Droplet Encoding‐Pairing Enabled Multiplexed Digital Loop‐Mediated Isothermal Amplification for Simultaneous Quantitative Detection of Multiple Pathogens

• Published in: Advanced science Vol. 10; no. 7; pp. e2205863 - n/a
• Main Authors: Cai, Dongyang, Wang, Yu, Zou, Jingjing, Li, Zhujun, Huang, Enqi, Ouyang, Xiuyun, Que, Zhiquan, Luo, Yanzhang, Chen, Zhenhua, Jiang, Yanqing, Zhang, Guohao, Wu, Hongkai, Liu, Dayu
• Format: Journal Article
• Language: English
• Published: Germany John Wiley & Sons, Inc 01.03.2023; John Wiley and Sons Inc; Wiley
• Subjects: droplet encoding‐pairing; droplet microfluidics; Flexibility; Generators; Libraries; machine learning algorithm; Microfluidics; multiplexed droplet digital nucleic acid analysis; Nucleic Acid Amplification Techniques - methods; Pathogens; quantitative detection of pathogens; Reagents; Streptococcus infections; droplet encoding-pairing; droplet microfluidics; multiplexed droplet digital nucleic acid analysis; quantitative detection of pathogens; machine learning algorithm
• ISSN: 2198-3844; 2198-3844
• DOI: 10.1002/advs.202205863

Despite the advantages of digital nucleic acid analysis (DNAA) in terms of sensitivity, precision, and resolution, current DNAA methods commonly suffer a limitation in multiplexing capacity. To address this issue, a droplet encoding‐pairing enabled DNAA multiplexing strategy is developed, wherein unique tricolor combinations are deployed to index individual primer droplets. The template droplets and primer droplets are sequentially introduced into a microfluidic chip with a calabash‐shaped microwell array and are pairwise trapped and merged in the microwells. Pre‐merging and post‐amplification image analysis with a machine learning algorithm is used to identify, enumerate, and address the droplets. By incorporating the amplification signals with droplet encoding information, simultaneous quantitative detection of multiple targets is achieved. This strategy allows for the establishment of flexible multiplexed DNAA by simply adjusting the primer droplet library. Its flexibility is demonstrated by establishing two multiplexed (8‐plex) droplet digital loop‐mediated isothermal amplification (mddLAMP) assays for individually detecting lower respiratory tract infection and urinary tract infection causative pathogens. Clinical sample analysis shows that the microbial detection outcomes of the mddLAMP assays are consistent with those of the conventional assay. This DNAA multiplexing strategy can achieve flexible high‐order multiplexing on demand, making it a desirable tool for high‐content pathogen detection. The developed droplet encoding‐pairing enabled multiplexed droplet digital nucleic acid analysis strategy, which can be adapted to any amplification methods, features high flexibility in constructing high‐order multiplexed droplet digital assays on demand, thus providing a desirable tool for simultaneous quantitative detection of complex and mutative infection‐causing pathogens.