Sample-to-answer on molecular diagnosis of bacterial infection using integrated lab­-on­-a-­disc

Loo, Jacky Fong‐Chuen; Kwok, H.C.; Leung, C.C.H.; Wu, S.Y.; Law, I.L.G.; Cheung, Yiu-ming; Chin, Miu L.; Kwan, Patrick; Hui, Mamie; Kong, Siu Kai; Ho, H.P.

doi:10.1016/j.bios.2016.09.001

Cited by 67 publications

(41 citation statements)

References 15 publications

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“…Extracted DNA was pre-amplified using consensus primer pairs and then split into 13 real-time PCR chambers for target amplification. Loo et al (2017) performed hybrid mechanical-chemical bacterial lysis, silica membrane-based DNA extraction, and real-time RT-LAMP amplification on an integrated LabDisk. After sample loading, this integrated platform could detect minimally 100 CFU/mL Acinetobacter baumannii in whole blood within 2 h from 10 μL of sample.…”

Section: Nucleic Acid Extraction From Human Bloodmentioning

confidence: 99%

“…(d) Schematic layout of a centrifugal microfluidic device showing various chambers for DNA extraction and amplification for tuberculosis detection in 2 h (reproduced with permission from Ref. ( Loo et al, 2017 ), © Elsevier 2017). (e) Paper microfluidic origami device for sputum sample preparation (reproduced with permission from Ref.…”

Section: Nucleic Acid Extraction From Oral and Nasal Samplesmentioning

confidence: 99%

“…Another technique commonly used for laboratory-based assay quantification is real-time detection (e.g., real-time PCR or quantitative PCR (qPCR)). For real-time detection, DNA probes such as molecular beacons, TaqMan probes, or DNA intercalating dyes are included in the amplification mixture ( Borysiak et al, 2015 ; Loo et al, 2017 ; Wu et al, 2013 ). However, conventional qPCR requires bulky, expensive, and sophisticated instruments.…”

Section: Introductionmentioning

confidence: 99%

“…After the first demonstration of a miniaturized total chemical analysis system (μ-TAS) by Manz et al (1990) , researchers in the last 30 years have developed numerous molecular detection systems utilizing microfluidic ( Kolluri et al, 2017 ; Koo et al, 2017 ; Liu et al, 2011 ; Q. Liu et al, 2018a , Liu et al, 2018c ; Petralia et al, 2013 ; Wu et al, 2014 ; Yan et al, 2017 ; Yin et al, 2019b ; Zhang et al, 2016 ) or paper-based devices ( Choi et al, 2016 ; Deng et al, 2017 ; Liu et al, 2017 ; Loo et al, 2017 ; Rodriguez et al, 2015 ). Furthermore, several commercial platforms such as GeneXpert Systems (Cepheid, USA), ARIES Systems (Luminex, USA), BioFire FilmArray Torch (BioFire Diagnostics, USA), and Integrated Cycler (Focus Diagnostics, USA) have been developed for rapid molecular diagnosis of human diseases.…”

Section: Introductionmentioning

confidence: 99%

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Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Paul

Ostermann

Wei

2020

Biosensors and Bioelectronics

124

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Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the “sample-in-result-out” diagnosis of human and plant diseases, especially in remote or resource-limited settings.

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Section: Nucleic Acid Extraction From Human Bloodmentioning

confidence: 99%

Section: Nucleic Acid Extraction From Oral and Nasal Samplesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Paul

Ostermann

Wei

2020

Biosensors and Bioelectronics

124

View full text Add to dashboard Cite

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“…Thus, LAMP has high potential in the field of medical diagnostics due to minimal sample processing and rapid DNA amplification. LAMP has also been previously demonstrated for detection of the Human Immunodeficiency Virus, Mycobacterium tuberculosis , ( Geojith et al, 2011 ), Plasmodium falciparum ( Poon et al, 2006 ), Bacillus anthracis ( Dugan et al, 2012 ), Pseudomonas aeruginosa, Escherichia coli ( Yan et al, 2016 ), Zika Virus ( Wang et al, 2016 ), Clostridium difficile ( Johansson et al, 2016 ), and Acinetobacter baumanii ( Loo et al, 2016 ), to name just a few.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

Etchebarne

Stedtfeld

et al. 2017

Front. Microbiol.

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Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a 4- to 8-h growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70–120 min) genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP) to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx). The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads and direct LAMP amplification without DNA purification from clinical blood, urine, wound, sputum and stool samples. The In-Dx panel was tested using two methods of detection: (1) real-time thermocycler fluorescent detection of LAMP amplification and (2) visual discrimination of color change in the presence of Eriochrome Black T (EBT) dye following amplification. In total, 239 duplicate samples were collected (31 blood, 122 urine, 73 mucocutaneous wound/swab, 11 sputum and two stool) from 229 prospectively enrolled hospital patients with suspected clinical infection and analyzed both at the hospital and by In-Dx. Sensitivity (Se) of the In-Dx panel targets pathogens from urine samples by In-Dx was 91.1% and specificity (Sp) was 97.3%, with a positive predictive value (PPV) of 53.7% and a negative predictive value (NPV) of 99.7% as compared to clinical microbial detection methods. Sensitivity of detection of the In-Dx panel from mucocutaneous swab samples was 65.5% with a Sp of 99.3%, and a PPV of 84% and NPV of 98% as compared to clinical microbial detection methods. Results indicate the LAMP-based In-Dx panel allows rapid and precise diagnosis of clinical infections by targeted pathogens across multiple culture types for point-of-care utilization.

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Technological Advances in Multiscale Analysis of Single Cells in Biomedicine

Loo

Kong

et al. 2019

Adv. Biosys.

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Single‐cell analysis has recently received significant attention in biomedicine. With the advances in super‐resolution microscopy, fluorescence labeling, and nanoscale biosensing, new information may be obtained for the design of cancer diagnosis and therapeutic interventions. The discovery of cellular heterogeneity further stresses the importance of single‐cell analysis to improve our understanding of disease mechanism and to develop new strategies for disease treatment. To this end, many studies are exploited at the single‐cell level for high throughput, highly parallel, and quantitative analysis. Technically, microfluidics are also designed to facilitate single‐cell isolation and enrichment for downstream detection and manipulation in a robust, sensitive, and automated manner. Further achievements are made possible by consolidating optically label‐free, electrical, and molecular sensing techniques. Moreover, these technologies are coupled with computing algorithms for high throughput and automated quantitative analysis with a short turnaround time. To reflect on how the technological developments have advanced single‐cell analysis, this mini‐review is aimed to offer readers an introduction to single‐cell analysis with a brief historical development and the recent progresses that have enabled multiscale analysis of single‐cells in the last decade. The challenges and future trends are also discussed with the view to inspire forthcoming technical developments.

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Sample-to-answer on molecular diagnosis of bacterial infection using integrated lab-on-a-disc

Cited by 67 publications

References 15 publications

Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

Technological Advances in Multiscale Analysis of Single Cells in Biomedicine

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Sample-to-answer on molecular diagnosis of bacterial infection using integrated lab­-on­-a-­disc

Cited by 67 publications

References 15 publications

Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

Technological Advances in Multiscale Analysis of Single Cells in Biomedicine

Contact Info

Product

Resources

About

Sample-to-answer on molecular diagnosis of bacterial infection using integrated lab-on-a-disc