Reference Number: PhD Project 01/2026
Director of Studies: James A. Berkley and Dr Caroline Tigoi
Location: Kilifi, Kenya
Country: Kenya
BRIEF DESCRIPTION OF THE PROJECT
Neonatal deaths remain unacceptably high in sub-Saharan Africa, with over one million newborns dying annually, many from sepsis driven by antimicrobial-resistant (AMR) bacteria, contributing to a global AMR burden projected to reach 10 million deaths per year by 2050. In Kenya, neonatal sepsis is a significant cause of mortality, and emerging evidence shows that mothers are key reservoirs and transmitters of resistant bacteria and genes to their babies during pregnancy, delivery, and early contact. However, little is known about how hospital environments in low- and middle-income countries shape maternal resistome carriage and facilitate this transmission. Studies such as BANARDS highlight the maternal microbiome as an important reservoir for multidrug-resistant pathogens, but major knowledge gaps persist regarding the dynamics of the microbiome resistome, nosocomial acquisition patterns, and the relationship between maternal factors and neonatal outcomes such as prematurity and low birth weight.
The successful candidate will have the opportunity to work with researchers from the University of Antwerp, the University of Oxford, and LMIC-based senior researchers to develop a project proposal and then undertake their research in a structured, mentored training environment. This PhD project will investigate the role of the maternal and maternity department microbiome in the acquisition and spread of AMR within Kenyan maternity wards. It will examine how mothers and newborns acquire bacteria and resistance genes from the hospital environment and from each other, characterise shared and distinct microbial and resistome profiles, and assess how maternal microbiota relate to major predictors of neonatal mortality such as prematurity and low birth weight. The project will also map the temporal dynamics of hospital environmental microbiomes, explore mechanisms such as horizontal gene transfer that sustain AMR reservoirs, and use machine learning to predict high-risk microbial and resistance patterns. This work will generate critical insights to inform strategies for reducing neonatal sepsis and AMR in resource-limited hospital settings.
The award of this studentship will be made through an international competition to candidates from African LMICs. The successful candidate will be expected to make substantial contributions to the development of their research project. The successful candidate will have the opportunity to work with researchers from the KEMRI/Wellcome Trust Research Programme, the University of Antwerp, and the University of Oxford to develop a project proposal and then undertake their research in a structured, mentored training environment.
ELIGIBILITY
Suitable applicants should be citizens or residents of an African LMIC and possess one or more of the following qualifications:
- A bachelor’s degree with at least a 2:1 (credit or equivalent) in clinical or veterinary medicine, or in basic or applied sciences, including bioinformatics, microbiology, molecular biology or biomedical sciences.
The following are not essential but are desired:
- A master’s degree with at least a credit (or equivalent experience) in a relevant discipline.
- Prior experience in health research, particularly working with neonatal surveillance data and lab skills, DNA extraction, PCR and library preparation
- Whole genome sequencing and AMR genomics experience
- Advanced bioinformatics knowledge, particularly workflow and pipelines development, bash scripting, tools and software for microbiome AMR analysis
- Biostatistics skills with experience in R and Python programming languages
- Machine learning and modelling skills
- Eligibility to register in Belgium
SCOPE OF SUPPORT
This is a three-year PhD studentship to be based at KWTRP. The selected candidate will be supported in applying for and registering for a PhD at the University of Antwerp. The candidate will be supervised by Dr Caroline Tigoi, research scientist at KWTRP, Prof. Surbhi Malhotra and Prof. James A. Berkley. The selected candidate will receive a stipend, medical insurance, and financial support to cover tuition, academic-related fees, travel expenses and research expenses. The candidate and their mentors may seek additional research funding from other sources to support the project.
METHOD OF APPLICATION
Interested applicants are required to submit the following.
- One-page application letter.
- An updated curriculum vitae with a contact email address and telephone number.
- A copy of the highest degree and a certified copy of an academic transcript.
- One-page personal statement stating the preferred area of research, reasons for selecting the area and future career ambitions.
- A letter of support from an academic referee stating the potential of the candidate to succeed in a research career.
SELECTION PROCESS
Shortlisted candidates will be invited for an interview either in person or by videoconference. The successful candidate in the interview will be offered PhD training support.
NOTE: ONLY ONLINE APPLICATIONS will be accepted.
STARTING DATE: March 2026.
APPLICATION DEADLINE: January 15, 2026
NOTE: Only shortlisted candidates will be contacted