMC7548029 DOI: 10.1016/j.aca.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.
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Affiliation(s)
- Micaela L Everitt
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Alana Tillery
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Martha G David
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Nikita Singh
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Aviva Borison
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Ian M White
- Fischell Department of Bioengineering, University of Maryland, United States.
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17
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Rabe BA, Cepko C. SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification. Proc Natl Acad Sci U S A 2020; 117:24450-24458. [PMID: 32900935 DOI: 10.1101/2020.04.23.20076877] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has had an enormous impact on society worldwide, threatening the lives and livelihoods of many. The effects will continue to grow and worsen if economies begin to open without the proper precautions, including expanded diagnostic capabilities. To address this need for increased testing, we have developed a sensitive reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay compatible with current reagents, which utilizes a colorimetric readout in as little as 30 min. A rapid inactivation protocol capable of inactivating virions, as well as endogenous nucleases, was optimized to increase sensitivity and sample stability. This protocol, combined with the RT-LAMP assay, has a sensitivity of at least 50 viral RNA copies per microliter in a sample. To further increase the sensitivity, a purification protocol compatible with this inactivation method was developed. The inactivation and purification protocol, combined with the RT-LAMP assay, brings the sensitivity to at least 1 viral RNA copy per microliter in a sample. This simple inactivation and purification pipeline is inexpensive and compatible with other downstream RNA detection platforms and uses readily available reagents. It should increase the availability of SARS-CoV-2 testing as well as expand the settings in which this testing can be performed.
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Affiliation(s)
- Brian A Rabe
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Constance Cepko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- Department of Ophthalmology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
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18
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Cano I, McCullough R, Mulhearn B, Gunning S, Waine A, Joiner C, Paley R. Non-lethal loop-mediated isothermal amplification assay as a point-of-care diagnostics tool for Neoparamoeba perurans, the causative agent of amoebic gill disease. JOURNAL OF FISH DISEASES 2020; 43:779-790. [PMID: 32364315 PMCID: PMC7383609 DOI: 10.1111/jfd.13175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Neoparamoeba perurans is the causative agent of amoebic gill disease (AGD). Two loop-mediated isothermal amplification (LAMP) assays targeting the parasite 18S rRNA and the Atlantic salmon EF1α, used as internal control, were designed. The N. perurans LAMP assay did not amplify close relatives N. pemaquidensis and N. branchiphila, or the host DNA. This assay detected 106 copies of the parasite 18S rRNA gene under 13 min and 103 copies under 35 min. Five "fast-and-dirty" DNA extraction methods were compared with a reference method and further validated by TaqMan™ qPCR. Of those, the QuickExtract buffer was selected for field tests. Seventy-one non-lethal gill swabs were analysed from AGD-clinically infected Atlantic salmon. The pathogen was detected under 23 min in fish of gill score >2 and under 39 min for lower gill scores. About 1.6% of the tests were invalid (no amplification of the internal control). 100% of positives were obtained from swabs taken from fish showing gill score ˃3, but only ~50% of positives for lower gill scores. The present LAMP assay could be implemented as a point-of-care test for the on-site identification of N. perurans; however, further work is required to improve its performance for lower scores.
