Staff Profile

Dr. Sivakumar S

Designation: Scientist E

Division/Unit: Bacteriology

Email: shanmugam[dot]sk[at]icmr[dot]gov[dot]in

Educational Qualification

MSc (Medical Microbiology), PhD (Microbiology and Immunology)

Personal Statement

I am presently heading department of Bacteriology which is a supranational reference laboratory that caters for monitoring and quality assurance of national TB laboratories and also supports TB laboratories in countries under WHO’s South East Asian region. I am a member Advisory Group on TB Diagnostics and Laboratory Strengthening of WHO TAG. My focus of research is molecular drug resistance, epidemiology, and molecular characterization of Mycobacterium tuberculosis. With the above research focus I got trained at CDC Atlanta for the next generation sequencing technology and have 4 project on surveillance of drug resistance and genomic characterization of mycobacterium tuberculosis. I am also the PI for TB diagnostic validation network of ICMR and WHO (WHO PQ) at ICMR -NIRT.

Research Focus

· Diagnostic Mycobacteriology

· Antimicrobial drug resistance

· Genomic characterization of Mycobacterium, including molecular epidemiology

· Biosafety laboratory

· Mycobacterial infection and Autophagy

Ongoing projects as Principal investigator

1. Culture-Free Detection of Drug-Resistance in Clinical Samples for MDR-TB patients
treated under the National Tuberculosis Elimination Program
2. Clinical Performance Evaluation of Molecular Tests for Diagnosis of Tuberculosis
(TB) and Drug Resistant TB Validation
3. The performance evaluation of molecular tests for the diagnosis of tuberculosis
(with or without resistance detection) for prequalification assessment, PQDx_385.
4. Manipulation of autophagy for host-directed therapy in Mycobacterium
tuberculosis.
5. Genomic investigation of sputum metagenomic profile of SARS-CoV-2, Tuberculosis
and in their co-infection.
6. Sentinel surveillance of drug-resistant tuberculosis in India by whole genome
sequencing.

Significant Publications

1. Charlotte Maserumule, Charlotte Passemar, Olivia SH Oh, Kriztina Hegyi, Karen Brown, Aaron Weimann, Adam Dinan, Sonia Davila, Catherine Klapholz, Josephine Bryant, Deepshikha Verma, Jacob Gadwa, Shivankari Krishnananthasivam, Kridakorn Vongtongsalee, Edward Kendall, Andres Trelles, Martin L Hibberd, Rafael Prados-Rosales, Kaliappan Andi, S Siva Kumar, Diane Ordway, Paul A MacAry, R Andres Floto. Phagosomal RNA sensing through TLR8 controls susceptibility to tuberculosis. Cell Reports. 2025 May 27;44(5).
2. Rajendran, P., Giridaran, P., Thomas, S. V., Nagaraj, N., Thiruvengadam, K., Radhika, G., ... & Shanmugam, S. (2025). Characterisation of M. tuberculosis isolates obtained from Tamil Nadu prevalence survey by whole genome sequencing analysis. Infection, Genetics and Evolution, 105763.
3. Daniel, B. D., Shanmugam, S., Mehta, R., Bhalla, M., Vijayalakshmi, M., Ramraj, B., & Padmapriyadarsini, C. (2025). Long term outcomes in drug resistant tuberculosis with Bedaquiline, Pretomanid and varying doses of Linezolid. Journal of Infection, 106509.
4. Rajendran P, Padmapriyadarsini C, Nagarajan N, Samyuktha R, Govindaraju V, Golla R, Ashokkumar S, Shanmugam S. Molecular characterisation of M. kansasii isolates by whole-genome sequencing. Pathogens. 2023 Oct 17;12(10):1249.
5. Gopalaswamy, R., Kumar, N., Vashistha, H., Rajendran, P., Kayesth, J., Peravali, C. J., ... & Shanmugam, S. (2023). Comprehensive assessment of invalid and indeterminate results

in Truenat MTB-RIF testing across sites under the national TB elimination program of India. Frontiers in Public Health, 11, 1255756.
6. Gopalaswamy, R., Palani, N., Viswanathan, D., Preysingh, B., Rajendran, S., Vijayaraghavan, V., ... & Shanmugam, S. (2023). Resistance profiles to second-line anti-tuberculosis drugs and their treatment outcomes: a three-year retrospective analysis from South India. Medicina, 59(6), 1005.
7. Shanmugam, S. K., Kumar, N., Sembulingam, T., Ramalingam, S. B., Selvaraj, A., Rajendhiran, U., ... & Ranganathan, U. D. K. (2022). Mycobacterium tuberculosis lineages associated with mutations and drug resistance in isolates from India. Microbiology Spectrum, 10(3), e01594-21.
8. Gopalaswamy, R., Palani, N., Viswanathan, D., Preysingh, B., Rajendran, S., Vijayaraghavan, V., ... & Shanmugam, S. (2023). Resistance profiles to second-line anti-tuberculosis drugs and their treatment outcomes: a three-year retrospective analysis from South India. Medicina, 59(6), 1005.
9. Venkataraman, A., Shanmugam, S., Balaji, S., Mani, K., Shanmugavel, A. K., Muthuramalingam, K., ... & Prendergast, A. J. (2022). Comparison of two mycobacterial strains in performance of the whole blood mycobacterial growth inhibition assay in Indian children. Tuberculosis, 137, 102255.
10. Palani, N., Premkumar, M., Vaishnavee, V., Dinesh, V., Thiruvengadam, K., Lavanya, J., ... & Shanmugam, S. (2022). Trends in rifampicin and isoniazid resistance in patients with presumptive TB. The International Journal of Tuberculosis and Lung Disease, 26(5), 446-453.