Siddhartha Thakur

Dr. Thakur will be responsible for the overall coordination and successful completion of the relevant project objectives that will be carried out in NC. He has extensive experience in conducting epidemiological based studies and will lead this project. He will be responsible for coordinating the sampling effort in NC, sample processing and pathogen isolation followed by characterization of the isolates. Dr. Thakur lab has the necessary infrastructure to perform phenotypic and genotypic characterization of Salmonella and Campylobacter isolates. His lab has an Illumina MiSeq that will be used for the 16sRNA and metagenomic sequencing of the samples collected in the proposed study. Finally, he will work closely with the rest of the team and will communicate research results in a timely manner.

Food animals, including retail pork, chicken, ground turkey and ground beef have been implicated as sources of Salmonella and Campylobacter and are the leading causes of bacterial foodborne illness. Both wild-caught and farm-raised salmon, shrimp, and tilapia have been implicated as sources of Vibrio and Aeromonas and are leading causes of sea-foodborne illness. Indicator pathogens, including Escherichia coli and Enterococcus spp., are also frequently isolated from these meat products. The situation is further complicated when the strains are also resistant to different antimicrobials. It is therefore important that we monitor the prevalence and trends of antimicrobial resistant (AMR) foodborne bacterial strains in the retail meat and seafood products that can eventually pass to the consumers along the farm-to-fork chain resulting in significant public health impact. The National Antimicrobial Resistance Monitoring System (NARMS) plays an important role in surveillance of AMR bacterial pathogens in humans, food animals and retail meats. North Carolina is an important food producing state situated along the eastern US seashore and ranks among the top states in pork and poultry production. As an existing NARMS laboratory, our major objective is to continue to enhance the surveillance of AMR pathogenic and indicator bacterial strains in retail meats and seafood in North Carolina and generate critical data to contribute to the NARMS mission. We propose to conduct this study in collaboration with the FDA GenomeTrakr program. The PI (Dr. Thakur) laboratory is a GenomeTrakr laboratory, which will provide the opportunity to generate the whole genome sequences (WGS) of the bacterial strains thereby significantly assisting us in tracking the emergence of potential new AMR bacteria and allowing the public health agencies to take appropriate steps.

Since 2016, North Carolina State University (NCSU) has helped expand the GenomeTrakr program on a national and global scale to target some of the leading causes of foodborne illnesses worldwide. The need for surveillance of foodborne pathogens is urgent because despite advances in hygiene, food and water quality and pathogen detection, foodborne illnesses remain a tremendous burden for public health. The environment and food products such as retail meats are implicated as sources of foodborne pathogens, and establishing standardized surveillance of these sources can help monitor key pathogens and trace contamination routes to prevent and control outbreaks. To date, NCSU GenomeTrakr laboratories have generated 3,328 whole genome sequencing (WGS) profiles of bacterial pathogens isolated from multiple sources. This includes profiles of 1,127 bacterial isolates from 9 countries outside the US over the last three years. They have also trained 23 students and professionals from 10 countries, which has led to 11 original publications of GenomeTrakr program data in peer-reviewed journals coauthored by the investigators and their US and international trainees. Since 2016, the investigators have worked to expand their global network to now include 13 countries spanning three continents. Consequently, the overarching aim of this project is to continue enhancing WGS-based surveillance of bacterial pathogens associated with foodborne illness at the national and global level using a One Health approach. This will be achieved through surveillance activities, partnership building and training students and professionals. The investigators will leverage their extensive leadership experience in surveillance protocols, advanced molecular techniques and data analysis, and their status as a WHO Collaborating Center for AMR and One Health to build capacity in the US and globally through world-class training for students and professionals. To achieve this, they will pursue the following specific aims. Aim 1 (Project): Expand the existing surveillance system of bacterial pathogens related to foodborne illness that have been isolated from food and environmental sources in the US and international locations. Aim 2 (Project): Compare WGS profiles of bacterial pathogens isolated from national and international samples to advance outbreak investigations and track emerging strains of public health importance. This work will be supported by two aims of the Administrative Core: Aim 1 (Admin): Provide leadership to complete the proposed aims in collaboration with national and international institutions. Aim 2 (Admin): Provide a framework to educate and equip the future surveillance workforce with the knowledge and skills needed for WGS analysis. Expected Outcomes: The investigators are committed to fulfilling the GenomeTrakr mission and expanding standardized surveillance systems across the globe. By characterizing 400 new isolates from US and international sources from new and existing collaborators, and by building capacity worldwide, this work will help public health agencies track the emergence of new strains, curb the distribution of foodborne pathogens and reduce the burden of foodborne illnesses in the US and globally.

