Transforming microbiology at Lira Hospital: How CwPAMS promotes diagnostic excellence in low-resource settings
Exploring how our Clinical Microbiology workstream supports the iAIMS project in Uganda
by Dr Nikki D’Arcy, Senior Technical Project Manager (Clinical Microbiology), CwPAMS
Since 2019, the Commonwealth Pharmacists Association (CPA) and Global Health Partnerships’ Commonwealth Partnerships for Antimicrobial Stewardship (CwPAMS) programme has empowered healthcare professionals to address the global health threat of antimicrobial resistance (AMR).
CwPAMS works by building strategic pharmacy-led partnerships between health institutions in the UK and those in eight African lower- and middle-income countries, fostering bidirectional learning between multidisciplinary healthcare teams to support strong antimicrobial stewardship (AMS) through an integrated bundle of activities that promote the prudent, safe use of medicines and effective infection prevention strategies.
An addition to phase 2.0 of CwPAMS was our Clinical Microbiology workstream, supporting the integration of laboratory data into our Health Partnerships’ AMS programmes, whilst fostering and strengthening links between hospital wards and laboratories. This workstream aims to improve the use of local microbiology services and antimicrobial prescribing data to inform clinical decisions.
Through CwPAMS 2.0, University Hospitals Dorset NHS Foundation Trust (UHD) in the UK has partnered with Lira Regional Referral Hospital (LRRH) in Uganda on the Integrated AMS, Infection Prevention and Control, and Microbiology Services (iAIMS) project, which is supported by the Ugandan Ministry of Health and the Infectious Diseases Institute as well as international partners.
The subsequent impact on the laboratory at LRRH has been transformational. What began as a run-down and under-resourced microbiology service has evolved into a centre of diagnostic excellence, delivering timely, reliable results and shaping antibiotic use across the region.Â
Before CwPAMS: underresourced and unsuitable
In May 2021, the microbiology laboratory at LRRH reopened, but under unsuitable conditions. The space was cramped and overheated, lacking basic equipment such as an autoclave, Bunsen burners, weighing scales, and purpose-built benches. Available diagnostic reagents, such as antibiotic discs and culture media, were often expired. Without reliable microbiological testing capacity, clinicians were forced to rely on empirical antimicrobial treatments. As such, their ability to track and respond to AMR was severely inhibited.
The situation at LRRH was not uncommon and is representative of a challenge faced by many in low-resource settings: how do health facilities build robust diagnostic systems despite limited infrastructure, constrained budgets, and insufficient specialist training?
iAIMS sought to address these gaps. The project is led by Dr Francis Kiweewa, Consultant at LRRH and Director at Strengthening Institutional Capacity for Research Administration and Dr Pasco Hearn, Consultant Microbiologist at UHD, and implemented by Mary Apaki, Medical Laboratory Technologist at LRRH, and a dedicated team of laboratory and clinical staff. Through their efforts, iAMS has provided a comprehensive solution to this challenge – one that has since become a model of impactful, scalable health system strengthening.
From dysfunction to diagnostics: the work of the iAIMS project
The revitalisation of microbiology services at LRRH began with basic interventions. An early initiative was the provision of plungers for the laboratory staff to use when applying antibiotic discs to agar plates. This greatly improved the efficiency and quality of antimicrobial sensitivity testing; before this intervention, needles had been used for the application of antibiotic discs, which was not time-efficient and often resulted in the incorrect positioning of the discs. Blood culture bottles, quality media and petri dishes were also provided, replacing expired and improvised alternatives.Â
At the inception of the iAIMS project, the laboratory at LRRH had recently been upgraded, with the provision of equipment and technology, including a WHONET computer with microbiology laboratory database software. However, orientation and training on how to utilise these improvements had not been given. Reflecting CwPAMS’ focus on partnership and bidirectional learning, Dr Hearn and Lindsey Osborne, a Senior Biomedical Scientist, conducted a face-to-face visit to LRRH to carry out in-person training in best practices, including how to perform internal quality assurance and create and apply laboratory standard operating procedures. This training, combined with encouragement from the AMS Committee, enabled Mary to lead this work locally, communicating closely with the clinical teams to drive a rapid improvement in laboratory performance.
