Laboratory performance of antimicrobial susceptibility testing for GLASS pathogens among participants in the EQuAfrica programme, 2021‒2025

The External Quality Assessment (EQA) for Africa (EQuAFRICA) project aimed at building regional capacity to provide a One Health bacteriology proficiency testing (PT) programme for reference and sentinel laboratories supporting antimicrobial resistance (AMR) surveillance and submission of data to the World Health Organization Global Antimicrobial Resistance and Use Surveillance System (WHO GLASS). We analysed the performance of participating laboratories in pathogen specific identification (ID) and qualitative antimicrobial susceptibility testing. The programme covered all GLASS and other bacterial pathogens of importance. One survey was distributed in 2021 and 2023 and two surveys in 2022, 2024 and 2025, with five isolates per survey. Participants were selected among reference and designated sentinel AMR laboratories from the 14 Fleming Fund recipient countries in Africa. The Clinical Microbiology Proficiency Testing (CMPT) marking scheme was used to score performance. The number of invited, enrolled and responding laboratories differed by survey; an average of 85% of enrolled laboratories submitted results. Participants scored 83% for organism ID across all cycles. Microbiology laboratories from the human health sector represented the majority in all cycles (75%). The average scores for antibiotic susceptibility testing (AST) was 73%, no participants that scored zero. Critical AST errors with clinical implications for directed treatment included vancomycin and cefoxitin for staphylococci. Our manuscript highlights that the use of EQA programmes to detecting gaps in laboratory processes and maintaining the quality and accuracy of AST is vital for effective AMR surveillance and control. This report illustrates that poorly performed AST at the beginning of the programme improved over the time. Building sustainable capacity for bacteriology testing, including AST, is critically important at all laboratory levels across Africa, from routine clinical and surveillance sites to national AMR reference laboratories.