
Dr. Paresh Sharma received his PhD (2010) from BITS Pilani, India. He did his Post-doctoral work in Malaria Biology at the NIAID, National Institute of Health (NIH), USA from 2010-2013. He joined the National Institute of Animal Biotechnology in 2013.
Dr. Paresh’s has extensive research experience in the field of Microbiology, Cell Biology, Immunology and Genomics. His research interest has been focused on understanding the molecular mechanisms behind major intracellular parasitic diseases for identifying new drug treatments, diagnostic tools, and vaccines. During his PhD and Postdoctoral work he has used genetic and genomic approaches to study the host parasite interaction and molecular mechanisms using the protozoan parasites Plasmodium falciparum, Leishmania donovani and Trypanosma brucei as a model.
Google Scholar Link:
https://scholar.google.co.in/citations?user=2tTBQ5MAAAAJ&hl=en
Research Focus
Welcome to the Host-Microbe Interactions and Epigenetics Laboratory
At the National Institute of Animal Biotechnology (NIAB), our laboratory is dedicated to deciphering the dynamic interplay between pathogens and their hosts. We employ cutting-edge genomic, epigenomic, and proteomic approaches to unravel the molecular foundations of infectious diseases, with the ultimate goal of developing innovative strategies for disease control.
Our Core Research Themes
1. Hemoprotozoan Parasites: Unraveling Complexity
We focus on understanding the pathogenesis of economically significant haemoprotozoan parasites. Our research encompasses:
Novel Antimicrobial Discovery:Tapping into the untapped potential of the gut microbiome, a gold mine for bioactive metabolites, to identify new antimicrobial compounds.
Our Mission
By integrating fundamental discovery with translational science, we aim to transform our findings into practical solutions, novel drugs, vaccines, and diagnostics that enhance animal health, ensure food security, and contribute to sustainable agriculture both nationally and internationally.
Bovine Theileriosis: Deciphering a Parasite-Induced Cancer
Theileria annulata is a master of cellular hijacking. This intracellular parasite doesn’t just infect bovine white blood cells; it transforms them. Infected cells lose control over their growth, become immortalized, and spread throughout the host’s body in a process that mirrors cancer metastasis.
Our lab is at the forefront of investigating this remarkable phenomenon. We seek to unravel the molecular toolkit T. annulata uses to reprogram its host, effectively creating a parasite-driven “cancer.” By understanding these mechanisms, we are uncovering fundamental principles of both infectious disease and cellular transformation.
Our Approach:
We employ cutting-edge integrative multi-omics combining genomics, epigenomics, and proteomics to answer key questions:
From Insight to Intervention:
Our research is translationally driven. We are leveraging our discoveries to develop tangible solutions for farmers:
By targeting the unique biology of this cancer-like parasite, our work aims to mitigate significant economic losses in the livestock sector and pioneer new strategies for sustainable animal health.
Theileria annulata Hijacks Host Signaling: Integrated Phosphoproteomics and Transcriptomics Unveils ERK1/2 as a Central Regulator of Host Transcription Factors
Theileria-transformed bovine leukocytes exhibit cancer-like characteristics, but the molecular mechanisms driving these transformations remain unclear. This study provides the first comprehensive phosphoproteomic analysis of both host and parasite in T. annulata–infected leukocyte cell lines. We show that T. annulata significantly induces changes in the host protein phosphorylation, impacting key cancer-related processes such as apoptosis suppression, CAMK signaling, and telomere maintenance. A pivotal finding is the parasite’s manipulation of the MAPK pathway via sustained ERK1/2 activation, which regulates the phosphorylation of critical transcription factors like RUNX3, FOSL2, BCL6, c-JUN, JUNB, and c-MYC. Transcriptomic analysis of genes controlled by these transcription factors confirmed their role in T. annulata replication. ERK inhibition disrupts phosphorylation, deactivates these transcription factors, and induces apoptosis in infected cells. This underscores the ERK-AP-1 axis as a central mechanism of Theileria pathogenesis and a promising therapeutic target. Additionally, parasite-specific phosphoproteins and kinases were identified, offering new insights into therapeutic strategies to combat infection.
