Whole genome sequencing-based Salmonella serotyping
Public health surveillance of foodborne illnesses relies on robust identification and classification of different subtypes of the pathogens. Salmonella is one of the most prevalent foodborne pathogens in the United States and worldwide. Salmonella serotyping, a laboratory routine for Salmonella classification, forms the foundation of the U.S. national Salmonella surveillance system for over five decades. A laboratory at the UGA Center for Food Safety created SeqSero, a highly innovative bioinformatics tool and the first of its kind that allows accurate, fast and straightforward prediction of bacterial pathogen serotype from raw whole genome sequencing (WGS) data. By making this tool publicly available, the food scientist and his team provided a free and in silico alternative to traditional Salmonella serotyping. This enables any laboratory and individual with access to WGS to do nearly full set Salmonella serotyping (more than 2,500 serotypes) and shortens the serotyping procedure from days to minutes or seconds. Since its inception in 2015, SeqSero has been adopted by over 60 governmental, academic and private institutions around the world including more than 20 national public health, research and regulatory agencies such as Centers for Diseases Control, Food and Drug Administration, U.S. Department of Agriculture, Public Health England, Public Health Agency Canada, Robert Koch Institute (Germany), Institut Pasteur (France), and Statens Serum Institute (Denmark). Significant cost saving and efficiency enhancement has been achieved by multiple users and the public health benefit of this tool will continue to increase as it is becoming the de facto reference method for molecular serotyping of Salmonella.