About

Gireesh Rajashekara is a Professor and Associate Dean for Research and Advanced Studies at the College of Veterinary Medicine, University of Illinois Urbana-Champaign, a position he has held since 2024. His research focuses on solving animal health and zoonotic disease problems in food-producing animals through One Health approaches. Specifically, his work involves the discovery of novel, narrow-spectrum antimicrobials, probiotics, and antimicrobial peptides to control foodborne and animal pathogens. Additionally, his studies explore the molecular mechanisms by which malnutrition and associated changes in microbiota contribute to gut integrity and intestinal homeostasis, and how these factors impact the pathogenesis of enteric pathogens. Dr. Rajashekara's academic career includes previous positions at Ohio State University, where he served as a Professor in the Center for Food Animal Health and the Food Animal Health Research Program, and as an Associate Professor and Assistant Professor in related departments. His educational background includes a B.V.Sc. and M.V.Sc. in Microbiology from the University of Agricultural Sciences in India, and a Ph.D. from the University of Minnesota. His research aims to advance understanding and develop solutions for animal health issues, emphasizing antimicrobial discovery and microbiota-related mechanisms affecting gut health.

Research topics

• Biology
• Microbiology
• Medicine
• Virology
• Ecology
• Environmental health
• Immunology
• Genetics
• Bioinformatics
• Internal medicine

Selected publications

• Spatial and Temporal Patterns of <i>Campylobacter</i> Infection and Projected Habitat Suitability of Dominant <i>Campylobacter</i> Species in Eastern Ethiopia

  GeoHealth · 2026-04-01

  articleOpen access

  Abstract Campylobacter is the most common bacterial cause of foodborne illness globally. Both symptomatic and asymptomatic infections with Campylobacter species have been associated with growth faltering of children in low‐resource settings, while previous prevalence studies primarily focused on diarrheal disease in children. Here, we leverage the data collected from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) project to characterize the spatial patterns of Campylobacter infections among infants with or without diarrhea in rural Eastern Ethiopia. Randomly enrolled infants ( n = 106) were followed from birth to around 13 months, with fecal samples collected monthly. Livestock feces, drinking water, and soil samples were collected biannually. Campylobacter was detected and quantified using genus‐specific PCR and species‐specific PCR for four species. We employed a spatial filtering approach using genus‐specific data to generate smoothed prevalence surfaces by month and age group. Temporally, an upward trend of prevalence was observed as the children grew older. Spatially, high‐prevalence areas were distributed across the whole study area. To relate disease risk to environmental conditions, we used ecological niche modeling with MaxEnt to estimate habitat suitability of the genus Campylobacter and two dominant species identified by PCR results. Elevation, vegetation index, and slope were the most important contributors, and all distribution models suggested areas in the north were more likely to support the pathogen. These results inform Campylobacter infection patterns and identify target areas with higher risk of Campylobacter in low‐resource settings. This further contributes to developing effective intervention strategies in the future.

  PublisherDOI

• Dairy manure, glyphosate, and antimicrobials (copper, streptomycin, and triazole) modulated the composition of antimicrobial resistance at the gene and microbial levels in a processing tomato field

