Research Article: Assessment of eight nucleic acid amplification technologies for potential use to detect infectious agents in low-resource settings

Date Published: April 22, 2019

Publisher: Public Library of Science

Author(s): Jason L. Cantera, Heather White, Maureen H. Diaz, Shivani G. Beall, Jonas M. Winchell, Lorraine Lillis, Michael Kalnoky, James Gallarda, David S. Boyle, Ruslan Kalendar.


Nucleic acid amplification technologies (NAATs) are high-performance tools for rapidly and accurately detecting infectious agents. They are widely used in high-income countries to diagnose disease and improve patient care. The complexities associated with test methods, reagents, equipment, quality control and assurance require dedicated laboratories with trained staff, which can exclude their use in low-resource and decentralized healthcare settings. For certain diseases, fully integrated NAAT devices and assays are available for use in environmentally-controlled clinics or emergency rooms where relatively untrained staff can perform testing. However, decentralized settings in many low- and middle-income countries with large burdens of infectious disease are challenged by extreme environments, poor infrastructure, few trained staff and limited financial resources. Therefore, there is an urgent need for low-cost, integrated NAAT tools specifically designed for use in low-resource settings (LRS). Two essential components of integrated NAAT tools are: 1) efficient nucleic acid extraction technologies for diverse and complex sample types; and 2) robust and sensitive nucleic acid amplification and detection technologies. In prior work we reported the performance and workflow capacity for the nucleic acid extraction component. In the current study we evaluated performance of eight novel nucleic acid amplification and detection technologies from seven developers using blinded panels of RNA and/or DNA from three pathogens to assess both diagnostic accuracy and suitability as an essential component for low-cost NAAT in LRS. In this exercise, we noted significant differences in performance among these technologies and identified those most promising for potential further development.

Partial Text

The accurate and rapid diagnosis of infectious disease can lead to improved patient care, appropriate use of antimicrobial drugs, and ultimately greater control of communicable diseases within populations [1]. The advent of molecular tests to accurately identify pathogen DNA or RNA has revolutionized clinical diagnostic testing, and molecular testing is now routine in many settings. Implementation is enabled in high-income countries by centralized laboratories with appropriate infrastructure and controlled environments to house complex equipment and cold chain–dependent reagents. These facilities also have highly skilled staff to operate and maintain the equipment under quality assurance protocols. In countries with sufficient resources, a centralized model offers high-quality diagnostic testing to most of the population because logistic infrastructure enables efficient shipping of samples and communication of test results. However, low-income countries face greater challenges because the burden of infectious diseases is much higher and access to healthcare is limited due to inadequate resources and poor infrastructure [2].

The overarching intent of this work and its companion study was to identify suitable component technologies for the development of affordable and effective fully integrated NAAT devices to diagnose globally-relevant infectious diseases in LRS [36]. In this report, the key components focus on the timely and effective amplification and detection of pathogen nucleic acids. We worked with a series of innovative developers to explore their proprietary platforms and NA amplification assays for influenza A, MTB, and salmonella. The assays and platforms were challenged with blinded replicate series of dilution panels to assess their performance with an emphasis on sensitivity, a critical parameter for the success of any NAAT-based technology. Although the developers’ identities were coded to encourage participation in this head-to-head challenge, further details can be requested from each. The assays and devices screened in this study were in varying phases of the development pipeline, and any limited performance observed in this study may be related simply to early prototypes still in the development, as compared to mature devices in production.




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