The position

The infant gut microbiome is important in protecting against infections with enteric pathogens, for the maturation of the human immune system, and in supporting nutrient metabolism and growth. Antibiotics massively disrupt the intestinal gut microbiome, impacting these functions of the gut microbiota and accelerating selection for antimicrobial resistance. Children in low- and middle-income countries have high burden of infectious diseases, high exposures in early-life to antibiotics, and high risk for infections with antimicrobial resistance. There is an urgent public health need to better characterize the impact of early life antibiotics on the developing microbiome in young infants in low- and middle-income settings to help prevent the development of antimicrobial resistance and preserve maturation and function of the infant gut.

The postdoctoral researcher will analyze metagenomic data of two large infant cohorts (> 1300 children, the ROTA-biotic study) in Zambia and Ghana, to characterize the association between antibiotic use and antimicrobial resistance (resistome), gut function, and risk of infection with enteric pathogens. The analysis will require the development and/or application of computational approaches to integrate quantitative readouts with antibiotic usage, vaccination status and demographic variables with the aim of better understanding the occurrence, stability, and evolution of antibiotic resistance genes. The sampling for the ROTA-biotic study has concluded, meaning that analysis can begin immediately.

Department

The Amsterdam University Medical Center is a leading academic medical center that combines complex highquality patient care, innovative scientific research, and education. Global Health, Microbiology, and Infectious Diseases represent one of the major research topics at the Amsterdam University Medical Center and are integrated in a multidisciplinary fashion at the Amsterdam Institute for Infection and Immunity (AII&I).

This research will take place at the Department of Global Health/Amsterdam Institute for Global Health and Development (AIGHD) and the Department of Medical Microbiology, Evolutionary Biology of the Amsterdam UMC.

The mission of the Dept of Global Health/AIGHD is to address challenges in global health and development by conducting collaborative interdisciplinary and intersectoral research, generating insights and solutions, and educating the next generation of global health experts. A key departmental research priority is curbing the global development and spread of antimicrobial resistance.

Dr. Harris and Dr. Mende will work closely with the postdoctoral researcher.

Dr. Harris’ group works on understanding how interactions between the intestinal microbiome and host immunity can drive vulnerabilities to infectious diseases in global health. The laboratory uses a translational approach, generating needed clinical data from relevant low- and middle-income country (LMIC) patient populations to fuel mechanistic hypotheses underpinning microbiome, pathogen, and host interactions. Epidemiologic studies are combined with computational, cell culture and animal model approaches. A key research area is understanding how antibiotic administration drives risk of infection with antibiotic-resistant enteropathogens. A second key research area is understanding whether the microbiome is a determinant of vaccine immunogenicity and if it can be employed to improve vaccine performance in LMIC.

Dr. Mende’s group studies the evolution and biology of microbial communities (e.g., the human microbiome) as well as pathogens. The focus of the group is on the analysis of metagenomics and genomics data. The group uses statistical and machine learning methods to integrate different datasets and data types to gain a better understanding of the biological principles behind microbial evolution and host/environment-microbe interactions. The group is further involved in the development of state-of-the-art methods for metagenomics data analysis such as the mOTUs tool. In a world, where sequencing data has become ubiquitous, our vision is to combine local expertise with global data to understand the mechanisms and underlying evolutionary history of our relationship with our microbial companions and opponents.