A rapid amplification/detection assay for analysis of Mycobacterium tuberculosis using an isothermal and silicon bio-photonic sensor complex

Shin, Yong Moon; Perera, Agampodi Promoda; Tang, Wen; Fu, Dong Liang; Liu, Qing; Sheng, Jack Kee; Gu, Zhonghua; Lee, Tae Yoon; Barkham, Timothy; Park, Mi Kyoung

doi:10.1016/j.bios.2015.01.030

Cited by 44 publications

(28 citation statements)

References 24 publications

(43 reference statements)

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“…Real time detection is mainly restricted to fluorescence detection, however, there are some reports of alternative real-time strategies ( Table 5). Real-time, label-free and highly sensitive detection of RPA can be achieved using ring-resonator technology [29], where primers are immobilised on a silicon ring resonator and the shift in the resonant wavelength is measured continuously during amplification. This approach has been demonstrated to have a sensitivity 100 times higher than benchtop RPA and conventional PCR methods and can be used to distinguish single point mutations [27].…”

Section: Alternative Real Time Detection Strategiesmentioning

confidence: 99%

Recombinase polymerase amplification: Basics, applications and recent advances

Lobato

O’Sullivan

2018

TrAC Trends in Analytical Chemistry

658

522

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a b s t r a c tRecombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37e42 C, with minimal sample preparation and capable of amplifying as low as 1e10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.

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Section: Alternative Real Time Detection Strategiesmentioning

confidence: 99%

Recombinase polymerase amplification: Basics, applications and recent advances

Lobato

O’Sullivan

2018

TrAC Trends in Analytical Chemistry

658

522

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“…3a). DMS is selected here not only for the specific binding process, but also because the binding is reversible at high pH (Shin et al, 2015b). Then, 40 μl of APTES-DE and 100 μl of DMS were added in that order.…”

Section: Characterization Of Dna Extraction Using a Complex Of Aptes-mentioning

confidence: 99%

A single-tube approach for in vitro diagnostics using diatomaceous earth and optical sensor

Zhao

Koo

Liu

et al. 2018

Biosensors and Bioelectronics

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Versatile, simple and efficient sample preparation is desirable for point-of-care testing of emerging diseases such as zoonoses, but current sample preparation assays are insensitive, labour-intensive and time-consuming and require multiple instruments. We developed a single-tube sample preparation approach involving direct pathogen enrichment and extraction from human specimens using diatomaceous earth (DE). Amine-modified DE was used to directly enrich a zoonotic pathogen, Brucella, in a large sample volume. Next, a complex of amine-modified DE and dimethyl suberimidate was used for nucleic acid extraction from the enriched pathogen. Using our single-tube approach, the pathogen can be enriched and extracted within 60min at a level of 1 colony formation unit (CFU) from a 1ml sample volume in the same tube. The performance of this approach is 10-100 times better than that of a commercial kit (10 to 10CFU/ml) but does not require a large centrifuge. Finally, we combined the single-tube approach with a bio-optical sensor for rapid and accurate zoonotic pathogen detection in human urine samples. Using the combination system, Brucella in human urine can be efficiently enriched (~ 8-fold) and the detection limit is enhanced by up to 100 times (1CFU/ml bacteria in urine) compared with the commercial kit. This combined system is fast and highly sensitive and thus represents a promising approach for disease diagnosis in the clinical setting.

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“…Ltd. The insertion loss (IL) spectrum was measured using an EXFO IQS-2600B DWDM passive component test system (Park et al, 2013;Shin et al, 2015a). The structures were then etched into the buried oxide layer by a reactive ion-etching process, followed by the deposition of 1.5 mm high-density plasma (HDP) oxide as a top cladding layer (Park et al, 2013;Shin et al, 2015a).…”

Section: Development and Operation Of Iroad Chipmentioning

confidence: 99%

“…Alternatively, real-time reverse transcriptase (RT) polymerase chain reaction (PCR) is the current gold standard because of its superior sensitivity, rapid turnaround time (2-4 h), and ability to identify multiple types of pathogens in a single test (Moesker et al, 2016;Olofsson et al, 2011;Pillet et al, 2013;Mentel et al, 2003). Among the methods, recombinase polymerase amplification (RPA) does not require thermal cycling and operates at a single temperature (Piepenburg et al, 2006;Shin et al, 2013aShin et al, , 2015a. However, these are not well implemented in all hospitals, as they require a molecular diagnostic laboratory with specialized personnel, equipment, and time to validate the products with large clinical samples.…”

Section: Introductionmentioning

confidence: 99%

“…Among the methods, recombinase polymerase amplification (RPA) does not require thermal cycling and operates at a single temperature (Piepenburg et al, 2006;Shin et al, 2013aShin et al, , 2015a. Furthermore, the fabrication of the SMRs by comple-mentary metal oxide-semiconductor (CMOS) technology ensures the ability to minimize costs while providing large scale-up capabilities and makes the microring resonator a good candidate for a disposable sensor in POC diagnostics (Park et al, 2013;Shin et al, 2015a;De Vos et al, 2007, 2009. Recently, reverse transcription-based RPA technique (RPA-RT) for RNA has been developed and applied for the amplification of RNA from Bovine coronavirus (BCoV), human immunodeficiency virus (HIV), influenza (IFN), dengue virus (DENV), and ebola virus (EVD) (Yang et al, 2016;Lillis et al, 2014;El Wahed et al, 2013;Teoh et al, 2015;El Wahed et al, 2015;Amer et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections

Koo

Jin

Lee

et al. 2017

Biosensors and Bioelectronics

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Recently, RNA viral infections caused by respiratory viruses, such as influenza, parainfluenza, respiratory syncytial virus, coronavirus, and Middle East respiratory syndrome-coronavirus (MERS-CoV), and Zika virus, are a major public health threats in the world. Although myriads of diagnostic methods based on RNA amplification have been developed in the last decades, they continue to lack speed, sensitivity, and specificity for clinical use. A rapid and accurate diagnostic method is needed for appropriate control, including isolation and treatment of the patients. Here, we report an isothermal, label-free, one-step RNA amplification and detection system, termed as iROAD, for the diagnosis of respiratory diseases. It couples a one-step isothermal RNA amplification method and a bio-optical sensor for simultaneous viral RNA amplification/detection in a label-free and real-time manner. The iROAD assay offers a one-step viral RNA amplification/detection example to rapid analysis (<20min). The detection limit of iROAD assay was found to be 10-times more sensitive than that of real-time reverse transcription-PCR method. We confirmed the clinical utility of the iROAD assay by detecting viral RNAs obtained from 63 human respiratory samples. We envision that the iROAD assay will be useful and potentially adaptable for better diagnosis of emerging infectious diseases including respiratory diseases.

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A rapid amplification/detection assay for analysis of Mycobacterium tuberculosis using an isothermal and silicon bio-photonic sensor complex

Cited by 44 publications

References 24 publications

Recombinase polymerase amplification: Basics, applications and recent advances

Recombinase polymerase amplification: Basics, applications and recent advances

A single-tube approach for in vitro diagnostics using diatomaceous earth and optical sensor

An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections

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