Abstract
Quantitative real-time PCR and genomic sequencing have become mainstays for performing molecular detection of biological threat agents in the field. There are notional assessments of the benefits, disadvantages, and challenges that each of these technologies offers according to findings in the literature. However, direct comparison between these two technologies in the context of field-forward operations is lacking. Most market surveys, whether published in print form or provided online, are directed to product manufacturers who can address their respective specifications and operations. One method for comparing these technologies is surveying end-users who are best suited for discussing operational capabilities, as they have hands-on experience with state-of-the-art molecular detection platforms and protocols. These end-users include operators in military defense and first response, as well as various research scientists in the public sector such as government and service laboratories, private sector, and civil society such as academia and nonprofit organizations performing method development and executing these protocols in the field. Our objective was to initiate a survey specific to end-users and their feedback. We developed a questionnaire that asked respondents to (1) determine what technologies they currently use, (2) identify the settings where the technologies are used, whether lab-based or field-forward, and (3) rate the technologies according to a set list of criteria. Of particular interest are assessments of sensitivity, specificity, reproducibility, scalability, portability, and discovery power. This article summarizes the findings from the end-user perspective, highlighting technical and operational challenges.
Highlights
Military, defense, and intergovernmental entities such as the United Nations, which coordinated missions to oversee disarmament in Iraq, frequently deploy field transportable and mobile laboratories [1,2] to address situations involving biological weapons of mass destruction (WMD)
Participants were asked to provide some basic background information to correlate with their responses. These were their highest level of education, their current position, and for what applications they use quantitative polymerase chain reaction (qPCR) and/or sequencing technologies
All 18 respondents (100%) had experience with qPCR, while 15 (80%) had experience with some sequencing technologies. This result was not surprising, as end-point PCR amplification is a routine molecular method and inherent to most sequencing methods; it is possible that someone could be proficient with sequencing techniques and not with qPCR
Summary
While these surveys are extensive and provide the manufacturers’ technical assessments of their products, there were only two designed with input from end-users [20,26] Qualitative metrics, such as real-world experience on testing samples according to sensitivity, specificity, accuracy, and ruggedness are valuable for end-users making assessments on appropriate technologies to incorporate into their field operations. The qualitative comparison included the following evaluation metrics: sensitivity, specificity, reproducibility, ease of use, time to detection, low cost per test, discovery power, scalability, portability, and ruggedness For this manuscript, we sought feedback from end-users on their actual experience with qPCR and sequencing technologies, both in the field and in laboratory settings. We sought feedback from end-users on their actual experience with qPCR and sequencing technologies, both in the field and in laboratory settings To gain this feedback, we designed a survey that asked respondents to evaluate the technologies using the evaluation criteria listed above. The survey results were compiled and analyzed to determine trends amongst the responses
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