THE FIRST 28 DAYS: Neonatal Health, New Science, and a Busy Few Months at CHRF
Our work at CHRF takes us between laboratories, communities and hospital wards, sometimes all in the same week. In the neonatal wards where we work, that often means meeting babies only a few days old, their families waiting for answers while clinicians try to understand what is making them sick and how best to treat them.
Bangladesh has made extraordinary progress in child survival. Vaccines, better nutrition and stronger health systems have helped reduce under-five mortality by almost 80%, from 147 deaths per 1,000 live births in 1990 to about 31 today. Yet the first 28 days of life remain especially vulnerable, and in our hospitals, we are increasingly seeing newborns with severe bacterial infections, rising antimicrobial resistance, and fewer antibiotics that work.
This is why neonatal health is one of CHRF’s major strategic priorities, and over the past few months many pieces of that work have started coming together. This Sepsis Awareness Month, we want to share that journey with you!
A paper we wish we did not have to write
For nearly two decades, CHRF teams and collaborators across four hospitals collected blood cultures from sick children, tested the bacteria for antibiotic resistance and carefully preserved isolates. This year, we brought those years of data together in a paper published in npj Antimicrobials and Resistance.
Among more than 122,000 children with suspected sepsis, we found a worrying rise in infections caused by the Klebsiella pneumoniae species complex. By 2021, 81% of isolates were resistant to carbapenems, some of our most important antibiotics, and mortality among infected children had risen substantially over the study period. Five years later, in 2026, these high levels of resistance remain.
But Klebsiella is only one part of the problem. In our hospitals, we also see serious neonatal infections caused by Acinetobacter, Pseudomonas, Burkholderia, E. coli and other bacteria, many of them increasingly resistant to antibiotics. Through routine microbiology, molecular testing and genomics, we are trying to understand this changing landscape: which pathogens are causing disease, how their populations are shifting over time, and how antimicrobial resistance is evolving.
Over the years, we have now sequenced more than 7500bacteria from neonatal and paediatric infections, allowing us to look beyond individual cases and begin building a much larger picture of how these pathogens are changing in Bangladesh.
So where do we start?
First Annual Meeting of ANISA
Our work on neonatal infections goes back many years. Through ANISA, one of the largest community-based studies of serious infections in young infants in South Asia, we followed more than 63,000 babies across Bangladesh, India and Pakistan, learning how often serious illness occurs and what bacteria and viruses may be responsible.
Today, we are also studying how infections spread inside hospitals. Through our neonatal programme and CAMO-Net collaboration with Imperial College London, supported by Wellcome, we combine clinical, microbiological, genomic and patient movement data to trace possible transmission.
PathoPath links bacterial genomes with where patients were in a hospital and when, helping reveal whether infections may be connected. The tool is open source and available on GitHub for anyone interested in using or adapting it to investigate hospital outbreaks.
Together, these approaches allow us to study neonatal infections at several levels, from understanding which organisms are causing disease to identifying possible transmission inside a hospital and finding practical ways to detect problems sooner.
But there is a sick baby today
Understanding the problem is important, but our research also needs to help the baby who is sick today. This is why CHRF, Bangladesh Shishu Hospital and Institute, and Sir Salimullah Medical College Mitford Hospital have joined NeoSep1, an international clinical trial across nine countries. Sponsored by GARDP and conducted with the MRC Clinical Trials Unit at UCL and St George’s, University of London, the trial is evaluating antibiotic combinations for neonatal sepsis, including new combinations involving fosfomycin, flomoxef and amikacin. In Bangladesh, it is led by Professor A.S.M. Nawshad Uddin Ahmed, working with CHRF early-career scientist Dr. Mohammad Shahidul Islam and the wider team.