Genomic characterization of host gene alterations in Theileria annulata-transformed leukocytes
T. annulata-infected host leukocytes exhibit cancer-like phenotypes, driven by mechanisms that remain incompletely understood. This study explores the genomic alterations underlying these transformations using whole-genome sequencing and bioinformatic analyses of six clinically relevant T. annulata-infected cell lines. Here we identify 7,867 exon-linked somatic mutations shared across all cell lines, with significant enrichment in oncogenes (e.g., FLT4, NOTCH2, MAP3K1, DAXX, FCGR2B, ROS1) and tumor suppressor genes (e.g., BARD1, KMT2C, GRIN2A, BAP1). These mutations are associated with critical cancer-related pathways. Functional studies revealed that inhibition of the mutated oncogene ROS1 using crizotinib induces death in infected leukocytes, confirming its role in transformation. Additionally, we observe mutations in genes linked to genomic instability and the DNA damage response (DDR) pathways, highlighting potential parallels with cancer biology. Suppression of TP53, a key tumor suppressor, is implicated in the immortalization of infected cells, while upregulation of the DNA mutator enzyme APOBEC3H suggests a parasite-driven, mutation-inducing mechanism. Our findings provide new insights into how T. annulata reprograms host cells through genomic instability and mutations, identifying ROS1 and TP53 as critical targets for therapeutic intervention. This work advances understanding of parasite-induced oncogenic transformation and offers pathways for future research.
Epigenetic Reprogramming of Host Chromatin by the Transforming Parasite Theileria annulata
T. annulata, a transforming apicomplexan parasite, extensively reprograms the chromatin architecture of bovine leukocytes to facilitate infection and cellular transformation. To elucidate the underlying epigenetic mechanisms, we characterized the chromatin landscape of infected lymphocytes using integrated proteomic, imaging, and functional assays. Our findings reveal that T. annulatalacks the DNA damage marker γH2A.X and its associated SQ/TQ motif, indicating an evolutionary divergence from canonical DNA repair signalling pathways.
High-resolution profiling of histone post-translational modifications (PTMs) demonstrated distinct nuclear compartmentalization, with host (H3K27me3, H3K9me1/2), parasite-predominant modifications (H3K4me3, H3K18me1, H3K27ac, H3K9ac, and H3K36me3), and shared modifications (e.g., H3K4me1/2, H3K36me2, H4K5/8/12/16ac, H3K9me3 and H4K91Ac) suggesting a coordinated epigenetic strategy driving host cell programs to sustain proliferation and survival. Our study delineates a novel host–parasite epigenetic interface, positioning T. annulata as a unique model of epigenetic parasitism. By bridging parasitology and cancer epigenetics, these findings unveil new therapeutic opportunities targeting chromatin vulnerabilities in parasite-induced transformation.
Drug Repurposing: A Fast-Track Strategy Against Protozoan Parasites
Confronting drug resistance and the high cost of new drug discovery, our lab is pioneering a systematic pipeline to identify existing clinical compounds for use against T. annulata and related parasites. By integrating high-content phenotypic screening with deep mechanistic validation, we rapidly pinpoint drugs that selectively target the infected cell while sparing healthy hosts.
Our pipeline has successfully identified three distinct classes of repurposed candidates:
Through this iterative strategy, we are building a robust portfolio of next-generation therapeutic candidates, offering new hope for controlling bovine theileriosis and providing a blueprint for tackling other protozoan diseases.
Genomic Surveillance of Protozoan Parasites: Decoding Diversity for Better Control
Our lab leverages advanced genomics, including Whole Genome Sequencing (WGS), to map the evolving genetic landscape of T. annulata and other protozoan parasites. By conducting large-scale population genomic studies on clinical isolates across India, we have uncovered critical insights into the parasite’s evolution and spread.
By integrating deep genomic surveillance via WGS with cutting-edge diagnostics, we are building a robust framework for the proactive and precise control of bovine theileriosis and related haemoparasites.
Combating Antimicrobial Resistance (AMR)
AMR is a critical One Health challenge, eroding the efficacy of treatments for bacterial infections in both animals and humans. In the livestock sector, AMR, particularly in mastitis-causing ESKAPE pathogens, leads to severe production losses and threatens food security.
