Erin Theiller 3; Elizabeth Qian 6; Andries Feder 7; Alice Slotfeld Viana 1; Agnes Marie Sá Figueiredo 1,2; Paul J. Planet 5,7,8; Ahmed M. Moustafa 3,4,5 1-Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Brazil 2- Faculdade de Medicina, Programa de Pós-graduação em Patologia, Universidade Federal Fluminense, Niterói, Brazil 3-Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA 4-Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA 5-Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 6-School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104 7-Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA 8-Sackler Genomic Institute, American Museum of Natural History, New York, NY, USA 10024
Poster # 92
Amid the escalating imperative for swift tracking of emerging hypervirulent and adapted pathogenic clones, the diminishing financial burden of whole-genome sequencing (WGS) presents a promising prospect. However, numerous low-to-middle income regions persistently lack access to such resources, thereby highlighting the urgent need for developing new bioinformatics tools that can leverage WGS data to quickly find diagnostic, apomorphic sequence mutations that create a new and unique restriction site in the clone of interest. These identified biomarkers can then be used to create a diagnostic screen. Addressing this challenge, we introduce the "Classification Using Restriction Enzyme Diagnostics" (CURED) tool that quickly identifies k-mers with restriction enzyme recognition sites that are exclusive to a specific clonal lineage. The culmination of this pipeline is the development of primers and PCR test that can amplify the region, where the unique k-mer that is highly specific to the clone of interest, is. This is then followed by endonuclease digestion showing a unique gel electrophoresis pattern in the clone of the interest. This novel pipeline promises to be the catalyst for equitable disease surveillance worldwide, revolutionizing the way developing public health risks are confronted and contained.
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