African EQA data expose uneven antimicrobial susceptibility testing across GLASS laboratories
Laboratory proficiency in antimicrobial susceptibility testing remains uneven across African sites participating in the EQuAFRICA external quality assessment programme, even as organism identification performed better overall. Across survey cycles from 2021 through 2025, participating laboratories averaged 83% for organism identification and 73% for AST, a gap that carries direct consequences for surveillance quality and bedside treatment decisions. The most concerning errors involved vancomycin and cefoxitin results for staphylococci, two outputs that can alter how clinicians interpret resistance and choose therapy.
The programme was built around a practical public health need: countries cannot monitor antimicrobial resistance reliably if reference and sentinel laboratories do not generate accurate, comparable data. EQuAFRICA was designed to strengthen regional capacity for a One Health bacteriology proficiency testing programme supporting laboratories that feed data into the WHO Global Antimicrobial Resistance and Use Surveillance System. In other words, the test panels were not a theoretical exercise. They were a live check on whether surveillance laboratories can identify pathogens correctly and report susceptibility patterns that can be trusted for national reporting, policy development, and treatment guidance.
One survey was distributed in 2021 and 2023, with two surveys in each of 2022, 2024, and 2025, and each survey included five isolates. Participants came from reference and designated sentinel AMR laboratories in the 14 Fleming Fund recipient countries in Africa. The Clinical Microbiology Proficiency Testing marking scheme was used to score performance. Enrollment and response changed from cycle to cycle, but the average response among enrolled laboratories reached 85%. Human health laboratories made up the majority of participants across all cycles, accounting for 75%.
The pattern of results points to a familiar laboratory problem: identification is often easier to standardize than susceptibility testing. Organism identification depends on workflows that can be corrected through algorithms, training, and familiar microbiology routines. AST is more vulnerable to variation in method execution, reagent handling, interpretive criteria, and laboratory process control. When AST slips, the consequences are immediate. A misleading susceptibility result can send clinicians toward an antibiotic that will not work or away from one that would have been effective.
One sentence captures the operational concern: poorly performed AST at the beginning of the programme improved over time.
That trend matters because quality improvement in AMR surveillance is only useful if it is durable. Laboratories that start with weaker performance and later improve suggest that external assessment can function as more than a scorecard. It can identify process gaps early enough to trigger retraining, method review, and tighter quality systems. The report also noted that no participant scored zero on AST, which suggests that even the weakest laboratories retained some baseline testing capacity rather than complete system failure.
Critical AST errors were not abstract misses. Vancomycin and cefoxitin for staphylococci were specifically identified as clinically important mistakes because they can influence directed treatment decisions. Cefoxitin is commonly used as a surrogate marker in evaluating methicillin resistance in staphylococci, while vancomycin susceptibility shapes one of the most consequential fallback choices in serious gram-positive infection. Errors in either direction can distort the clinical picture, making resistance appear more or less likely than it truly is. In a surveillance system, those mistakes do not stay inside the lab. They can propagate into antibiograms, treatment algorithms, and policy decisions built on flawed data.
The findings also reinforce why AST quality cannot be treated as a narrow technical issue reserved for specialized reference centers. Sustainable bacteriology capacity has to extend from routine clinical laboratories to surveillance sites and national reference laboratories. If each step in the chain is inconsistent, the surveillance network loses sensitivity and credibility. For AMR control programs, that means the difference between recognizing resistance trends early and missing them until treatment failures accumulate.
EQuAFRICA’s design reflects a broader public health reality across the region: laboratory strengthening is not finished when instruments are installed or staff are trained once. Performance needs repeated external measurement, especially in a field where interpretive accuracy drives infection control and antimicrobial stewardship. The programme’s results show that structured external quality assessment can reveal weak links, track improvement, and keep attention focused on tests with immediate clinical implications.
For surveillance systems linked to GLASS, the message is direct. Organism identification was relatively strong, but AST still left room for error, and those errors were clinically meaningful. The work supports continued investment in proficiency testing, laboratory supervision, and consistent quality systems across African AMR networks. It also leaves an important operational question for future cycles: whether the performance gains seen over time can be maintained once the external pressure of a proficiency programme is reduced.