PhD position - targeting the microbiome for diarrhea and AMR

Infants in low- and middle- income countries (LMIC) are disproportionately burdened by bacterial diarrheal diseases and infections with antimicrobial resistance (AMR). Bacterial diarrheal pathogens contributes significantly to infant mortality, with many classified as WHO AMR priority pathogens. Interventions are needed to prevent infections with bacterial enteropathogens and AMR. 

Our previous research showed that there are differences in the E coli colonization of infants’ microbiome between LMIC vs. high-income countries (HIC).  The airm of this PhD project is to understand how E. coli colonization contributes tot he risk of diarrheal disease and  infections with AMR and use this knowledge to design interventions that protectLMIC infants from both.  

This is a 4 year PhD project based at the Amsterdam UMC's Department of Global Health, building on collaborations with the Centers for Infectious DIsease Research in Zambia, the University of Ghana, and Kenya Medicral Research Institute. 

Would you like to know more about the different phases within the PhD trajectory? You can read more about this on this page.

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.

We 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.