Our lab is at the forefront of AMR research, employing an integrative strategy to decipher resistance mechanisms and pioneer novel countermeasures. Our approach is built on four key pillars:
Through this comprehensive research, we aim to generate the knowledge and tools needed to curb the spread of AMR, improve animal welfare, and ensure the sustainability of livestock production.
Genomic Surveillance of AMR pathogens to Point-of-Care Detection
Our lab has pioneered genomic surveillance strategies for Staphylococcus aureus, a major cause of bovine mastitis. Through a series of interconnected studies, we have moved from uncovering hidden AMR threats to developing rapid field-deployable diagnostics, establishing a comprehensive framework for managing this pathogen.
Collectively, this body of work underscores our lab’s dedication to building a modern genomic surveillance framework for livestock health, one that enhances detection accuracy, tracks the evolution of resistance in real-time, and ultimately empowers evidence-based strategies to safeguard bovine health and productivity.
Mechanistic Decoding of AMR Pathways
A core focus of our lab is to deconstruct the molecular mechanisms that major bacterial pathogens use to evade antimicrobials. We employ integrated genomics, transcriptomics, and phenotyping to unravel the complex resistance pathways in priority pathogens, providing a foundational knowledge for countering AMR.
The OS-MRSA Enigma: A Case Study in Cryptic Resistance
Our work on oxacillin-susceptible MRSA (OS-MRSA) exemplifies this approach, deciphering the unique biology of a cryptic pathogen that carries the mecA resistance gene yet tests as susceptible to antibiotics. We seek to understand how this “sleeper agent” evades detection and rapidly activates its resistance under therapeutic pressure.
Our findings reveal a sophisticated two-stage survival strategy:
Stage 1: The Trojan Horse
In its dormant state, OS-MRSA significantly downregulates the femXAB operon, a key complex for peptidoglycan cross-linking. This creates a compromised, weakened cell wall that is inherently vulnerable to β-lactam antibiotics, explaining its apparent susceptibility. Crucially, the mecA gene is present but functionally latent, allowing the bacterium to masquerade as a treatable infection.
Stage 2: Activation Under Fire
Upon exposure to oxacillin, OS-MRSA undergoes a dramatic adaptive shift. It activates key pathways, including altered expression of ltaS and sceD, which remodel the cell envelope. This response triggers a coordinated survival phenotype:
Physiological Changes: Reduced growth rate and increased cell size.
Resistance Emergence: A significant increase in the Minimum Inhibitory Concentration (MIC).
Stealth Retention: Critically, this induced resistance does not compromise virulence, allowing the pathogen to persist during infection and evade standard treatment regimens.
Impact: By exposing this molecular switch, we have redefined OS-MRSA as a high-threat, cryptic reservoir of resistance. This work provides the essential mechanistic foundation needed to develop next-generation diagnostics that can detect this latent threat and more effective therapeutic strategies to prevent its dangerous activation.
A One Health Strategy: Drug Repurposing at the Human-Animal Interface
The global fight against Antimicrobial Resistance (AMR) is uneven. Disparities in drug accessibility and regulatory frameworks between low- and middle-income countries (LMICs) and high-income countries (HICs) create hotspots for AMR emergence. In LMICs, factors like over-the-counter antibiotic availability and limited healthcare access often lead to unregulated use, while HICs operate under stricter stewardship. Our research tackles this complex challenge through a One Health lens, focusing on drug repurposing as a rapid, cost-effective strategy to discover new weapons against resistant pathogens like Staphylococcus aureus.
From Global Insight to Drug Discovery
We bridge the gap between AMR epidemiology and practical therapeutic solutions. By systematically screening compound libraries like the MMV Pathogen Box, we have identified several potent anti-staphylococcal leads, including:
MMV676501
MMV102872
MMV687807
MMV1804559
Our work goes beyond identification; we are actively deciphering their mechanisms of action, revealing how they disrupt key metabolic pathways and virulence systems in S. aureus.
Expanding the Arsenal: Beyond Conventional Compounds
In parallel, we are exploring novel chemical spaces. We have demonstrated that macrocyclic copper (II) complexes and other repurposed chemical scaffolds exhibit strong antibiofilm activity, presenting promising candidates for treating persistent, device-associated infections that are notoriously difficult to eradicate.
