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
• Computational biology
• Animal science
• Internal medicine
• Family medicine

Selected publications

• Comparison of PCR and culture for detection of <i>Campylobacter jejuni</i> in canine feces

  Journal of Veterinary Diagnostic Investigation · 2026-04-15

  articleOpen access

  Campylobacter jejuni is a leading cause of human foodborne illness, and pet dogs can be a source of infection. Despite recognition of this zoonotic potential, tests for detection of C. jejuni are not performed routinely in dogs. We compared bacterial culture and molecular methods for the detection of C. jejuni directly from canine feces and from Bolton enrichment broth inoculated with feces in a multi-laboratory randomized-method test. Although culture offers the advantage of collection of isolates for further epidemiologic study, real-time PCR (rtPCR) to detect cpn60 from DNA isolated directly from canine feces was more sensitive than culture and more accurate than rtPCR using DNA isolated from enrichment cultures. The limit of detection for our cpn60 rtPCR was 320 cfu/g.

  PublisherOA PDFDOI

• Risk factors for fluoroquinolone- and macrolide-resistance among swine <i>Campylobacter coli</i> using multi-layered chain graphs

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-16

  preprintOpen access

  Abstract Campylobacter spp . resistant to fluoroquinolones and macrolides are serious public health threats. Studies aiming to identify risk factors for drug-resistant Campylobacter have narrowly focused on antimicrobial use at the farm level. Using chain graphs, we quantified risk factors for fluoroquinolones- and macrolide-resistance in Campylobacter coli isolated from two distinctive swine production systems, conventional and antibiotic-free (ABF). The chain graphs were learned using genotypic and phenotypic resistance data from 1082 isolates and host exposures obtained through surveys for 18 cohorts of pigs. The gyrA T86I point mutation alone explained at least 58 % of the variance in ciprofloxacin minimum inhibitory concentration (MIC) for ABF and 79 % in conventional farms. For macrolides, genotype and host exposures explained similar variance in azithromycin and erythromycin MIC. Among host exposures, heavy metal exposures were identified as risk factors in both conventional and ABF. Chain graph models can generate insights into the complex epidemiology of antimicrobial resistance by characterizing context-specific risk factors and facilitating causal discovery. Author summary Antimicrobial resistance is influenced by multiple factors, including exposures to selecting agents, such as antibiotics, antiseptics, or heavy metals, and factors affecting the transmission of resistant pathogens, such as biosecurity and hygiene measures. Understanding what specific factors are associated with resistance in a given context is challenging. We developed an approach based on probabilistic graphical models to investigate context-specific antimicrobial resistance risk factors. We applied the approach to Campylobacter coli isolated from pigs in antibiotic-free and conventional farms. We demonstrated how for fluoroquinolones, risk factors were similar across both types of farms, but risk factors for macrolides were different across settings.

  PublisherDOI

• Clonal spread of blaCTX-M-65 producing Salmonella enterica serovars detected in poultry retail meat in North Carolina, USA

  Scientific Reports · 2025-07-21 · 6 citations

  articleOpen accessSenior author

  The rise of antimicrobial resistance (AMR) in Salmonella enterica poses a significant public health threat, particularly through the dissemination of extended-spectrum β-lactamase (ESBL) genes such as blaCTX-M-65. This study investigated the prevalence, resistance profiles, and genomic characteristics of S. enterica isolates from retail poultry products in North Carolina, collected between 2020 and 2024. Among 132 isolates representing 25 serovars, 14 were identified as multidrug-resistant (MDR) strains harboring blaCTX-M-65. Whole-genome sequencing revealed that these isolates belonged to three serovars—S. Infantis (n = 11), S. I -:r:1,5 (n = 2), and S. Senftenberg (n = 1)—with associated sequence types ST32 and ST14. Genomic analyses identified additional resistance determinants, including quinolone resistance-determining region (QRDR) mutations, and a range of mobile genetic elements, such as IncFIB(pN55391) plasmids. The genetic environment of blaCTX-M-65 was conserved, with IS1380-blaCTX-M-65-IS5 structures, highlighting its mobility potential. Phylogenetic analysis showed that isolates clustered by serovar, with strong associations to international lineages. These findings emphasize the ongoing clonal dissemination of blaCTX-M-65 and MDR Salmonella in the food supply chain, necessitating enhanced surveillance and mitigation strategies to curb the spread of resistance genes in food production environments.

