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Dr Jivan Shakya

Dr Itu Singh has almost 20 years of leprosy research experience, and joined the Stanley Browne Laboratory, The Leprosy Mission Trust India in 2012, and has been Scientist-In-Charge since February 2020. Before joining The Leprosy Mission, she worked at the National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra (Nov 2003-June 2009).

Her research projects include early diagnosis, drug resistance and immunological aspects of leprosy.

Dr Itu has published 37 papers in high impact factor journals. and as Principal Investigator, she has received several research grants from national and international bodies. She is currently mentoring two PhD students.

Email: jivans@tlmnepal.org
ORCiD: https://orcid.org/0000-0001-9469-2148

Dr. Jivan Shakya is an immunologist and infectious disease researcher specializing in host–pathogen interactions, molecular epidemiology, and antimicrobial resistance in mycobacterial diseases. He currently serves as Head of the Mycobacterial Research Laboratories (MRL) at Anandaban Hospital, part of The Leprosy Mission Nepal, where he leads laboratory and translational research aimed at improving understanding, diagnosis, and control of Leprosy.

He obtained his PhD in Immunology from Technion – Israel Institute of Technology, where his research focused on immune regulation and host–pathogen interactions. Building on this foundation, his current research integrates immunology, molecular microbiology, and genomics to investigate disease mechanisms and transmission dynamics of Mycobacterium leprae. His work includes molecular surveillance of antimicrobial resistance, strain typing for transmission studies, and the development of improved molecular diagnostic approaches.

A defining strength of Dr. Shakya’s research program is its multidisciplinary nature. By combining immunological insights with molecular and genomic tools, his work bridges laboratory discovery with epidemiological investigation. This integrated perspective is particularly important for leprosy, a disease characterized by complex host immune responses, long incubation periods, and persistent transmission in endemic communities. Through this approach, his research contributes to improved surveillance strategies, earlier detection of infection, and better understanding of transmission pathways.

Beyond laboratory research, Dr. Shakya contributes to global strategic initiatives aimed at interrupting leprosy transmission. He is actively involved in the Transmission Breakthrough Taskforce of The Leprosy Mission International, an expert working group focused on identifying and implementing innovative interventions to accelerate progress toward zero transmission. Through this role, he contributes scientific expertise to the development of evidence-based strategies addressing key components of the transmission cycle, including early detection, prevention, and improved diagnostics.

Dr. Shakya has authored and co-authored multiple peer-reviewed publications across immunology, microbiology, and infectious disease research. His work also includes investigations into antimicrobial resistance mechanisms and alternative antimicrobial strategies, including bacteriophage-based approaches against multidrug-resistant pathogens such as Pseudomonas aeruginosa and Salmonella Typhi.

In addition to his research activities, Dr. Shakya is committed to strengthening research capacity in infectious diseases. He mentors early-career scientists, supports laboratory training, and promotes collaborative research networks linking laboratories in endemic countries with international research institutions. Through his combined scientific, mentoring, and policy contributions, he aims to advance the global effort to better understand and ultimately interrupt the transmission of leprosy.

Publications (2015- 2026):

