Prevalence of extended-spectrum β-lactamase and carbapenemase-producing Klebsiella pneumoniae in humans, animals and the environment in Northwest Amhara, Ethiopia

Abstract

Extended-spectrum β-lactamase-producing K. pneumoniae (ESBL-PKP) and carbapenemase-producing K. pneumoniae (CPKP) are major causes of life-threatening infections in humans and animals. In 2019, the bacterium was responsible for 100,000 to 200,000 deaths globally attributable to antimicrobial resistance (AMR). Ethiopia, home to the largest livestock population in Africa, is characterized by close human-animal interaction and common practices of raw milk and meat consumption that favor the transmission of resistant bacteria. Despite these risks, the epidemiology of ESBL-PKP and CPKP has not been investigated using a one-health approach. This study aimed to determine the prevalence of ESBL-PKP and CPKP among humans, animals, and the environment in northwest Amhara, Ethiopia. A cross-sectional study was conducted from January 1 to August 30, 2025. A total of 972 samples (508 humans, 158 animals, and 306 environmental samples) were analyzed. Sociodemographic and related data were collected from human participants using a structured questionnaire. Urine, blood, environmental swab, wastewater, and rectoanal mucosal swab samples were collected and processed for the isolation of K. pneumoniae using standard microbiological methods. ESBL-PKP and CPKP were identified phenotypically using a combination disk diffusion test and a modified carbapenem inactivation method, respectively, in accordance with the Clinical Laboratory Standard Institute guidelines. Data were analyzed using SPSS version 25 and R software. The prevalence of ESBL-PKP and CPKP among human isolates (n = 71) was 49.3% (35/71, 95% CI: 38-60.7) and 40.8% (29/71, 95% CI: 30.2-52.5), respectively. Meanwhile, the prevalence of ESBL-PKP and CPKP among environmental isolates (n = 56) was 39.3% (22/56, 95% CI: 27.6-52.4) and 25% (14/56, 95% CI: 15.5-37.7), respectively. No ESBL-PKP or CPKP were detected in animal samples. All ESBL-PKP and CPKP isolates were multidrug resistant (MDR) with more than 70% co-resistance to ciprofloxacin, co-trimoxazole, gentamicin, and tetracycline. Among K. pneumoniae isolates, 93% (56/61) of humans, and 73.2% (41/56) of environmental isolates were MDR. Though the number of animal isolates was small, all K. pneumoniae isolates from animals (n = 5) were MDR. Nearly all (40/43, 93%) CPKP isolates were resistant to the last-resort antibiotics, ceftazidime-avibactam and meropenem-vaborbactam. Neonates had higher odds of culture-positive K. pneumoniae compared with adults aged 18-49 years (adjusted odds ratio [AOR]: 27.79, 95% CI: 3.47-222.42, p = 0.002). The high prevalence of ESBL-PKP and CPKP in humans and hospital environments, coupled with widespread multidrug resistance, underscores the presence of a serious public health threat. The nearly universal resistance of CPKP isolates to the last-resort antibiotics is particularly alarming. However, molecular characterization was not performed, limiting the inference about specific carbapenemase genes. Cleaning of the targeted hospital environment and implementing integrated AMR surveillance under a one health framework are essential to prevent cross-sectoral spillover.