  PublisherOA PDFDOI

• Whole genome sequencing reveals virulence–mobile element linkages and phylogenetic diversity in multidrug-resistant Escherichia coli from Nigeria

  Frontiers in Microbiology · 2025-05-07 · 11 citations

  articleOpen accessSenior author

  Background Multidrug-resistant Escherichia coli poses a critical public health threat in Nigeria, where limited genomic surveillance hinders the understanding of virulence-resistance interplay. Methods This cross-sectional study employed whole-genome sequencing to characterize 107 MDR-E isolates from a Nigerian tertiary hospital (2019–2020), analyzing virulence genes, mobile genetic elements (MGEs), phylogroups, sequence types (STs), pathotypes, and antimicrobial resistance (AMR). Results We identified 2,021 virulence genes across nine functional categories, dominated by immune evasion ( terC , 96.3%), adherence ( fimH , 86%), and iron acquisition ( fyuA , 63.6%). Strikingly, 81.3% of virulence genes were linked to MGEs, including MITEEc1 (75.7% of isolates) and IS30 (56.1%), with IncFII (17.8%) and Col156 (12.1%) plasmids co-harboring virulence (e.g., traJ/traT , senB ) and AMR genes (e.g., blaTEM-1B ). Phylogroup B2 (32.7%) dominated, exhibiting high resistance to ampicillin (97.1%) and emerging meropenem resistance (11.4%). Globally disseminated STs (ST131, ST410, ST648) carried significantly more diverse virulence genes than minor clones ( p = 0.028) and were strongly associated with double-serine QRDR mutations ( gyrA_S83L : 97.6%, parC_S80I : 97.6%), which correlated with more virulence genes (24.2 vs. 22.3 genes) and resistance (MAR index: 0.7 vs. 0.5) compared to minor clones. Notably, 92% (61/66) of high-risk clones harbored these mutations, versus 57% (21/37) of low-risk clones, suggesting a fitness advantage enabling major clones to sustain larger genetic cargoes. Pathotyping revealed 54.2% as extraintestinal pathogenic E. coli (ExPEC), with 72.4% of these being uropathogenic (UPEC) and 5.2% ExPEC/EAEC hybrids, alongside 43.9% atypical ExPEC strains. Hierarchical clustering demonstrated phylogroup B2’s genetic diversity and co-localization of plasmid-borne virulence/AMR genes. Discussion These findings underscore Nigeria’s MDR-E crisis, driven by MGE-facilitated gene transfer, hybrid pathotypes, and globally disseminated high-risk clones harboring double-serine QRDR mutations. There is continued need for robust genomic surveillance, stringent infection control measures, enhanced antibiotic stewardship, and exploration of antivirulence strategies (e.g., targeting fimH or yeh ) to curb the spread of these highly adaptable pathogens in resource-limited settings and beyond.

  PublisherOA PDFDOI

• Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs

  PLoS Computational Biology · 2025-08-13 · 1 citations

  articleOpen accessCorresponding

  Campylobacter spp. resistant to fluoroquinolones and macrolides are serious public health threats. Studies aiming to identify risk factors for drug-resistant Campylobacter have narrowly focused on antimicrobial use at the farm level. Using chain graphs, we quantified risk factors for fluoroquinolones- and macrolide-resistance in Campylobacter coli isolated from two distinctive swine production systems, conventional and antibiotic-free (ABF). The chain graphs were learned using genotypic and antimicrobial susceptibility data from 1082 isolates and host exposures obtained through surveys for 14 cohorts of pigs. The gyrA T86I point mutation alone explained at least 58% of the variance in ciprofloxacin minimum inhibitory concentration (MIC) for ABF and 79% in conventional farms. For macrolides, genotype and host exposures explained similar variance in azithromycin and erythromycin MIC. Among host exposures, heavy metal exposures were identified as risk factors in both conventional and ABF. Chain graph models can generate insights into the complex epidemiology of antimicrobial resistance by characterizing context-specific risk factors and facilitating causal discovery.

