Uganda’s antimicrobial resistance crisis: How poor-quality microbiology laboratories are struggling

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OPINION

By Ronald Samuel Lugwana

Like many low-and middle-income countries, Uganda faces a growing crisis of antimicrobial resistance (AMR), a threat that silently erodes the effectiveness of life-saving medicines. While the misuse of antibiotics often receives the most blame, a less discussed but equally critical factor is the role of underperforming microbiology laboratories.

When poorly equipped and mismanaged, these facilities can inadvertently contribute to the very problem they are meant to prevent. To reverse this trend, targeted investment in the capacity and quality of microbiology laboratories is needed.

Antimicrobial resistance occurs when bacteria, viruses, fungi, or parasites evolve to resist the drugs used to treat them, turning treatable infections into deadly threats. Globally, AMR is projected to cause 10 million deaths annually by 2050 if no urgent action is taken. In Uganda, efforts to combat AMR are hindered by fragmented data reporting, weak coordination across health facilities, and the inadequate capacity of microbiology laboratories, which limits the timely detection and reporting of resistant pathogens.

A major obstacle lies in the inadequate capacity of microbiology laboratories to generate accurate and timely antimicrobial susceptibility data. These laboratories are responsible for identifying pathogens and determining which antimicrobial agents will work, guiding clinicians in appropriate treatment. However, when laboratories operate without standardised procedures, modern equipment, or well-trained personnel, they risk producing unreliable results. This can lead to incorrect prescriptions, fueling resistance rather than containing it.

A scientific study covering 14 sub-Saharan African countries, including Uganda, found that only 1.3% of approximately 50,000 medical laboratories in these networks conduct the routine bacteriological testing necessary for pathogen identification and antimicrobial susceptibility testing. Many laboratories do not follow internationally accepted procedures for antibiotic testing, such as those recommended by the Clinical and Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing.

Others do not participate in national surveillance or report results to government health information systems, making it difficult for authorities to track resistance patterns and respond effectively.

Uganda’s health system faces significant gaps. According to the Fleming Fund Uganda AMR Diagnostic Capacity Report (2019), only 14 regional referral hospital laboratories are equipped to perform blood cultures and antimicrobial susceptibility testing, and even these operate only when reagents (special chemicals or substances that health workers use to test for diseases in the laboratories) are available.

Many facilities lack microbiology laboratories altogether or rely on outdated manual methods. Even where laboratories exist, staff shortages often mean complex procedures are performed by underqualified personnel. These systemic issues compromise the quality of testing and hinder data sharing, further weakening the national AMR response.

To address this, targeted investment is urgently needed. Microbiology laboratories must be strengthened through the implementation of standard operating procedures, regular internal and external quality assurance, training in current testing protocols and data management, procurement of up-to-date modern laboratory equipment, and mandatory participation in government health information systems AMR reporting.

Improving laboratory quality is not just a technical matter — it is a matter of public safety. Without accurate diagnostics, clinicians are forced to guess, often defaulting to broad-spectrum antibiotics, which accelerates resistance. Surveillance — the systematic monitoring of health data to detect and respond to emerging threats — is only meaningful when the data is reliable and complete. By equipping laboratories and ensuring timely data sharing at the national level, Uganda can make significant strides in its fight against AMR.

Antimicrobial stewardship, public education, and robust health policies are all essential, but none will be fully effective without strong laboratory systems at their foundation. A well-functioning microbiology laboratory is not merely a testing unit; it is a strategic asset in the fight against antimicrobial resistance.

Antimicrobial stewardship, public education, and health policies are all essential, but none will be fully effective without robust laboratory systems at their foundation. A well-functioning microbiology laboratory is not merely a testing unit; it serves as a strategic asset in the fight against antimicrobial resistance.

The writer is a Laboratory Leadership Fellow with the Uganda Public Health Fellowship Program-Laboratory Leadership Program. The views expressed here are views of the author not the institution.