  Microbiology Spectrum · 2026-03-17

  articleOpen accessSenior author

  ABSTRACT Intensive pesticide use drives antimicrobial resistance (AMR) in agriculture, yet the effects of specific practices remain poorly understood. This study evaluated the impact of dairy manure and agrochemicals (glyphosate, copper, streptomycin, and propiconazole) on the composition of culturable AMR bacteria (CARB), AMR genes (ARGs; n = 87), and the microbiome in a processing tomato field ( n = 64 experimental plots). Glyphosate-treated plots harbored the lowest levels of CARB, but the highest prevalence of ARGs (especially tetA , tetB , OXA-50, and OXA-58) in the tomato leaves ( P &lt; 0.05). Manure-treated plots had the highest levels of CARB and ARGs in the soil and in tomato leaves (especially ACT-1, LAT, MIR, aadA1, and aphA6 ). The prevalence of multiple ARGs (IMP-12, ACT-1, DHA, MIR, MOX, OXA-58, OXA-60, ermB , oprj, and oprm ) was lower in streptomycin- or propiconazole-treated plots compared to non-treated plots. Shifts in the soil and leaf microbiome correlated with changes in ARG composition, particularly aminoglycoside-, fluoroquinolone-, and beta-lactamase-associated genes. These findings show that dairy manure, glyphosate, and propiconazole significantly alter the tomato field microbiome and ARG landscape, indicating that fungicide and herbicide applications may contribute to AMR development and dissemination similar to conventional antibacterial agents in agricultural ecosystems. IMPORTANCE Plant agricultural practices are commonly used by farmers to assure the yield and quality of crops; however, they are also associated with the emergence and dissemination of antimicrobial-resistant (AMR) pathogens. AMR is a critical concern in plant agriculture, as it can affect food safety, security, and sustainability. To combat this issue, it is critical to understand the impact of agricultural practices on AMR. Our study demonstrated that biological amendment (dairy manure) and pesticides (glyphosate, copper, streptomycin, and propiconazole) significantly exacerbated the AMR burden in the applied tomato field, which could increase the food safety risk of the fruit. Findings from this study will raise awareness among farmers, policymakers, and consumers, promote responsible and judicious use of antimicrobial agents in plant agriculture, and prioritize the development of sustainable practices to mitigate current and future AMR challenges.

  PublisherDOI

• Antimicrobial peptides isolated from probiotics as an alternative to antibiotics against <i>Salmonella</i> infection

  Applied and Environmental Microbiology · 2026-01-30 · 1 citations

  articleOpen accessSenior author

  ABSTRACT Non-typhoidal Salmonella (NTS) is the leading cause of deaths associated with foodborne illnesses in the United States. NTS is primarily transmitted in humans through the consumption of contaminated poultry and poultry products. Antibiotics and vaccines are used to control Salmonella infection in poultry. However, the evolution of antibiotic-resistant Salmonella and the lack of cross-protection by vaccines necessitate the development of novel antimicrobials for Salmonella infection. Antimicrobial peptides are considered viable alternatives due to the reduced propensity for resistance development, broad-spectrum activity, and lower toxicity. Our previous study detected 33 small peptides in the culture supernatants of Lacticaseibacillus rhamnosus GG and Bifidobacterium lactis (Bb12). Among them, we characterized the efficacy of two peptides (PN3 and PN5) against Salmonella in vitro and in vivo . Our results demonstrated that PN3 and PN5 inhibited the growth of Salmonella Typhimurium (ST) and nine other Salmonella serotypes. PN3 was cidal to ST within 30 min of incubation, and PN5 in 8 h in the time-kill kinetics assay. Additionally, both peptides completely cleared intracellular ST and ST inside the biofilm. PN3 and PN5 possessed stability at high temperatures and against proteolytic enzyme. In resistance assays, ST did not acquire resistance to both peptides. PN3 and PN5 were non-toxic to wax moths and increased their survivability and reduced ST load following challenge. Moreover, the oral administration of PN3 and PN5 significantly reduced ST load in the cecum of infected chickens. Overall, our study showed that PN3 and PN5 are promising candidates to control Salmonella infection in poultry. IMPORTANCE Non-typhoidal Salmonella (NTS) is the leading cause of foodborne-associated deaths in the United States, with 420 deaths reported annually. Although antibiotics are used to control NTS invasive infection, overuse of antibiotics has accelerated the evolution of multidrug-resistant (MDR) Salmonella , necessitating the development of novel alternatives to antibiotics. Antimicrobial peptides (AMPs) are promising alternatives to antibiotics due to their activity against MDR Salmonella , lower chances of acquiring resistance, selectivity, and stability. This study investigated the effect of two AMPs, PN3 and PN5, against Salmonella . Our results demonstrated that PN3 and PN5 inhibit the growth of Salmonella , are stable at higher temperatures, and are resistant to proteolytic enzyme activity. Salmonella exposed to peptides were not prone to acquire resistance. Peptides were effective against Salmonella in the wax moth model and chickens. This study characterized two AMPs identified previously with potential for developing a novel approach to control Salmonella in poultry, prevent foodborne illnesses, and mitigate the rising antimicrobial resistance problem.