  PublisherDOI

• Impact Evaluation of Ayurveda Outreach Clinic for the Management of Non- Communicable Diseases Program in Nepal

  Tribhuvan University Journal · 2024-12-31

  articleOpen access

  Department of Ayurveda and Alternative Medicine (DOAA), one of the departments of the Ministry of Health and Population (MOHP), manages Ayurveda and alternative medicine services and promotes health through Ayurveda health institutions across the country. The department also carries out planning, programming, coordination, supervision, monitoring of Ayurveda service programs. Ayurveda Outreach clinic for the management of non-communicable diseases (NCDs) is a major program which focuses on the preventive aspect of health care and aims to develop and promotes a healthy lifestyle in people and tries to prevent and manage NCDs. This program is being delivered from Ayurveda hospitals, Ayurveda health centres and outreach clinics (ORC). The key activities are to provide the Ayurveda health services to the unreached population. General health check-up and medicine distribution were the main activities of the ORC. The ORC mainly served elderly women and poor people. High blood pressure, gastritis, asthma, osteoarthritis, rheumatoid arthritis, gouty arthritis and constipation were the chief health complaints of the people. The activities of the program are relevant to bring notable changes in the community as people who visit the ORC site are being informed about the health and Ayurveda and are also receiving the quality services. Provision of Snehana and Swedena in some places has increased the utilization of the health services and the activities of the program have been performed effectively to bring the desired result to prevent and manage the NCDs.

  PublisherOA PDFDOI

• Relevancy and Sustainability of Ayurveda Education and Alternative Medicine in Nepal

  Curriculum Development Journal · 2024-12-31

  articleOpen access

  The study focuses on the preventive aspect of health care and aims to promote healthy lifestyles in school children and tries to prevent and manage the incidence and prevalence of diseases. This research study was done to evaluate the relevancy and sustainability of the program. This study took data from schools of 7 districts, one from each province in Nepal with SAHYP between March to July 2019. Students felt the SAHYP is necessary for them as it makes them aware of medicinal plants, helps them to learn Yoga skills, and remain healthy. The program and its activities are very relevant in context to Nepal as the student needs to learn about the medicinal plants and students have also felt the need of such programs which help them to be healthy and develop healthy habits. The SAHYP should be conducted more frequently with provision of Ayurveda, Yoga teacher and educational materials. Program activities and changes have possibility of being sustainable. Major challenges for sustainability identified include insufficient funds, inadequate physical infrastructures, and lack of trained human resources. Community and institutional ownership and coordination with the local government are required for the sustainability of the programme.

  PublisherOA PDFDOI

• Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing

  mSystems · 2024-02-06 · 10 citations

  articleOpen access

  ABSTRACT The resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens Salmonella and Escherichia coli , the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping Salmonella enterica and E. coli . We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting Salmonella serotypes on in silico test data and identified key pathogenic serovars of Salmonella and E. coli in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable. IMPORTANCE In order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.

  PublisherDOI

• Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States

  PLoS ONE · 2024-06-03 · 5 citations

  articleOpen accessSenior authorCorresponding

  Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.

  PublisherOA PDFDOI

• The genomic diversity and antimicrobial resistance of Non-typhoidal Salmonella in humans and food animals in Northern India

  One Health · 2024-09-12 · 5 citations

  articleOpen access

  Introduction: (NTS) serovars are the leading global cause of gastroenteritis and have established reservoirs in food animals. Gap statement: Due to a lack of surveillance, there is limited information on the distribution of NTS serovars in India. Aim: Here, we investigated the epidemiology, sequence types, serovar distribution, phylogenetic relatedness, and antimicrobial resistance patterns of NTS in humans and animals across a large geographic area in Northern India. Methodology: We collected stool samples from patients with diarrhea who presented to 14 laboratories in Chandigarh and from five states in India (Punjab, Haryana, Uttarakhand, Himachal Pradesh, and Rajasthan). We sequenced the genomes and analyzed 117 NTS organisms isolated from humans and animals. Minimum inhibitory concentrations (MICs) were estimated using a Vitek2 system. Results: Virchow, causing human infections from north India for the first time. Among the different food-producing animals, pigs appeared to be a key source of human infections. Twenty-eight percent (28 %) of the NTS isolates were multi-drug resistant (MDR), and human isolates showed a higher proportion of resistance. A higher level of contamination of meat samples in our study (8.4 %) potentially suggests a close association of NTS serovars with the food chain and high transmission risk in north India. Conclusions: This study provides information on AMR genes and plasmid replicons associated with different serovars and highlights the role of food animals in AMR dissemination in our region.

  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