One particularly transformative step was the development of the hospital’s first antibiogram, a laboratory report that shows the susceptibility of bacteria to various antibiotics. With mentorship and support, local staff gained the skills to develop an antibiogram and use it to interpret AMR. This quickly became central to clinical and operational decisions, guiding the hospital’s antibiotic procurement for the 2023/2024 fiscal year and informing newly established protocols that restrict the use of critical antibiotics (i.e., meropenem) in the absence of a laboratory-confirmed requirement.
The commitment of all involved in this partnership is to be commended and used as an example of what can be achieved with a great team. In particular, it is important to recognise Mary’s dedication to improving herself and the facility. She has heightened awareness of microbiology services throughout the facility, which has led to an increase in the number and the quality of samples sent to the laboratory, ultimately giving patients the best chance of optimal treatment.
In keeping with our bidirectional learning approach, as part of CwPAMS, Mary travelled to the UK to spend time with the UHD team and returned to Uganda with additional knowledge and skills to continue to improve the service at LRRH.Â
Beyond the lab: the wider impact of iAIMS
The success of the iAIMS project went beyond just restoring LRRH’s microbiology service. By strengthening the lab-clinician interface, sample volumes increased dramatically from 314 samples in 2021 to 1,391 by mid-2024.Â
Monthly meetings between laboratory teams and clinicians have improved communication and collaboration, and have built confidence in diagnostic services. In parallel, community engagement activities, including radio talk shows, have helped to increase public awareness of AMR and the importance of diagnostics in supporting AMS initiatives.
The antibiogram and microbiology test menu developed through iAIMS were disseminated to 38 lower-level health facilities, extending the reach of data-driven treatment protocols and laboratory support to the broader health system. Through these measures, LRRH now serves as a regional centre of excellence for AMR surveillance and responsible antibiotic use.
“When you come to Lira Regional Referral Hospital and you ask, ‘Which department is really doing wonders?’ Anyone in Lira Hospital will tell you, microbiology is doing wonders. Everyone says “Wow” to microbiology!”
Mary Apaki
Medical Laboratory Technologist, Lira Hospital
Although the laboratory’s performance has improved significantly, challenges remain. LRRH’s status as a regional centre of excellence has resulted in an increased demand for diagnostics and other health institutions looking to LRRH to process their samples, straining stock levels. Additionally, more awareness is needed across hospital departments and in the wider community to sustain sample submission and responsible antibiotic use.
This success story is not the end point, but a foundation and an example of how iAIMS’ model can be used to support the implementation of diagnostics to strengthen health systems in the management of infections. The LRRH/UHD Health Partnership experience demonstrates what can be achieved with focused investment and international collaboration, and provides a practical, cost-effective model for how diagnostic capacity can be scaled across Uganda and beyond.
The transformation at LRRH demonstrates that revitalising diagnostic services is not only possible but vital. Microbiology laboratories are the frontline defence in the fight against AMR: when they function well, they improve patient outcomes, inform cost-effective treatment decisions and protect the effectiveness of life-saving medicines.
This story is also a proof of concept. Provision of infrastructure and equipment alone cannot make a fully functional laboratory with meaningful results, but with modest financial input, strategic mentorship, operational support and good communication systems between laboratory and clinical teams, these initiatives can yield an outsized impact. As the global health community grapples with the growing threat of AMR, scalable, sustainable models like iAIMS’ microbiology revival at LRRS are more critical than ever.
Continued support, both technical and financial, is needed to preserve these gains and extend them locally, nationally and globally. The return on investment is not just measured in data points or laboratory reports but in lives saved, drugs used wisely, and systems strengthened for the future.
Dr Nikki D’Arcy
Senior Technical Project Manager (Clinical Microbiology), CwPAMS
About the author
Nikki is an experienced project manager with molecular and microbiology research experience in hospitals, academia and biotechnology. She has a background in infectious disease research and a PhD in infection control and the microbiology of indoor environments.
In addition to leading the Clinical Microbiology workstream on the Commonwealth Pharmacists Association’s CwPAMS programme, Nikki is Director of Operations at a biotech firm, Logistics and Operations Lead at Tessellate Bio, and a freelance Early Stage Drug Discovery Consultant.
About CwPAMS and the Fleming Fund
The Department of Health and Social Care’s Fleming Fund is a UK aid programme supporting up to 25 countries across Africa and Asia to tackle antimicrobial resistance (AMR), a leading public health threat across the world. The Fleming Fund invests in strengthening data surveillance systems through a portfolio of country grants, regional grants and fellowships managed by Mott MacDonald, and global projects managed by partners.