Some of our Neosep1 team members
We are also beginning to think beyond antibiotics. With support from our donors, CHRF has sequenced over 1500 Klebsiella and E. coli isolates from neonates, giving us a unique resource to ask which parts of these bacteria might make promising targets for future vaccines, monoclonal antibodies and other therapeutics. This work is led by our Senior Scientist Dr. Yogesh Hooda through a grant from the Gates Foundation.
What began as an effort to understand why babies are becoming sick is increasingly becoming an effort to find better ways to diagnose, treat and, ultimately, prevent these infections.
Bangladesh to the world
While this work has been growing in Dhaka, CHRF scientists have also been carrying research and experiences from Bangladesh into conversations around the world.
CHRF was strongly represented at ISPPD-14 in Copenhagen, where our team members shared decades of pneumococcal research through talks and posters. Our Lab Officer, Hafizur Rahman gave his first oral talk!
Dr. Senjuti Saha spoke at ESCMID Global in Munich, Microb’UP hosted by Pasteur Institute, and gave a seminar at ETH Zurich in Basel hosted by Pathoplexus. Dr. Yogesh Hooda spoke at the Post Graduate Institute of Medical Education & Research in India, where he presented on integrating patient movement and pathogen genomics to track neonatal Klebsiella pneumoniae infections in hospitals. He also took part in a Gates Foundation convening in London, while back home, Dr. Arif Mohammad Tanmoy presented at the Network of Young Biotechnologists of Bangladesh (NYBB).
And the world came to us
Dr. Genay Pilarowski and Dr. Juliana Gil from the Chan Zuckerberg Biohub spent a week working alongside our genomics team on RNA metagenomics. The visit was hands-on, with experiments, troubleshooting and plenty of discussion, but it also took our visitors beyond the laboratory to Mirzapur, where they could see how surveillance works in the communities where much of our research begins. And because no visit to Bangladesh should be entirely about pipettes and protocols, there were Jamdani sarees too.
For us, the visit felt particularly special. Years ago, CHRF scientists travelled abroad to learn genomics and bring those skills home. Today, collaborators are coming to Bangladesh to work with us, exchange ideas and build new science together.
A little celebration
There was also time for celebration. As many of you know, Dr. Senjuti Saha received the 2026 Sabin Rising Star Award, with Professor Mathuram Santosham introducing her at the ceremony. It was a lovely full-circle moment, connecting generations of scientists who share a belief that research and vaccines can transform child health.
There have also been quite a few conversations about our science beyond conference halls.
The Lancet Regional Health – Southeast Asia invited Dr. Senjuti Saha to talk about CHRF's community RSV study in rural Bangladesh, why hospital surveillance alone cannot tell us the whole story, and what the findings could mean as Bangladesh thinks about RSV prevention. In the European Medical Journal, the conversation turned to Powering Local Genomics: why Dr. Senjuti Saha returned to Bangladesh, what it takes to build genomics capacity locally, and why mentorship matters as much as machines. And The Pathologist asked another question very close to our hearts: Can Bangladesh build its own diagnostics? Our answer, unsurprisingly, is that we certainly intend to try.
The growing Building Scientists for Bangladesh (BSB) network
This quarter, we also travelled to Kishoreganj for a science camp at Guzadia Secondary School. The camp was organised in collaboration with ShikkaBridge, founded by BSB alumna Tahiyah Hafiz.
For many of the students, it was their first time looking through a microscope. Through hands-on experiments, they observed bacteria, tested salt for iodine, and extracted DNA from a banana.
And for us, it was a small glimpse of what a growing network can do: taking science beyond our labs and bringing it closer to more young minds.
In conclusion
Looking back at all these moments, the same spirit runs through much of the work in this newsletter. Whether we are trying to protect a newborn from an untreatable infection, involving families and communities in research, building new tools in our laboratories or watching a young person use a pipette for the first time, we are trying to build science that is useful, rooted in Bangladesh and able to grow beyond any one project or generation.
There is still a lot to learn and much more to do, but these past few months have given us many reasons to be hopeful about what comes next.
Onward with purpose and passion, CHRF Communications Team
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