Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods

• Published in: Journal of microbiology and biotechnology Vol. 33; no. 1; pp. 83 - 95
• Main Authors: Park, Dong-Geun, Ha, Eun-Su, Kang, Byungcheol, Choi, Iseul, Kwak, Jeong-Eun, Choi, Jinho, Park, Jeongwoong, Lee, Woojung, Kim, Seung Hwan, Kim, Soon Han, Lee, Ju-Hoon
• Format: Journal Article
• Language: English
• Published: Korea (South) The Korean Society for Microbiology and Biotechnology 28.01.2023
• Subjects: Escherichia coli - genetics; Fermented Foods; Food Microbiology; High-Throughput Nucleotide Sequencing - methods; Listeria monocytogenes - genetics; Multiplex Polymerase Chain Reaction - methods; Research article; Salmonella typhimurium - genetics; Sensitivity and Specificity; qPCR validation; NGS panel; foodborne pathogens; multiple detection
• ISSN: 1017-7825; 1738-8872
• DOI: 10.4014/jmb.2211.11009

These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic , , and serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 10 -10 CFU of target strains. However, a few false-positive results were shown at 10 -10 CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.