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Affiliation(s)
- Irene Cano
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
| | - Robin McCullough
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
| | - Brian Mulhearn
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
| | - Susie Gunning
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
| | - Ava Waine
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
| | - Claire Joiner
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
| | - Richard Paley
- International Centre of Excellence for Aquatic Animal HealthCefas Weymouth LaboratoryWeymouthUK
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19
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Basing LAW, Simpson SV, Adu-Sarkodie Y, Linnes JC. A Loop-Mediated Isothermal Amplification Assay for the Detection of Treponema pallidum subsp. pertenue. Am J Trop Med Hyg 2020; 103:253-259. [PMID: 32314703 DOI: 10.4269/ajtmh.19-0243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The eradication of yaws caused by Treponema pallidum subsp. pertenue is constrained by the lack of rapid, accurate diagnosis. We sought to develop a molecular point-of-care test for the diagnosis of yaws. A loop-mediated isothermal amplification (LAMP) assay with primers targeting the conserved gene, tp0967, with visual detection by lateral flow test strip was developed and optimized. The limit of detection was evaluated while 63 samples from clinical cases of yaws and five samples with polymerase chain reaction (PCR)-confirmed syphilis were used to determine the sensitivity and specificity of the assay compared with the current molecular testing protocol. The developed LAMP assay was found to be optimal when run at 65°C for 30 minutes. The limit of detection from extracted DNA was 2.7 × 104 DNA copies/mL. The sensitivity of the LAMP assay using unextracted and DNA extracted samples were 0.67 and 1.00, respectively. None of the syphilis samples tested positive in any of the assays. We show the development of a fast and sensitive LAMP assay for yaws detected by lateral flow test strip. Using extracted DNA, the assay sensitivity is at par with real-time PCR-based detection. The assay can be adapted to minimal sample processing required for infield detection without DNA extraction.
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Affiliation(s)
| | | | | | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
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20
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Zhu H, Fohlerová Z, Pekárek J, Basova E, Neužil P. Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens Bioelectron 2020; 153:112041. [PMID: 31999560 PMCID: PMC7126858 DOI: 10.1016/j.bios.2020.112041] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.
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Affiliation(s)
- Hanliang Zhu
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Jan Pekárek
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Evgenia Basova
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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21
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Seok Y, Jang H, Oh J, Joung HA, Kim MG. A handheld lateral flow strip for rapid DNA extraction from staphylococcus aureus cell spiked in various samples. Biomed Phys Eng Express 2019. [DOI: 10.1088/2057-1976/aaf3be] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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22
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Kaur N, Toley BJ. Paper-based nucleic acid amplification tests for point-of-care diagnostics. Analyst 2019; 143:2213-2234. [PMID: 29683153 DOI: 10.1039/c7an01943b] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There has been a recent resurgence in the use of paper as a substrate for developing point-of-care medical diagnostic tests, possibly triggered by expiring patents published in the 1990s. A hallmark of this resurgence has been the development of advanced shapes and structures made from paper to conduct multi-step fluidic operations using the wicking action of porous materials. Such devices indicate a distinct improvement over lateral flow immunoassays, which are restricted to conducting one-step operations. New developments in paper-based diagnostic devices have triggered interest in the development of paper-based point-of-care nucleic acid amplification tests (NAATs). NAATs can identify extremely low levels of specific nucleic acid sequences from clinical samples and are the most sensitive of all available tests for infectious disease diagnosis. Because traditional PCR-based NAATs require expensive instruments, the development of portable paper-based NAAT's has become an exciting field of research. This article aims to review and analyse the current state of development of paper-based NAATs. We project paper-based NAATs as miniaturized chemical processes and shed light on various schemes of operation used for converting the multiple steps of the chemical processes into paper microfluidic devices. We conclude by elaborating on the challenges that must be overcome in the near future so that progress can be made towards the development of fully functional and commercial paper-based NAATs.
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Affiliation(s)
- Navjot Kaur
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India560012.
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23
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Land KJ. The Many Roads to an Ideal Paper-based Device. PAPER-BASED DIAGNOSTICS 2018. [PMCID: PMC7119996 DOI: 10.1007/978-3-319-96870-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The recent Zika and Ebola virus outbreaks highlight the need for low-cost diagnostics that can be rapidly deployed and used outside of established clinical infrastructure. This demand for robust point-of-care (POC) diagnostics is further driven by the increasing burden of drug-resistant diseases, concern for food and water safety, and bioterrorism. As has been discussed in previous chapters, paper-based tests provide a simple and compelling solution to such needs.