  PublisherDOI

• Synthesis of carbazole and naphthyl-pyrimidine-based inhibitors of Xanthomonas for tomato bacterial spot management

  Molecular Diversity · 2026-04-04

  articleOpen accessSenior authorCorresponding

  Bacterial spot of tomato (BST), caused by Xanthomonas species, is a devastating disease in tomato production, leading to severe yield losses and reduced crop quality. Current control strategies, including cultural management and chemical applications, are increasingly challenged by the emergence of copper- and antibiotic-resistant strains. To address this issue, we are exploring the development of novel small molecule antibacterial as a promising alternative control strategy. Through structural expansion and modification of previously identified anti-Xanthomonas leads (X2, X5, and X12), we synthesized a library of small molecules featuring key pharmacophores, including pyrimidine, oxazole, and imidazole. The synthesized compounds were evaluated for their inhibitory activity against Xanthomonas hortorum pv. gardneri (Xhg). Three derivative 4-(2-(1-(2-hydroxy-3-((2-(naphthalen-1-yl)pyrimidin-5-yl)methoxy)propyl)piperidin-2-yl)ethyl)phenol (X2-c), 4-(2-(1-(3-(9H-carbazol-9-yl)-2-hydroxypropyl)piperidin-2-yl)ethyl)phenol (X12-k), and 1-(9H-carbazol-9-yl)-3-(2-(2-(pyridin-2-yl)ethyl)piperidin-1-yl)propan-2-ol (X12-l) demonstrated promising antibacterial effects, exhibiting minimum inhibitory concentrations (MIC) of 25–50 µM and minimum bactericidal concentrations (MBC) of 50–100 µM. X12-l exhibited rapid bactericidal activity against Xhg within 1 h, whereas X2-c and X12-k required 4 h and 6 h, respectively, in a time–kill assay. Furthermore, in silico predictions for compounds X2-c, X12-k, and X12-l indicate an optimal balance of molecular size, polarity, and lipophilicity, conforming to Lipinski’s rule and exhibiting acceptable absorption, distribution, metabolism, and excretion (ADME) profiles. These small molecules can be potentially developed into a useful tool for controlling Xanthomonas in tomato production. Future studies will focus on elucidating their mode of action and evaluating their safety and efficacy in seeds and seedlings.

  PublisherOA PDFDOI

• Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia

  Microbiome · 2025-11-03 · 2 citations

  articleOpen accessSenior authorCorresponding

  BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types. RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings. CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.

  PublisherOA PDFDOI

• Assessing fecal contamination from human and environmental sources using Escherichia coli as an indicator in rural eastern Ethiopian households—a cross-sectional study from the EXCAM project

  Frontiers in Public Health · 2025-01-06 · 7 citations

  articleOpen accessSenior authorCorresponding

  Introduction Enteric pathogens are a leading causes of diarrheal deaths in low-and middle-income countries. The Exposure Assessment of Campylobacter Infections in Rural Ethiopia (EXCAM) project, aims to identify potential sources of bacteria in the genus Campylobacter and, more generally, fecal contamination of infants during the first 1.5 years of life using Escherichia coli as indicator. Methods A total of 1,310 samples (i.e., hand rinses from the infant, sibling and mother, drinking and bathing water, food and fomite provided to or touched by the infants, areola swabs, breast milk and soil) were collected from 76 households between May 2021 and June 2022. Samples were assigned to two groups by infant age: TP1 (time point 1), infants between 4 and 8 months of age, and TP2, infants between 11 and 15 months of age. Fluorometric and semi-selective colorimetric approaches were used to quantify E. coli in the field samples. Results Overall, E. coli was ubiquitous within selected households (56.8% across the study). E. coli was more frequently detected than average (&amp;gt;53%) with high concentration (&amp;gt;2-log CFU) in soil (g) and per pair of hand, while the opposite trend (&amp;lt;33%; &amp;lt;1.5-log CFU) was observed in food provided to the infants (g or mL), per areola, and breast milk (mL; p &amp;lt; 0.01). E. coli was frequently detected in fomites touched by the infants, drinking and bathing water (&amp;gt;51%), but at low concentration (&amp;lt;1.5-log CFU). Correlation analysis between E. coli concentration in different sample types suggested that the mother’s hands and fomites might play a key role in the transmission of E. coli to the infants ( p &amp;lt; 0.01; r 2 &amp;gt; 0.3). Discussion Using E. coli as surrogate, our study identified mother (hands and areola) as reservoirs likely to be involved in frequent transmission of fecal contaminants to infants within rural Ethiopian households.

