Antimicrobial resistance in Burundi: a mixed-methods protocol for assessing   prevalence, risk factors and association with infection prevention and control

Abstract Background Antimicrobial resistance (AMR) is a major global health threat, yet data on its prevalence and associated factors remain scarce in Burundi. This study aims to describe a mixed-methods protocol assessing the prevalence of multidrug-resistant (MDR) bacterial infections, associated risk factors, and the implementation level of infection prevention and control (IPC) measures at Kamenge Teaching Hospital (KTH), Burundi. Methods This is a cross-sectional analytical study conducted at KTH from March to June 2026. A total of 120 patients aged 5 years and older with suspected bacterial infections and an indicated microbiological sample were consecutively enrolled. A structured questionnaire collected sociodemographic, clinical, and therapeutic data. Blood, urine, pus, sputum, or cerebrospinal fluid samples were cultured. Bacterial identification and antimicrobial susceptibility testing followed EUCAST disk diffusion guidelines. MDR was defined as resistance to at least three antibiotic classes. Descriptive statistics, bivariate analysis (Chi-square), and multivariate logistic regression were performed to identify factors associated with MDR. Results Among 120 enrolled patients, the mean age was 42.5 years (SD ± 18.3) and 58.3% were male. The overall prevalence of MDR among positive cultures was 41.2% (35/85). Escherichia coli was the most frequent isolate (36.5%), followed by Klebsiella pneumoniae (21.2%). Among MDR isolates, 60.0% were ESBL-producing Enterobacteriaceae and 14.3% were methicillin-resistant Staphylococcus aureus (MRSA). Prior antibiotic exposure within three months before admission was reported by 44.2% of patients, of whom 60.4% practiced self-medication. The cumulative survival probability at day 28 was 93.0%. In multivariate analysis, prior antibiotic exposure (aOR: 4.82; 95% CI: 2.15–10.82), self-medication (aOR: 3.45; 95% CI: 1.56–7.63), and length of hospital stay > 7 days (aOR: 3.12; 95% CI: 1.38–7.05) were independently associated with MDR infection. Conclusion MDR prevalence is high (41.2%) at KTH, driven by prior antibiotic exposure, self-medication, and prolonged hospitalization. This protocol will guide a comprehensive assessment of AMR at KTH. The findings will inform empirical antibiotic therapy, strengthen IPC programs, and contribute to the national fight against AMR in Burundi.