ESKAPE pathogens and their antimicrobial resistance patterns at the university teaching hospital of Kigali, Rwanda: a five -year analysis (2020–2024)

Abstract

Background Antimicrobial resistance (AMR) in Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa , and Enterobacter spp ., known as ESKAPE pathogens, continue to pose a health threat globally. In Rwanda, data on long-term trends and resistance profiles among these pathogens remain limited. This study has assessed the temporal trends in the distribution and AMR patterns of ESKAPE pathogens at the University Teaching Hospital of Kigali (CHUK) from 2020 to 2024. Methodology A retrospective laboratory-based surveillance study was conducted using microbiology laboratory data. All culture-positive clinical specimens processed over the five years were included. Descriptive analysis was performed to assess pathogens' distribution, resistance rates, phenotypic resistance patterns, and temporal trends according to antibiotic categories. Results A total of 3,778 culture-positive isolates were analyzed. Klebsiella pneumoniae was the most prevalent (43.8%), followed by Staphylococcus aureus (26.4%) and Acinetobacter baumannii (15.1%). The overall AMR rate was 56.5%, with the highest resistance observed in Enterococcus spp . (74.6%), Acinetobacter baumannii (69.9%), and Enterobacter spp . (64.4%). Resistance to access antibiotics increased from 54.7 % in 2020 to 83.3 % in 2024, while resistance to watch antibiotics rose from 42.5 % to 57.2%. ESKAPE Pathogens exhibited a comparatively lower resistance rate to the Reserve antibiotics, including polymyxin B and ceftazidime-avibactam. Phenotypic resistance analysis identified extended-spectrum β-lactamase-producing Enterobacterales (32.9 %), methicillin-resistant Staphylococcus aureus (31.1%), carbapenem-resistant Enterobacterales (15.6%), and vancomycin-resistant E nterococci (5%). Conclusion This study demonstrates a high and increasing burden of multidrug-resistant ESKAPE pathogens, characterized by escalating resistance to first-line and second-line antibiotics and early indications of emerging resistance to last-resort antimicrobials. These findings highlight the urgent need to strengthen antimicrobial stewardship, infection prevention, and control measures.