  PublisherOA PDFDOI

• Transmission pathways of Campylobacter jejuni between humans and livestock in rural Ethiopia are highly complex and interdependent

  Research Square · 2025-01-01 · 1 citations

  preprintOpen access
  PublisherOA PDFDOI

• Antimicrobial peptides disrupting the bacterial membrane reduce <i>Salmonella</i> colonization in chickens

  Microbiology Spectrum · 2025-11-03 · 3 citations

  articleOpen accessSenior author

  ABSTRACT Salmonella is a significant food safety and public health concern. Poultry products have been considered the main vehicles of Salmonella infections in humans. Salmonella being present in visually healthy poultry is suggested as the preeminent human transmission risk factor, allowing bacteria to easily transmit from eggs and poultry to humans. Antimicrobial peptides (AMPs) have been suggested as promising alternatives to current antibiotics because of their low propensity for resistance development. In this study, we tested the efficacy of Lactobacillus rhamnosus GG (LGG)-derived small peptides (P1-NPSRQERR, P2- PDENK, and P4-MLNERVK) against Salmonella Typhimurium (ST) and Salmonella Enteritidis (SE) both in vitro and in chickens. Peptides inhibited ST, SE, and other public health–relevant Salmonella serovars in vitro . The antibacterial activity of peptides is likely due to their effect on Salmonella membranes. Importantly, P1 and P2 effectively reduced the colonization of ST by 2.2 and 1.8 logs, respectively, in chickens at 7 days post-infection. P1, P2, and P4 possessed no adverse effect on chicken cecum microbial community, but chickens not treated and challenged with Salmonella showed a difference in microbial richness and evenness compared to the unchallenged chickens. Furthermore, peptides retain their activity upon exposure to heat and protease treatments—characteristics necessary for the use of antimicrobial products in the poultry industry. In summary, these small peptides can provide a promising approach to develop novel strategies for controlling Salmonella infections in chickens. IMPORTANCE Salmonella is the most frequently reported bacterial cause of foodborne illness in the United States. Poultry products (eggs and poultry meat) have been considered the main vehicles of Salmonella infections in humans. There is a need for developing and implementing effective antibiotic alternatives to reduce Salmonella in chickens, minimize human exposures, and simultaneously contribute to alleviating antibiotic resistance. AMPs have been suggested as promising alternatives to current antibiotics because of their low propensity for resistance development. Our study showed that LGG-derived peptides (P1-NPSRQERR, P2-PDENK, and P4-MLNERVK) significantly inhibit ST, SE and other Salmonella serovars in vitro and in chickens. Overall, our results demonstrate that small peptides can facilitate the development of promising approaches to control Salmonella infections in poultry, thus contributing to improved food safety and public health.

  PublisherDOI

• The probiotic <i>Lacticaseibacillus rhamnosus</i> GG supplementation reduces <i>Salmonella</i> load and modulates growth, intestinal morphology, gut microbiota, and immune responses in chickens

