# Analytical Track 4:  Whole Genome Sequencing

> **NIH FDA U19** · NORTH CAROLINA STATE UNIVERSITY RALEIGH · 2020 · $151,816

## Abstract

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 prov...

## Key facts

- **NIH application ID:** 10175629
- **Project number:** 1U19FD007113-01
- **Recipient organization:** NORTH CAROLINA STATE UNIVERSITY RALEIGH
- **Principal Investigator:** Siddhartha Thakur
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** FDA
- **Fiscal year:** 2020
- **Award amount:** $151,816
- **Award type:** 1
- **Project period:** 2020-09-01 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10175629

## Citation

> US National Institutes of Health, RePORTER application 10175629, Analytical Track 4:  Whole Genome Sequencing (1U19FD007113-01). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10175629. Licensed CC0.

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