Salmonella serotype in just two hours and the entire identification process within eight hours

An article published in Food Microbiology volume 89, August 2020(@ https://www.sciencedirect.com/science/article/pii/S0740002020300411?via%3Dihub) scientists from Cornell University, the Mars Global Food Safety Center in Beijing and the University of Georgia developed a method for completing whole genome sequencing (WGS) to determine salmonella serotypes in just two hours and the entire identification process within eight hours. Emerging long-read sequencing platforms developed by Oxford Nanopore Technologies (ONT) provide an alternative WGS method to meet the needs of industry for rapid and accurate Salmonella confirmation and serotype classification. Advantages of the Oxford Nanopore Technologies (ONT) sequencing platforms used in this study include portability, real-time base-calling, and long-read sequencing. All 38 Salmonella strains, representing 34 serotypes, were accurately predicted to the serotype level using WGS (Whole Genome Sequencing). The turnaround time of this method from pure culture to prediction results was within one day. The study systematically assessed the accuracy of using the combination of ONT sequencing method and corresponding data analysis pipelines for Salmonella serotype prediction. The study identified the most efficient data analysis workflow to achieve a balance between accuracy and turnaround time, delivering a more rapid, molecular-based Salmonella confirmation and serotype classification.