A Holistic Vision
By connecting the dots between global AMR drivers, systematic drug discovery, and mechanistic validation, our lab embodies a holistic approach. We are committed to developing accessible, next-generation therapeutic strategies that mitigate the threat of bacterial pathogens across human, animal, and environmental interfaces.
The Gut Microbiome: A New Front in the Fight against AMR
Our lab mines the bovine gut microbiome for novel antimicrobials while monitoring the impact of antibiotic treatments. Using an integrated multi-omics approach, we:
Discover New Therapeutics: Using 16S rRNA sequencing, proteomics, and metabolomics, we identify and characterize natural antimicrobial producers, uncovering novel bacteriophages, antimicrobial peptides, and metabolites.
Assess Antibiotic Impact: We simultaneously use these tools to understand how antibiotic exposure disrupts gut microbial balance and promotes resistance.
This dual-strategy positions the gut microbiome as a central pillar in developing sustainable anti-infective strategies and upholding One Health principles.
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Lab Members:
S. Akash | Senior Research Fellow
M.Sc. (Biotechnology), The Maharaja Sayajirao University of Baroda, Gujarat.
Research interest: Antimicrobial Resistance
Linkedin Profile: https://www.linkedin.com/in/akash-suresh-5816ba15b/

Sakshi Singh | Senior Research Fellow
M.Sc. (Genetics), Maharshi Dayanand University, Haryana.
Research interest: Host Pathogen Interaction
Linkedin Profile: https://www.linkedin.com/in/sakshi-singh-4152a9382/

Madhusmita Subudhi | Senior Research Fellow
M.Sc. (Life Science), NIT Rourkela, Orissa.
Research interest: Host Pathogen Interaction (Epigenetics)
Linkedin Profile: https://www.linkedin.com/in/madhusmita-subudhi-a3970413a/

Vengatachala Moorthy A | Senior Research Fellow
M.Sc. (Biochemistry), PSG Coimbatore, Tamil Nadu.
Research interest: Host Pathogen Interaction
Linkedin Profile: https://www.linkedin.com/in/vengatachala-moorthy-a-138b431a4/

Samoel Lareb | Project Associate- II
M.Sc. (Biomedical Sciences) University of Delhi
Research interest: Host Pathogen Interaction
Linkedin Profile: https://www.linkedin.com/in/samoel-lareb-51410b307/

Jaya Limbu | Junior Research Fellow
M.Sc. (Biotechnology), Mizoram University, Aizawl, Mizoram.
Research interest: Host Pathogen Interaction (Epigenetics)
Lab Alumni:
Dr. Debabrata Dandasena | PhD Student
Sonam Kamble | PhD Student
Srimathi Rameshan | Project Associate
Amruthanjali | Project Associate
Umarani Brahma | Project Associate
Shweta Nori | DST-Inspire Young Women Scientist
Dr. Sonti Roy | PhD Student
Dr. Madhumani Barman | Project Associate
Dr. Vasundhra Bhandari | DST-Inspire Faculty
1. Identification of Virulence factors associated with Theileria annulata ( From DBT, India)
2. Genome-wide association study for identification of novel loci associated with resistance to Theileriosis in India. ( From DBT, India)
3. Virulence/disease pathogenesis during Bovine Mastitis ( From DBT, India)
4. Evaluation of Anti-inflammatory Natural Compounds for Therapeutic use in Mastitis of Dairy Animals. (From Ayush, India)
Room 204, 2nd Floor B Wing
National Institute of Animal Biotechnology
Survey No. 37, Opp. Journalist Colony
Extended Q City Road, Near Gowlidoddy
Gachibowli, Hyderabad
Telangana – 500032
Email: paresh[at]niab[dot]org[dot]in
Tel: +91-(0)40-2312-0144

We welcome applications from enthusiastic candidates (JRFs/SRFs/ PDF/Trainees) who are interested in research at our lab. Candidates seeking a position can write to paresh@niab.org.in with a brief CV and one-page research statement explaining how you fit in our lab and why you want to join…
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Ministry of Science and Technology, Government of India
+91 40 2312 0103
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