The Foreign Animal Disease Diagnostic Laboratory (FADDL) is a national reference laboratory for USDA Veterinary Services and the National Animal Health Laboratory Network (NAHLN), and an international reference laboratory for the Food and Agriculture Organization (FAO) of the United Nations and the World Organization for Animal Health (OIE). FADDL is currently located at the Plum Island Animal Disease Center (PIADC), the only U.S. location approved for handling high-consequence foreign animal diseases* (FAD), including foot and mouth disease (FMD) and Rinderpest viruses. The majority of the U.S. FAD subject matter diagnostic expertise (SME) for livestock diseases resides at PIADC-FADDL, within approximately 20 scientists that include microbiologists, veterinarians, and veterinary scientists (DVM/PhD). Based on anecdotal data from discussions with these FADDL employees, it is likely that most (>80%) of FADDL������������������s subject matter experts (SMEs) will not relocate to the new National Bio and Agro-Defense Facility (NBAF) in Kansas, creating an FAD SME gap throughout the transition process and during stand-up of FADDL at NBAF. This gap is compounded by the fact that few new veterinary school graduates are pursuing careers in FADs or other high-consequence animal diseases. According to 2017 market research statistics on the employment of U.S. veterinarians, less than 0.016% of all positions are with the federal government (AVMA). Within that group, even fewer veterinarians work with livestock and FADs. The trending emphasis of new veterinarians exclusively pursuing small animal private practice is expected to continue. In addition to the need to recruit FAD SMEs, the FADDL mission will expand at NBAF to include zoonotic and emerging diseases, with a new emphasis on biosafety level (BSL)-4 pathogens. SMEs knowledgeable in these agents and with expertise in working in BSL-4 laboratories are critical to develop BSL-4 programs at NBAF. APHIS has developed a graduate training program, APHIS NBAF Scientist Training Program (NSTP), to minimize the SME gap and identify highly qualified candidates to fill key roles in the new NBAF facility. NSTP fellows will receive full tuition and supplementary support to complete a MS, PhD or DVM/PhD program in target laboratory-based fields of study, including but not limited to microbiology, virology, molecular biology, diagnostics, and bioinformatics. APHIS will work with partner universities and laboratories to ensure the fellows������������������ research projects address specific FADs and capability needs. Upon successful completion of the programs, each fellow will be required to fulfill a service commitment at NBAF and/or PIADC-FADDL, dependent on agency needs and timing of degree completion. North Carolina State University (NCSU), located in Raleigh, North Carolina has a strong affiliation with the new NBAF facility. NCSU faculty are uniquely poised to support NSTP fellow training, given significant expertise in emerging infectious diseases. Collaboration with NCSU on the NSTP will strengthen relationships between USDA and NCSU and ensure rapid development of necessary expertise to support NBAF stand-up.

The purpose of this contract is to conduct SARS-CoV-2 variant quantification and sequence analysis on wastewater samples collected twice a week throughout the state of North Carolina as part of NCWMN. Results will be shared weekly with NCDHHS for submission to CDC NWSS. Additionally, these results will supplement other COVID-19 surveillance strategies for NCDHHS and be shared with academic partners of the NC WW Path for further development of predictive models and spatial applications for public health surveillance.

Food-borne pathogens enact substantial harms on the American people in the form of illness, lost productivity, and expenses related to mitigation and regulatory compliance. Surveillance and tracing of foodborne pathogens is a key control strategy, but its efficacy is reduced by the longtimes associated with current culture and whole-genome-sequencing approaches. Rapid, accurate and comprehensive pathogen detection would improve the safety and lower the costs of our food supply. We aim to develop a targeted metagenomics methodology that can rapidly (<24 hrs) and precisely identify a broad range of foodborne pathogens from heterogeneous environmental samples. In order to achieve this, we propose to combine the GenomeTrakr and NCBI RefSeq databases with cuttingedge bioinformatics tools developed by the PD that achieve single-nucleotide resolution from amplicon sequencing data of full-length genes to identify E. coli and Salmonella strains to the serovar level (e.g. E. coli O157:H7 or S. enterica Heidelberg). We will validate the resolution and accuracy of this new methodology in silico, on isolates of various pathogenic serovars, and in environmental samples of various types for which pathogen presence and identity were previously established by standard culture-based methods. Our methodology will be distributed to the broader food safety community as open-source and actively-supported software, alongside extensive documentation of its efficacy and best-practices guidance. Successful completion of this project will yield a powerful, usable, and broad-spectrum pathogen surveillance technique that will improve food safety by detecting foodborne pathogens before they reach consumers, and by rapidly tracing outbreaks to their source.

The project is to support the state of North Carolina in surveillance of SARS-CoV-2 variants in the population. We will sequence SARS-CoV-2 from clinical specimens collected as part of the NCSU surveillance lab (surveillance lab director Megan Jacob is a co-PI) and partner WakeMed hospitals. We estimate to sequence 3700 samples over the course of the project.

his national network for antimicrobial resistance-related food safety outreach is being designed to include at least two individuals from each of the four U.S. regions illustrated below: North Central, Western, Southern, and Northeastern. Because programming conducted through these projects is intended to engage both consumers and producers, it will be important for each region to be represented by someone capable of leading consumer-facing food safety outreach and someone capable of leading producer-facing outreach.

Under this agreement, North Carolina State University will provide training to foodborne surveillance scientists and laboratory personnel in the Asia Pacific Economic Cooperation (APEC) countries to conduct Whole Genome Sequencing (WGS) analysis of the foodborne pathogens isolated from the environment

NC State CVM is ideally placed to provide strong collaboration in animal health and One Health-focused methodologies in AMR research and surveillance in Malawi. The expertise of CVM faculty and staff span a variety of relevant areas, from molecular epidemiology and microbiology to livestock health and infectious diseases. Objective 1: Strengthened One Health governance structure for AMR, AMU and AMC surveillance. Objective 2: Strengthened AMR Surveillance system in the Animal Health sector.