Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs)

Sol Park,Anita Rana,Way Sung,Mariya Munir

doi:10.3390/applmicrobiol1030028

Abstract

With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.

Highlights

Many studies and global communities noted that the prevalence and ubiquity of antibiotic resistance genes (ARGs) are increasing over time due to human activities of producing and overdosing antibiotics [1,2,3,4,5,6,7,8,9] (Figure 1)
Methods is that the lower limit of detection of Droplet digital PCR (ddPCR) is 10 times more effective compared to quantitative PCR (qPCR) [42,46,48,50,74,91,101,104]
The consensus observed from the literature on the use of qPCR and ddPCR technologies is that both methods have great potential for multiple applications. qPCR’s strength lies in its broader detection range of genetic materials, lower upfront costs, and shows specificity to some target genes over ddPCR

Summary

Introduction

Many studies and global communities noted that the prevalence and ubiquity of antibiotic resistance genes (ARGs) are increasing over time due to human activities of producing and overdosing antibiotics [1,2,3,4,5,6,7,8,9] (Figure 1). Maximization of profits by promoting production and selling of antibiotics is intensifying antibiotic resistance (AR), which is contradictory to policies of governments and health services that incentivize conservation of the common good [10]. The wastewater and soil surrounding humans, agricultural land, and industrial manufacturing are contaminated with antibiotics, and AR is accumulating in the environment and in organisms over time (Figure 1).

Objectives

Results

Conclusion