Recently, AI&I researchers Prof. Joost Wiersinga, Dr. Bob Kullberg and Dr. Vanessa Harris joined the Wellcome Leap Focused Antibiotics consortium, a $50M international initiative to develop microbiome‑sparing antibiotics. In this article, we highlight their new grants, research aims and global collaborations to reduce antimicrobial resistance and improve patient care.

Approximately 85-90% of human bacterial infections are local, affecting areas such as the bladder, middle ear, skin, or respiratory tract. Yet nearly all antibiotics are administered systemically, through oral tablets or intravenous injections, exposing the entire body to treatment and turning the gut into a "resistance factory."

The Focused Antibiotics program brings together researchers from across disciplines to pursue a different approach: reformulating antibiotics so they primarily reach the site of infection while sparing the gut microbiome, without compromising treatment efficacy. 

Prof. Wiersinga, Dr. Kullberg and Dr. Harris participate in the Focused Antibiotics consortium and are in the unique position of joining a group of world-leading experts in a $50 million initiative. The consortium aims  to better understand the consequences of systemic antibiotic use and to develop more focused antibiotics that cause less collateral damage.

If successful, scaling these new formulations for the most common outpatient bacterial infections could reduce the global annual occurrence of antibiotic-driven resistant infections by as much as 40%, potentially avoiding more than 100 million resistant infections within a decade of use.

Project of Prof. Wiersinga and Dr. Kullberg

The main goal of the research project led by Prof. Wiersinga and Dr. Kullberg is to develop a microbiome-based marker that predicts the risk of resistant infections after antibiotic use. The researchers will test and validate this marker across different populations and in a controlled antibiotic study. 

‘The microbiome and resistance patterns vary a lot between people and countries. A challenge will be to find a predictor that works reliably across these different setting'
Prof. Joost Wiersinga
Head of the Department of Internal Medicine at Amsterdam UMC

To achieve this goal they bring together international expertise in microbiome research, antimicrobial resistance, and clinical studies, with collaborators based in Finland, India, the UK and the US. The team received $3 million to conduct this research. Dr. Bob Kullberg: 'In the end, we hope that this project will help develop antibiotics that treat infections effectively while causing less damage to the microbiome and less resistance’.

Project of Dr. Harris

Dr. Harris and the PREVENT-AMR team received $1.2 million to study children in low-resource settings, where there is limited capacity for infectious disease surveillance, minimal access to diagnostics, and some of the highest rates of infectious diseases and antibiotic exposures. 

In these settings, antibiotic-resistant infections are harder to treat, place substantial financial burden on families and health systems, and shorten lives. It is known that the gut microbiome plays an important role in the development and spread of antibiotic-resistant (AMR) infections. Antibiotics that can treat high-risk children while sparing the microbiome are a promising way to protect children from current infections and future AMR. 

The researchers’ main goal in this project is to identify gut microbiome biomarkers that can predict diarrhoeal infections with AMR. These biomarkers can be used to assess how likely new antibiotics are to induce resistant infections and support interventions to decrease the risk of diarrhoeal infections with AMR. 

Besides PREVENT-AMR, a five-year clinical trial, TARGET, officially began on 1 July 2026, co-led by Dr. Harris. The project will enroll 2,800 children aged 2 to 59 months across Kenya and Tanzania to test whether two widely available antibiotics, azithromycin and ciprofloxacin, can reduce death and hospitalization in children with both acute watery diarrhoea and malnutrition. 

The Wellcome Leap funded PREVENT-AMR study uses existing microbiome data from children treated with antibiotics to identify biomarkers that predict which children are likely to develop diarrhoeal infections with antimicrobial resistance. 

Although TARGET and PREVENT-AMR are very different studies, they are ultimately complementary: TARGET evaluates the potential benefits of antibiotic treatment, while PREVENT-AMR assesses its costs in terms of antimicrobial resistance. Together, they help weigh the risks and benefits of antibiotic use in children.  

A major challenge for PREVEN-AMR is to identify biomarkers that are relevant for children across different ages and geographic settings. For this reason, the team collaborates with researchers in multiple regions:

  • In Asia, with Dr. Najeeha Iqbal and Dr. Asad Ali at the Aga Khan University in Pakistan,researchers who study malnutrition and diarrhoeal disease and have worked with mothers and children in informal settlements in Karachi for many years.

  • In sub‑Saharan Africa, with Caroline Chisenga and Mwelwa Chibuye, who study AMR and infectious diseases in communities near Lusaka and across Zambia.

  • At Keio University in Tokyo, Japan, with Daniel Mende and Kenya Honda, experts in bacterial ecology, metabolomics and colonization resistance.

  • At the University of Virginia, with epidemiologist Josh Colston, who helps to quantify the potential impact of introducing a microbiome‑sparing antibiotic.

'We hope that we can support the development of low-cost, effective antibiotics that treat children's infections without placing them or their communities at increased risk for infections with AMR. We are also excited about supporting novel drug development and believe our research will provide mechanistic insights into how antimicrobial resistance is induced and spread by bacteria in the gut.’ 
Dr. Vanessa Harris
Internist and infectious diseases physician

Text: Joost Wiersinga, Bob Kullberg, Vanessa Harris and Esmée Vesseur