Analytical Track 4: Whole Genome Sequencing

摘要:项目

Summary: Project Since 2016, North Carolina State University (NCSU) has participated in the Food and Drug Administration (FDA) GenomeTrakr program and helped expand the program on a global scale. There is an urgent need for national and international surveillance of foodborne pathogens because despite major advances in hygiene, food and water quality and pathogen detection, foodborne illnesses remain a tremendous burden for public health. Bacterial pathogens such as Salmonella, Listeria and Shiga toxin-producing Escherichia coli (STEC) are among the leading causes of foodborne illnesses worldwide and importantly, do not respect international boundaries. The environment and food products such as retail meats and fresh produce have been implicated as sources of foodborne bacterial pathogens, and establishing standardized surveillance of these sources can help monitor key pathogens and trace contamination routes to prevent and control outbreaks. The overarching aim of this project is to enhance WGS-based surveillance of bacterial pathogens associated with foodborne illness at the national and global level using a One Health approach. This will improve and protect public health by strengthening the surveillance of drug-resistant bacterial pathogens in human, animal and environmental sectors in the US and worldwide. The investigators have an extensive global network comprised of organizations in 13 countries spanning three continents. This includes the Institut Pasteur de Dakar (IPD) in Senegal, a major biomedical research center for West Africa. Altogether, this global network has enabled NCSU laboratories to sequence 1,127 bacterial isolates from international locations over the last three years. To achieve the overarching goal of the project, the investigators will pursue the following specific aims. Aim 1: Expand the existing surveillance system of Salmonella, Listeria, STEC and other bacterial pathogens related to foodborne illness that have been isolated from food and environmental sources in the US and international locations. The investigators will generate WGS profiles of 400 isolates, including 300 from the US and 100 from outside the US. Through collaborations with global partners, they will continue to expand the GenomeTrakr database of WGS profiles for specific bacterial pathogens on a global scale. Aim 2: Compare WGS profiles of Salmonella, Listeria and STEC isolated from national and international samples to advance outbreak investigations and track emerging strains of public health importance. The investigators will continue to conduct bioinformatics-based analysis of WGS profiles and corresponding metadata to identify new emerging bacterial strains in the US and globally. Findings will be shared via the NCBI platform and with public health agencies to inform control and intervention strategies. Expected outcomes: By characterizing 400 new isolates from national and international sources, this work will provide the food safety community with information to facilitate the identification of new, clinically relevant emerging bacterial strains, and safeguard US and global public health.