A team of scientists led by researchers at the University of Georgia Center for Food Safety in Griffin has developed a machine-learning approach that could lead to quicker identification of the animal source of certain Salmonella outbreaks. In the research, published in the January 2019 issue of Emerging Infectious Diseases, Xiangyu Deng and his colleagues used more than a thousand genomes to predict the animal sources, especially livestock, of Salmonella Typhimurium. Deng, an assistant professor of food microbiology at the center, and Shaokang Zhang, a postdoctoral associate with the center, led the project, which also included experts from the Centers for Disease Control and Prevention, the U.S. Food and Drug Administration, the Minnesota Department of Health and the Translational Genomics Research Institute. According to the Foodborne Disease Outbreak Surveillance System, close to 3,000 outbreaks of foodborne illness were reported in the U.S. from 2009 to 2015. Of those, 900 -- or 30 percent -- were caused by different serotypes of Salmonella, including Typhimurium, Deng said.

Enteroviruses are important drivers of global health, but few countries undertake enterovirus surveillance. Pons-Salort and Grassly used Japanese surveillance data to model the interplay between the ratio of susceptible and immune individuals, accounting for declining birth and death rates, incomplete surveillance, and seasonality of infection (see the Perspective by Nikolay and Cauchemez). Enteroviruses have highly predictable yet highly nonlinear dynamics. The model also reveals signatures of increased pathogenicity and of antigenic change and transmissibility. Science, this issue p. 800; see also p. 755 Human enteroviruses are a major cause of neurological and other diseases.

We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix (e.g. BLOSUM62). The kernel is used in learning machines to predict binding affinities of peptides to human leukocyte antigens DR (HLA-DR) molecules. On both fixed allele (Nielsen and Lund 2009) and pan-allele (Nielsen et.al. 2010) benchmark databases, our algorithm achieves the state-of-the-art performance. The kernel is also used to define a distance on an HLA-DR allele set based on which a clustering analysis precisely recovers the serotype classifications assigned by WHO (Nielsen and Lund 2009, and Marsh et.al. 2010). These results suggest that our kernel relates well the chain structure of both peptides and HLA-DR molecules to their biological functions, and that it offers a simple, powerful and promising methodology to immunology and amino acid chain studies.