Our research focus is on rapid identification of modifiable factors of mortality in neonatal sepsis. We have developed molecular assays for virulent pathogens and antimicrobial resistance for detection of bacteria causing lethal neonatal sepsis in India. We plan to link the activity of our laboratory with the national UMMID initiative of the Department of Biotechnology, Government of India for making these assays easy-to-access in clinical diagnosis. Sepsis is caused by a dysregulated host response to infection. We focus on understanding sepsis with data-driven approaches using public health and host transcriptome data, and cutting edge tools, like artificial intelligence.
Tripathi H, Mukhopadhyay S, Mohapatra SK. Sepsis-associated pathways segregate cancer groups. BMC Cancer. 2020 Apr 15;20(1):309. doi: 10.1186/s12885-020-06774-9. PMID: 32293345; PMCID: PMC7160985.
Mukhopadhyay S, Thatoi PK, Pandey AD, Das BK, Ravindran B, Bhattacharjee S, Mohapatra SK. Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock. PLoS One. 2017 Feb 15;12(2):e0171689. doi: 10.1371/journal.pone.0171689. PMID: 28199355; PMCID: PMC5310888.
Li XL, Ezelle HJ, Kang TJ, Zhang L, Shirey KA, Harro J, Hasday JD, Mohapatra SK, Crasta OR, Vogel SN, Cross AS, Hassel BA. An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20816-21. doi: 10.1073/pnas.0807265105. Epub 2008 Dec 15. PMID: 19075243; PMCID: PMC2634919.x.
Mohapatra SK, Krishnan A. Microarray data analysis. Methods Mol Biol. 2011; 678:27-43. doi: 10.1007/978-1-60761-682-5_3. PMID: 20931370.
Mohapatra SK, Cole LE, Evans C, Sobral BW, Bassaganya-Riera J, Hontecillas R, Vogel SN, Crasta OR. Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection. BMC Infect Dis. 2010 Jan 18;10:10. doi: 10.1186/1471-2334-10-10. PMID: 20082697; PMCID: PMC2826305.
Sepsis is a lethal disorder in all age groups including the newborn, and accounts for one-fifth of all deaths globally. One approach to reduce mortality is by rapid detection of the virulent pathogens (especially of the ESKAPE group) causing neonatal sepsis in India. Virulent phenotype is coded by certain genes in the bacteria. In our first attempt, we have developed a molecular diagnostic assay based on multiplex PCR for rapid detection of ESKAPE pathogens in clinical isolates. We plan to go deeper with genomic characterization of hyper-virulent bacteria causing sepsis.
What is the consequence of infection by a virulent pathogen? The host response to a serious bacterial pathogen, such as Klebsiella, is complex and dynamic. A series of molecular and cellular events shape the clinical trajectory of sepsis. In sepsis patients, some patterns emerge from analysis of blood transcriptomic datasets of the patients, such as up-regulation of pro-inflammatory cytokines and down-regulation of adaptive immunity. The current motivation is to dissect the clinically meaningful patterns and to discover the biological processes underlying non-survival from sepsis [PMID:28199355] and related disorders like COVID-19 (DOI: 10.1101/2020.10.13.20211425).
In addition to pathogen virulence and host immune-inflammatory responses, failure of antimicrobial treatment is an important cause of mortality due to sepsis. Antimicrobial
resistance, like virulence, is also encoded by genes in the bacteria, and are targeted for rapid detection.
Modern biological investigations are premised on generation of genome-scale data and sophisticated computational algorithms. For example, pathway-centric analysis of transcriptome data conducted at our laboratory revealed insights into sepsis [PMID:28199355] and sepsis-like cancers [PMID: 32293345] that were not possible with gene-level analysis alone. Ultimately, we are grounded on the notion that computational analysis must be driven by the quest for biological insights and societal impact.
A diagnostic panel for rapid detection of early onset sepsis in high-risk neonates (DBT and ICMR)
|1993||M.D.||Banaras Hindu University|
Assistant Professor, National Institute of Biomedical Genomics, Kalyani, West Bengal, India (2010 - present)
Research Associate, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA (2005 - 2009)
Research Associate, Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA (2003 - 2005)
SRA, Scientists' Pool Scheme, CSIR, India (2000 - 2002)
Assistant Professor, Department of Biochemistry, BP Koirala Institute of Health Sciences, Dharan Nepal (1997 - 1999)
Senior Resident, Department of Biochemistry, Maulana Azad Medical College, New Delhi, India (1994 - 1997)
Member, Society of Biological Chemists (India)
Member, Indian Society of Human Genetics
|1986||Honors in Biochemistry (1st Professional)|
Leukocyte transcriptome signature of outcome of severe sepsis/septic shock (DBT)
A unified web-portal for analysis, integration and visualization of multiomics data (DBT)
Samanwoy Mukhopadhyay (recently submitted thesis)