How CPA Strengthens Diagnostic Capacity Across LMICs
Examining the successes of the CwPAMS Clinical Microbiology workstream
by Dr Nikki D’Arcy, Senior Technical Project Manager (Clinical Microbiology), CwPAMS
Since 2022, the Commonwealth Partnerships for Antimicrobial Stewardship (CwPAMS) programme has supported Health Partnerships in strengthening their microbiology capability and capacity by fostering international partnerships, sharing expertise, and promoting sustainable improvements in diagnostics and antimicrobial stewardship (AMS).Â
Across Kenya, Nigeria, Uganda, and Zambia, laboratories have evolved from under-resourced, unsupported facilities into centres of diagnostic excellence, shaping clinical decisions and patient outcomes.
Keep reading to explore an overview of case studies from these participating countries, reflecting on the successes of the programme so far.
Uganda
Before the intervention of CwPAMS, the microbiology laboratory at Lira Regional Referral Hospital (LRRH) in northern Uganda was not fully functional due to space, lack of equipment and inconsistent availability of reagents. In the absence of reliable diagnostics, clinicians were treating infections empirically with broad-spectrum antibiotics, thereby accelerating antimicrobial resistance (AMR) by undermining targeted therapy and promoting the emergence of resistant strains.
With mentorship from UK specialists, the provision of essential tools, and intensive on-site training, LRRH soon developed robust microbiology systems and a culture of quality in the laboratory. In no small part due to the leadership of Mary Apaki, Medical Laboratory Technologist, this culture was quickly locally implemented, clinical colleagues were engaged, and internal quality assurance processes were established to ensure that staff adopted best practices.
Within a short time, the laboratory achieved a 100% pass rate in external quality assessments, developed its first hospital antibiogram, and became a regional reference point for AMR surveillance. Sample volumes grew from 314 in 2021 to 1,391 by mid-2024, while monthly meetings between laboratory staff and clinicians strengthened collaboration and confidence in diagnostic services. Community engagement, including radio programmes, further amplified public awareness of AMR – particularly the importance of diagnostics and responsible antibiotic use.
Utilising peer-to-peer learning networks, LRRH also extended its experience and influence to Entebbe Regional Referral Hospital (ERRH), central Uganda. In December 2025, a team from LRRH, including Apaki and Dr Francis Kiweewa, LRRH Consultant and Director at Strengthening Institutional Capacity for Research Administration, visited ERRH to share practical knowledge in microbiology and AMS. They provided hands-on guidance in transferring data from the existing automated laboratory information system to the WHONET microbiology database software, as well as in developing antibiograms and improving lab-clinician communication. ERRH staff gained practical skills in data management and laboratory workflows, paving the way for sustainable collaboration and knowledge exchange.
Laboratory-supported data use led to the implementation of restrictions on the broad-spectrum antibiotic piperacillin/tazobactam, which in turn led to an overall 9% reduction in resistance rates among pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Sensitivity to alternative antibiotics such as aminoglycosides, meropenem and cefepime showed marked improvement, indicating restored effectiveness of these agents when piperacillin/tazobactam was conserved for only essential cases. Antibiotic utilisation data revealed a 35% reduction in piperacillin/tazobactam use post-restriction, with a corresponding increase in the use of narrower-spectrum antibiotics.
Kenya
At Kitale County Referral Hospital, microbiology capacity has also expanded due to the success of Health Partnerships established through CwPAMS. Between 2022 and 2023, sample workload grew from 1,592 to 2,027, driven by support from the Kenya Medical Research Institute, A Clinically-Oriented AMR Network (ACORN), the United States Agency for International Development’s Infectious Disease Detection and Surveillance project, and CwPAMS, as training programmes and reagent provision enabled laboratory staff to increase blood culture testing.
However, after partner projects ended in 2024, sample volumes dropped, highlighting the ongoing need for sustainable local investment.