  Infection and Immunity · 2025-04-04 · 17 citations

  articleOpen accessSenior author

  ABSTRACT Salmonella, a leading cause of foodborne illnesses, is primarily transmitted to humans through the consumption of contaminated poultry products. The increasing resistance of Salmonella to antibiotics and lack of cross-protection by vaccines necessitate new control strategies in poultry production systems. This study assessed the efficacy of probiotics against Salmonella Typhimurium (ST) and Salmonella Enteritidis (SE). Lactobacillus acidophilus (LA), Lacticaseibacillus rhamnosus GG (LGG), and Bifidobacterium animalis subsp. lactis (Bb12) showed inhibition of ST and SE in agar well diffusion assay, with stable inhibitory properties. In co-culture assay, both LGG and Bb12 completely suppressed ST and SE growth. Liquid chromatography-with tandem mass spectrometry (LC-MS/MS) analysis of the LGG and Bb12 cell-free culture supernatant identified novel bioactive peptides with anti- Salmonella properties. Administering LGG in drinking water of chickens raised on built-up litter floor in experimental conditions significantly reduced the ST load (5.95 logs and 3.74 on 7 days post-infection [dpi] and 14 dpi, respectively). Gut microbiota analysis revealed increased abundance of several beneficial genera such as Butyricicoccus , Erysipelatoclostridium , Flavonifractor, and Bacillus in LGG-treated groups. Histomorphometry analysis demonstrated increased villus height (VH) and VH by crypt depth ratio in the ileum of the LGG-treated group on 14 dpi. These results highlight LGG as a promising probiotic for controlling Salmonella in chickens and reducing transmission to humans. The beneficial properties of LGG are attributed to the production of antimicrobial peptides, microbiota modulation, and enhanced intestinal integrity. IMPORTANCE Salmonella is the leading cause of foodborne illnesses in the United States and worldwide. It is primarily transmitted through contaminated poultry and poultry products (eggs and poultry meat). Increasing resistance of Salmonella to antibiotics and lack of cross-protection by vaccines necessitate new control strategies to reduce Salmonella in poultry production system and minimize human infections. Probiotics, which are live beneficial microorganisms when administered in an optimum amount, have been increasingly used in recent years as alternatives to antibiotics to promote health. Our study showed that LGG exhibited superior probiotics properties and significantly reduced Salmonella load in chickens. Thus, LGG supplementation is a promising approach to prevent Salmonella infection and enhance performance of poultry thereby enhance food safety, proper antibiotic stewardship and public health.

  PublisherDOI

• Long-term impacts of untreated dairy manure on the microbiome and Shiga toxin-producing <i>Escherichia coli</i> persistence in agricultural soil

  Applied and Environmental Microbiology · 2025-08-07 · 2 citations

  articleOpen access

  ABSTRACT Biological soil amendments of animal origin (BSAAO) improve the soil health of agricultural fields for plant growth. However, as natural reservoirs for bacterial foodborne pathogens, BSAAO application can introduce and support microbes of public health concern, such as pathogenic Shiga toxin-producing Escherichia coli (STEC), in agricultural soils. Using shotgun metagenomic sequencing, this project investigated the microbiome of soil with and without BSAAO, focusing on STEC and the E. coli population over time alongside changes in the soil microbiome and soil abiotic properties. Two farms in Ohio, one using an untreated dairy manure amendment and one that does not use a BSAAO, were sampled for over a year for metagenomic analysis of the soil microbiome. All manure samples were positive for stx genes, indicating the presence of STEC. Impacts of the manure on the soil lasted four weeks by several measures including higher E. coli diversity and more frequent STEC detection. Outside of these four weeks post-amendment, Shiga toxin genes ( stx ) were identified periodically in both fields throughout the year. STEC detection significantly correlated with higher in silico E. coli O-serogroup diversity, as well as lower soil cation exchange capacity and concentrations of calcium, magnesium, and organic nitrogen. Differential abundance analysis of the soil metagenomes identified several taxa influenced by amendment but did not identify taxa correlated with detection of stx genes. This work provides insights into the timing of and ecological factors associated with STEC persistence in the agricultural environment. IMPORTANCE Shiga toxin-producing E. coli (STEC), including E. coli O157:H7, is a major etiological agent of foodborne human disease outbreaks associated with fresh produce and can be transferred to produce via contaminated agricultural soil. Given the devastating impacts of foodborne STEC outbreaks on public health and growers, it is necessary to understand the longevity of the impacts of manure application on the pathogen risk in the soil as well as better understand the ecological and environmental conditions that contribute to STEC survival in the agricultural soil environment. This work expands upon the knowledge of conditions that support STEC persistence in the produce-growing environment and its longevity following amendment in commercial fields with naturally occurring STEC contamination.

  PublisherDOI

Recent grants

• Gut microflora: Impact on neonatal immunity, viral gastroenteritis and vaccines

  NIH · $2.2M · 2012–2018

Frequent coauthors

• Anand Kumar

  Los Alamos National Laboratory

  78 shared

• Löıc Deblais

  College of Wooster

  64 shared

• Gary A. Splitter

  University of Wisconsin–Madison

  62 shared

• Fernando A. Goldbaum

  49 shared

• Trevor E. Swartz

  49 shared

• Gastón Paris

  Consejo Nacional de Investigaciones Científicas y Técnicas

  49 shared

• Anastasia N. Vlasova

  49 shared

• Diego J. Comerci

  National University of General San Martín

  49 shared