  1. Rana, D. R., Shakya, J., Baral, S., Shrestha, R., Koju, K., Joshi, J., ... & Shah, M. (2026). “Clinico‐Epidemiological and Molecular Evidences for Reactivation of Herpesviruses in Dapsone‐Induced Hypersensitivity Reactions in Nepalese Leprosy Patients: An Observational Study.” Immunity, Inflammation and Disease, 14(2), e70385. https://doi.org/10.1002/iid3.70385
  2. Shrestha P, Tandukar S, Shrestha M, Shrestha S, Subedee A, Shakya J, Tuladhar R. “Bacteriophage as an anti-biofilm agent against Pseudomonas aeruginosa from wound infection.” PLoS One. 2025 Oct 9;20(10):e0334139. https://doi.org/10.1371/journal.pone.0334139
  3. Manandhar, S., Karn, D., Shrestha, M. R., Shakya, J., & Singh, A. (2025). “Biofilm formation, methicillin resistance and SCC mec types among Staphylococcus aureus isolated from clinical samples from a tertiary care hospital, in Nepal.” BMC Infectious Diseases, 25(1), 534. https://doi.org/10.1186/s12879-025-10943-1
  4. Tandukar, S., Thakali, O., Tiwari, A., Baral, R., Malla, B., Haramoto, E., Shakya, J., Tuladhar, R., Joshi, D.R., Sharma, B. and Shrestha, B.R., 2024. Application of Skimmed-Milk Flocculation Method for Wastewater Surveillance of COVID-19 in Kathmandu, Nepal. Pathogens, 13(5), p.366. https://doi.org/10.3390/pathogens13050366
  5. Tandukar, S., Sthapit, N., Thakali, O., Baral, R., Tiwari, A., Shakya, J., Tuladhar, R., Joshi, D.R., Sharma, B., Shrestha, B.R. and Sherchan, S.P., 2024. Long-term longitudinal monitoring of SARS CoV-2 in urban rivers and sewers of Nepal. Science of The Total Environment, p.175138. https://doi.org/10.1016/j.scitotenv.2024.175138
  6. Shrestha S, Da Silva KE, Shakya J, Yu AT, Katuwal N, et al. (2024) Detection of Salmonella Typhi bacteriophages in surface waters as a scalable approach to environmental surveillance. PLOS Neglected Tropical Diseases 18(2): e0011912. https://doi.org/10.1371/journal.pntd.0011912
  7. Ghimire, S., Yadav, B.K., Shrestha, S., Shakya, J., Poudel, C.M., Tuladhar, E.T., Sharma, V.K., Raut, M., Bhattarai, A., Manandhar, K.D. and Pant, V., 2023. Effect of ABCA1-R219K Polymorphism in Serum Lipid Parameters in Patients under Statin Therapy Visiting Tertiary Cardiac Center of Nepal. Journal of Laboratory Physicians, 15. DOI: 10.1055/s-0043-1768630
  8. LeBoa C, Shrestha S, Shakya J, Naga SR, Shrestha S, et al. (2023) “Environmental sampling for typhoidal Salmonellas in household and surface waters in Nepal identifies potential transmission pathways.” PLOS Neglected Tropical Diseases 17(10): e0011341. https://doi.org/10.1371/journal.pntd.0011341
  9. Bista, S., Yadav, B., Syangtan, G., Shakya, J., Tuladhar, R., Joshi, D. R., & Lekhak, B. (2023). “Emergence of ISAba1-linked oxacillinase genes among carbapenem resistant Acinetobacter baumannii isolates in a tertiary cardiac center, Nepal.” bioRxiv, 2023-03.
  10. Carey ME, Dyson ZA, Ingle DJ, et al. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. Elife. 2023;12:e85867. Published 2023 Sep 12. https://doi.org/10.7554/eLife.85867
  11. Aiemjoy, K., Seidman, J.C., Saha, S., Munira, S.J., Sajib, M.S.I., Al Sium, S.M., Sarkar, A., Alam, N., Jahan, F.N., Kabir, M.S., Tamrakar, D., Shakya, J., et al., “Estimating typhoid incidence from community-based serosurveys: a multicohort study.”, The Lancet Microbe. (2022) https://doi.org/10.1016/S2666-5247(22)00114-8
  12. da Silva, K., Tanmoy, A.M., Pragasam, A.K., Iqbal, J., Sajib, M.S.I., Mutreja, A., Veeraraghavan, B., Tamrakar, D., Qamar, F.N., Dougan, G. and Bogoch, I., Seidman, J.C., Shakya, J., Vaidya, K., et al., “The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi.” The Lancet Microbe. (2022) https://doi.org/10.1016/S2666-5247(22)00093-3
  13. Andrews, J.R., Yu, A., Saha, S., Shakya, J., Aiemjoy, K., Horng, L., Qamar, F., Garrett, D., Baker, S., Saha, S., Luby, S.P. (2020). “Environmental surveillance as a tool for identifying a high-risk settings for typhoid transmission”, Clinical Infectious Diseases  Volume 71, Issue Supplement_2, 15 August 2020, Pages S71-S78 https://doi.org/10.1093/cid/ciaa513
  14. Ben-Shaanan, T.L., Schiller, M., Azulay-Debby, H., Korin, B., Boshnak, N., Koren, T., Krot, M., Shakya, J., Rahat, M.A., Hakim, F. and Rolls, A., (2018). “Modulation of anti-tumor immunity by the brain’s reward system.” Nature communications, 9(1), p.2723. https://doi.org/10.1038/s41467-018-05283-5
  15. Thapa, K., Manandhar, S., Bista, M., Shakya, J., Sah, G., Dhakal, M., Sharma, N., Llewellyn, B., Wultsch, C., Waits, L.P. and Kelly, M.J., (2018). “Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape”. PloS one, 13(3), p.e0193495. https://doi.org/10.1371/journal.pone.0193495
  16. Simanovich, E., Brod, V., Rahat, M. M., Drazdov, E., Walter, M., Shakya, J., & Rahat, M. A. (2016). “Inhibition of tumor growth and metastasis by EMMPRIN multiple antigenic peptide (MAP) vaccination is mediated by immune modulation.” Oncoimmunology, 6(1), e1261778. https://doi.org/10.1080/2162402X.2016.1261778
  17. Michal A. Rahat and Jivan Shakya (2016). “Parallel Aspects of the Microenvironment in Cancer and Autoimmune Disease.” Mediators of Inflammation, vol. 2016, Article ID 4375120, 2016. https://doi.org/10.1155/2016/4375120
  18. Karmacharya D, Manandhar S, Shakya J, Thapa K, Bista M, Sah GP, Sharma AN, Sherchan A, Dhakal M, Hero JM, Hughes J. (2016) “Incidental discovery of non-focal carnivore species during genetic study of Bengal tiger (Panthera tigris tigris) and snow leopard (Panthera uncia) in Nepal.” Asian Journal of Conservation Biology, 2016 December. 5 (2)
  19. Kinkel HT, Karmacharya D, Shakya J, Manandhar S, Panthi S, Karmacharya P, Sitaula D, Thapaliya R, Prawachan KC, Rai A, Dixit S. (2015) “Prevalence of HIV, hepatitis B and C infections and an assessment of HCV-genotypes and two IL28B SNPs among people who inject drugs in three regions of Nepal.” PLoS One. 2015 Aug 11;10(8):e0134455. https://doi.org/10.1371/journal.pone.0134455