About your role
The PhD student will first use existing datasets to identify bacterial, host and environmental determinants of E. coli carriage, bacterial diarrheal infections, and AMR gene (ARG) carriage in infants. They will then support two clinical studies in Kenya and Zambia, assessing whether E. coli carriage contributes to Enterobacteriaceae colonization and ARG transmission. Finally, the PhD student will use agent-based modeling to simulate colonization resistance and ARG transmission dynamics, guiding the design of microbiome-based interventions. Collectively, this work will clarify the role of E. coli in infant gut ecology, support dvelopment of ARG endpoints in late-stage enteric vaccine trials and identify new strategies to reduce AMR and bacterial infections in at-risk LMIC infants.
About youWe are looking for an ambitious PhD candidate to study the interaction between E coli carriage, bacterial gastroenteritis and risk of AMR infections in infants in LMIC settings.
Supportive expertise for the position include:
- Microbiology, microbiome & AMR expertise: Strong understanding of gut microbial ecology, antimicrobial resistance, and ideally metagenomics or microbial genomics.
- Quantitative, statistical & bioinformatics skills Experience analysing complex longitudinal datasets, proficiency in R and/or Python, and familiarity with bioinformatics workflows for microbiome, genomic, or ARG data.
- Computational modeling & systems thinking Strong quantitative aptitude and interest in agent-based modeling, simulation, and integrating bacterial, host, and environmental determinants of colonization and transmission.
- Clinical research Ability to support clinical studies in international/LMIC settings
Key qualities for the researcher include:
- Capacity for interdisciplinary work, international collaboration, & strong communication skills. The candidate should work effectively in interdisciplinary teams, manage research activities independently, and communicate findings clearly in writing and presentations. Capacity to work within an international, multidisciplinary teams while progressively taking ownership of analyses and research questions. The candidate should be organized, curious, analytically rigorous and comfortable learning unfamiliar methods. Good written and spoken English is essential.
- Research motivation: a clear interest in global health, infant health, microbiome science and AMR, with an ability to translate mechanistic findings into clinically relevant questions and potential interventions.
Our offer- You will be employed by Amsterdam UMC Research BV.
- A contract for 12 months, with the intention to extend for a total of four years. The Guideline PhD contract applies to this vacancy.
- Classification in salary scale OIO: € 3.217 in the first year to € 4.077 gross in the fourth year for full-time employment. In addition to a good basic salary, we offer 8.3% end-of-year bonus. Calculate your net salary here.
- Holiday hours: 194.4 per year for full time and a possibility to save additional hours.
- 100% reimbursement for public transport travel costs. If you travel by foot, bicycle, or car, a mileage allowance of €0.21 per km applies (up to a maximum of 40 km one way by car).
- Do you prefer walking or cycling? Take advantage of our good bike scheme.
- Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.
Watch this video with more information about joining Amsterdam UMC Research BV.