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Affiliation(s)
- Kevin J. Land
- Council for Scientific and Industrial Research, Pretoria, South Africa
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24
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Kim Y, Kim S. An electro-conductive plane heating element for rapid thermal lysis of bacterial cells. J Microbiol Methods 2018; 153:99-103. [DOI: 10.1016/j.mimet.2018.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
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A bench-top automated workstation for nucleic acid isolation from clinical sample types. J Microbiol Methods 2018; 148:174-180. [PMID: 29678500 DOI: 10.1016/j.mimet.2018.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 11/23/2022]
Abstract
Systems that automate extraction of nucleic acid from cells or viruses in complex clinical matrices have tremendous value even in the absence of an integrated downstream detector. We describe our bench-top automated workstation that integrates our previously-reported extraction method - TruTip - with our newly-developed mechanical lysis method. This is the first report of this method for homogenizing viscous and heterogeneous samples and lysing difficult-to-disrupt cells using "MagVor": a rotating magnet that rotates a miniature stir disk amidst glass beads confined inside of a disposable tube. Using this system, we demonstrate automated nucleic acid extraction from methicillin-resistant Staphylococcus aureus (MRSA) in nasopharyngeal aspirate (NPA), influenza A in nasopharyngeal swabs (NPS), human genomic DNA from whole blood, and Mycobacterium tuberculosis in NPA. The automated workstation yields nucleic acid with comparable extraction efficiency to manual protocols, which include commercially-available Qiagen spin column kits, across each of these sample types. This work expands the scope of applications beyond previous reports of TruTip to include difficult-to-disrupt cell types and automates the process, including a method for removal of organics, inside a compact bench-top workstation.
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McKenna JP, Cox C, Fairley DJ, Burke R, Shields MD, Watt A, Coyle PV. Loop-mediated isothermal amplification assay for rapid detection of Streptococcus agalactiae (group B streptococcus) in vaginal swabs - a proof of concept study. J Med Microbiol 2017; 66:294-300. [PMID: 28126051 DOI: 10.1099/jmm.0.000437] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Neonatal sepsis caused by Streptococcus agalactiae [group B streptococcus (GBS)] is a life-threatening condition, which is preventable if colonized mothers are identified and given antibiotic prophylaxis during labour. Conventional culture is time consuming and unreliable, and many available non-culture diagnostics are too complex to implement routinely at point of care. Loop-mediated isothermal amplification (LAMP) is a method that, enables the rapid and specific detection of target nucleic acid sequences in clinical materials without the requirement for extensive sample preparation. METHODOLOGY A prototype LAMP assay targeting GBS sip gene is described. RESULTS The assay was 100 % specific for GBS, with a limit of detection of 14 genome copies per reaction. The clinical utility of the LAMP assay for rapid direct molecular detection of GBS was determined by testing a total of 157 vaginal swabs with minimal sample processing using a rapid lysis solution. Compared to a reference quantitative real-time PCR assay, the direct LAMP protocol had a sensitivity and specificity of 95.4 and 100 %, respectively, with positive and negative predictive values of 100 and 98.3 %, respectively. Positive and negative likelihood ratios were infinity and 0.05, respectively. The direct LAMP method required a mean time of 45 min from the receipt of a swab to generation of a confirmed result, compared to 2 h 30 min for the reference quantitative real-time PCR test. CONCLUSION The direct LAMP protocol described is easy to perform, facilitating rapid and accurate detection of GBS in vaginal swabs. This test has a potential for use at point of care.
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Affiliation(s)
- James Patrick McKenna
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Ciara Cox
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Derek John Fairley
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Rachael Burke
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK.,Centre for Experimental Medicine, Queens University Belfast, Belfast, UK
| | - Michael D Shields
- Centre for Experimental Medicine, Queens University Belfast, Belfast, UK.,Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK
| | - Alison Watt
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Peter Valentine Coyle
- Regional Virus Laboratory, Department of Microbiology, Belfast Health and Social Care Trust, Belfast, UK
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