Dr James Njunge


Dr James Njunge


Research Group:


My group focusses on identifying molecular mechanisms to help children survive and thrive. My portfolio lies at the interface of infection, immunity, and nutrition, examining mechanisms underlying clinical outcomes during and following acute illness. Specifically, we focus on the relationships between infection, nutrition, mortality, and poor growth among acutely ill children. I joined the Programme in 2013 as an early post-doc and started biomarker research among critically ill children including biomarkers distinguishing bacterial meningitis from cerebral malaria with Dr. Evelyn Gitau. From 2016, under the mentorship of Prof. Jay Berkley, I successfully led the existing samples and data analysis workplan of the Childhood Acute Illness and Nutrition (CHAIN) Network. My work revealed that acutely ill undernourished children who die soon after hospital discharge have a sepsis-like inflammatory profile at discharge implicating untreated infections or ongoing microbial component exposures. I have further shown that children with severe malnutrition and HIV have evidence of metabolic stress, affecting pathways related to inflammation and lipid metabolism. I am currently leading a large nested systems biology study within CHAIN on mechanisms of inpatient and post-discharge mortality among acutely ill children across the nutritional spectrum in Africa and south Asia. Early data suggests death is associated with failure in energy metabolism alongside inflammation. This will be the largest biological study to date elucidating mechanisms underlying mortality despite treatment protocols being followed. Together, this work has generated new thinking about interventions addressing specific pathways to reduce mortality and leading to translational trials. In the next 5 years, I aim to conduct a programme of work focussed on the relationship between systemic inflammation, a natural response to infections and should resolve with recovery, and growth following acute illness in children. I aim to determine whether systemic inflammation persists after hospital discharge, is greater among undernourished children, if it affects post-discharge growth and identify causes of systemic inflammation. I will utilise a large set of existing high-quality data and biological samples from a recent large study of children admitted to hospitals in sub-Saharan Africa and South Asia and followed up for 6 months after discharge.  

I head the liquid chromatography-mass spectrometry platform and have developed analytical pipelines to investigate infections, support antigen discovery in malaria, among others.  


External: Bryan Gonzales, Holm Uhlig, Trevor Lawley, Judd Walson, Robert Bandsma 


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  • Njunge JM, Gonzales G, Ngari M, Thitiri J, Bandsma R, Berkley J: Systemic inflammation is negatively associated with early post discharge growth following acute illness among severely malnourished children - a pilot study. Wellcome open research 2020, 5(248). https://doi.org/10.12688/wellcomeopenres.16330.1. 
  • Gonzales GB, Njunge JM, Gichuki BM, Wen B, Potani I, Voskuijl W, Bandsma RHJ, Berkley JA: Plasma proteomics reveals markers of metabolic stress in HIV infected children with severe acute malnutrition. Scientific reports 2020, 10(1):11235. 
  • Njunge JM, Gwela A, Kibinge NK, Ngari M, Nyamako L, Nyatichi E, Thitiri J, Gonzales GB, Bandsma RHJ, Walson JL, Gitau EN, Berkley JA: Biomarkers of post-discharge mortality among children with complicated severe acute malnutrition. Scientific reports 2019, 9(1):5981. https://doi.org/10.1038/s41598-019-42436-y. 
  • Njunge JM, Oyaro IN, Kibinge NK, Rono MK, Kariuki SM, Newton CR, Berkley JA, Gitau EN: Cerebrospinal fluid markers to distinguish bacterial meningitis from cerebral malaria in children. Wellcome open research 2017, 2:47. 


Wilson Gumbi – Laboratory lead for the molecular pathogen diagnostics platform. Support testing of clinical samples using molecular techniques to identify and quantify pathogens.  


Elisha Omer – Provides laboratory research support on molecular pathogen diagnostics and liquid chromatography tandem mass spectrometry platforms. 


Justine Getonto – Provides laboratory support for clinical and immunology related research 


Bonface Gichuki: – Wellcome Trust MSc Fellow at The University of Aberdeen, Scotland. I aim to understand the gut microbiome profiles and enteric pathogens that are associated with hospital readmissions among acutely ill children in sub-Saharan Africa and South-Asia. 


Cecillia Wechessa: – MSc Immunology student fellow with our Training Department under The Initiative to Develop African Research Leaders (IDEAL) and Pwani University. I aim to determine biological mechanisms underlying late post-discharge mortality among children treated for complicated severe malnutrition that could inform interventions to prevent mortality. 


Eunice Njuguna: MSc Bioinformatics student fellow with our Training Department, The Eastern Africa Network for Bioinformatics Training (EANBiT) programme, and Pwani University – I am developing a reusable pre-processing workflow for liquid chromatography tandem mass spectrometry proteomics data