At Nanyuki Teaching and Referral Hospital, the development of an antibiogram has highlighted the impact of targeted interventions. Preliminary data from the hospital revealed alarming AMR patterns among common pathogens; a low uptake of targeted antimicrobial therapy underscored the need for evidence-driven practice. After the installation of a VITEK automated microbiology system, CwPAMS supported consumables, clinician training, and technical mentorship.
This resulted in the laboratory reducing turnaround times to 5 hours for isolate identification and 48-72 hours for sensitivity testing. Over 500 samples have since been processed, including 200 positive isolates, laying the foundation for a facility-specific antibiogram and improved patient outcomes. Challenges remain, including funding limitations and industrial strikes, but progress is significant. A comparison of the point prevalence survey (PPS) data from 2024 revealed that only 28.3% of patients were prescribed antibiotics as inpatients compared with 53.3% in 2023.
Elsewhere, at Kakamega County General Teaching and Referral Hospital, similar investments have transformed microbiology laboratory service delivery. The introduction of a VITEK-2 machine reduced turnaround times from 9 days to 48 hours, while sample volumes and pathogen detection increased dramatically. Key World Health Organisation-priority pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, and Staphylococcus aureus, were reliably identified. Staff exchanges with the UK facilitated knowledge sharing and strengthened laboratory practices.
Zambia
At Ndola Teaching Hospital, laboratory upgrades supported by the Fleming Fund and the Centre for Infectious Disease Research in Zambia achieved remarkable outcomes. Renovations modernised the laboratory infrastructure, equipment such as incubators, autoclaves, biosafety cabinets, and automated blood culture systems improved capacity, and the first hospital-wide antibiotic guidelines were developed using local antibiogram data.
Over two years, microbiology test requests increased from 13,387 to 15,283, while PPS demonstrated a 17% reduction in broad-spectrum antibiotic use and increased clinician confidence in diagnostics. The laboratory now plays a critical role in outbreak detection and management, including early identification of multidrug-resistant pathogens in neonatal units, and has achieved ISO 15189 accreditation.
Nigeria
At the University of Calabar Teaching Hospital, microbiology capacity strengthening has underpinned broader AMS efforts. Initially, lack of consumables and poor laboratory infrastructure led to the widespread use of empirical treatment, especially in neonatal wards.
Through CwPAMS’ support, laboratories were equipped to process blood, urine, and wound samples, generating data on 230 isolates, including Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumanii, with notable resistance profiles. Data were disseminated to prescribers across departments, enabling targeted therapy, enhancing infection prevention and control practices (IPC), and informing AMS interventions. Sample referral networks from spoke sites further enhanced access to advanced diagnostics. At the same time, IPC training, antimicrobial guidelines, and community pharmacist engagement ensured that laboratory gains translated into improved clinical practice and reduced inappropriate antibiotic use.
Across all these sites, common themes were noted. Strategic investment in laboratory infrastructure, staff mentorship and training, the introduction of standard operating procedures, and the integration of microbiology with clinical teams all drive transformative change. With improved access to microbiology data, AMS and IPC initiatives at an individual and population level become more contextually relevant and appropriate to the setting.
Whether through revitalising an under-resourced laboratory in Uganda, implementing automated systems in Kenya, modernising facilities in Zambia, or linking laboratory data to clinical practice in Nigeria, the CwPAMS programme has demonstrated that robust microbiology services are essential to combating AMR through better use of antimicrobials and improving patient outcomes.
These success stories highlight the value of bidirectional learning, targeted support, and partnership models that prioritise sustainability, capacity building, and local leadership, laying the foundation for stronger health systems across Africa.
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 UK Department of Health and Social Care (DHSC)’s Fleming Fund is a UK International Development programme partnering with more than 30 countries across Africa, Asia-Pacific and the Caribbean to tackle antimicrobial resistance (AMR),a leading contributor to deaths from infectious diseases worldwide. The Fleming Fund invests in strengthening AMR surveillance systems through a portfolio of country grants, regional grants, and fellowships managed by Mott MacDonald, and global projects managed by DHSC.