Siddhartha Thakur

About

Dr. Siddhartha "Sid" Thakur is a Professor of Molecular Epidemiology and the Executive Director of the Global One Health Academy at the College of Veterinary Medicine at NC State. His research focuses on filling critical knowledge gaps related to antimicrobial-resistant (AMR) bacterial foodborne pathogens at the interface of humans, animals, plants, and the environment. He investigates the phenotypic and genotypic diversity of AMR bacterial strains reported in animals and humans, characterizing mechanisms of resistance at the molecular level, analyzing DNA fingerprint patterns, and identifying risk factors for infections. Additionally, Dr. Thakur employs phylogenetics to study the evolution of drug-resistant bacterial strains at the population level using molecular approaches to analyze pathogen evolution. His work aims to develop evidence-based recommendations for tackling current and future global health threats. He holds a Degree in Veterinary Medicine and a Master of Veterinary Public Health from India, and a Ph.D. from NC State. Dr. Thakur has authored or co-authored 80 peer-reviewed publications and edited two books on Food Safety. He has received numerous awards, including the Larry Beuchat Young Researcher Award by the International Association for Food Protection and the Outstanding Global Engagement award by NC State.

Research topics

• Medicine
• Biology
• Microbiology
• Veterinary medicine
• Environmental health
• Genetics
• Nursing
• Ecology
• Intensive care medicine
• Biotechnology

Selected publications

• Impact of the COVID-19 pandemic on the surveillance, prevention and control of antimicrobial resistance: a global survey

  Journal of Antimicrobial Chemotherapy · 2021 · 175 citations

  OBJECTIVES: The COVID-19 pandemic has had a substantial impact on health systems. The WHO Antimicrobial Resistance (AMR) Surveillance and Quality Assessment Collaborating Centres Network conducted a survey to assess the effects of COVID-19 on AMR surveillance, prevention and control. METHODS: From October to December 2020, WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) national focal points completed a questionnaire, including Likert scales and open-ended questions. Data…

  DOI

• Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments

  Antimicrobial Resistance and Infection Control · 2021 · 144 citations

  Senior authorCorresponding

  BACKGROUND: Inappropriate use of antimicrobial agents in animal production has led to the development of antimicrobial resistance (AMR) in foodborne pathogens. Transmission of AMR foodborne pathogens from reservoirs, particularly chickens to the human population does occur. Recently, we reported that occupational exposure was a risk factor for multidrug-resistant (MDR) Escherichia coli (E. coli) among poultry-workers. Here we determined the prevalence and genetic relatedness among MDR E. coli is…

  DOI

• Ultra-accurate microbial amplicon sequencing with synthetic long reads

  Microbiome · 2021 · 129 citations

  BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. METHODS: Here, we describe and analytically validate LoopSeq, a commercially availa…

  DOI

• Evidence of sheep and abattoir environment as important reservoirs of multidrug resistant Salmonella and extended-spectrum beta-lactamase Escherichia coli

  International Journal of Food Microbiology · 2021 · 29 citations

  PublisherDOI

• Uncovering changes in microbiome profiles across commercial and backyard poultry farming systems

  Microbiology Spectrum · 2023-08-21 · 24 citations

  articleOpen accessSenior author

  ABSTRACT The microbiome profiles of poultry production systems significantly impact bird health, welfare, and the environment. This study investigated the influence of broiler-rearing systems on the microbiome composition of commercial and backyard chicken farms and their environment over time. Understanding these effects is vital for optimizing animal growth, enhancing welfare, and addressing human and environmental health implications. We collected and analyzed various samples from commercial…

  PublisherDOI

Recent grants

• Enhance the surveillance of foodborne bacterial pathogens isolated from food and environmental samples using whole genome sequencing (WGS) to prevent foodborne outbreaks and promote public health

  NIH · $355k · 2020–2025

• Enhance the surveillance of foodborne bacterial pathogens isolated from food and environmental samples using whole genome sequencing (WGS) to prevent foodborne outbreaks and promote public health

  NIH · $1.1M · 2020–2025

Frequent coauthors

• Wondwossen A. Gebreyes

  The Ohio State University

  46 shared

• Mabel Kamweli Aworh

  North Carolina State University

  26 shared

• Lyndy Harden

  North Carolina State University

  25 shared

• W. E. Morgan Morrow

  Mississippi State University

  20 shared

• René S. Hendriksen

  Technical University of Denmark

  17 shared

• Julie A. Funk

  17 shared

• Paula J. Fedorka–Cray

  North Carolina State University

  16 shared

• Emmanuel C. Okolocha

  Ahmadu Bello University

  16 shared

Labs

• Thakur Molecular EpidemiologyPI

Education

• Ph.D., Animal Science

  University of California, Davis

  2006

• M.S., Animal Science

  University of California, Davis

  2002

• B.S., Animal Science

  University of California, Davis

  2000

Awards & honors

• Larry Beuchat Young Researcher Award by the International As…
• Outstanding Global Engagement award by NC State

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• Casey Therioth-35
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