Molecular Characterisation of Carbapenemase-Producing Multi-Drug Resistant Klebsiella pneumoniae from Human, Animal, and Environmental Samples from Ekiti and Ondo State, Nigeria

Background The escalating global threat of human infections caused by multi-drug-resistant (MDR) Enterobacteriaceae, particularly Klebsiella pneumoniae , poses a serious challenge to public health. The study investigated the prevalence and molecular characteristics of carbapenemase-producing Klebsiella pneumoniae in human, animal, and environmental samples from Ekiti and Ondo States, Nigeria. Methods A total of 1329 samples comprising 399 clinical human samples, 404 non-clinical human samples, 393 animal samples, and 133 environmental samples were examined. The samples were processed using standard microbiological techniques, and antibiotic susceptibility testing was performed in accordance with the Clinical and Laboratory Standards Institute (CLSI) guidelines. Antibiotic resistance genes ( OXA-48, NDM-1, VIM , and KPC ) were determined in all K. pneumoniae isolates that were phenotypically positive for carbapenemase production. Whole-genome sequencing (WGS) was performed on two K. pneumoniae isolates from the same household, which exhibited similar resistance patterns. Data analysis was performed in Excel and the Statistical Package for Social Sciences (SPSS) version 23. Results The overall prevalence of K. pneumoniae was 105 (7.9%), with higher rates in animal samples 38 (9.4%) than in human samples 59 (7.3%) and in the environmental sample 8 (6.0%). Antibiotic resistance was significantly higher in human isolates than in animal and environmental isolates (p < 0.05). All isolates were susceptible to colistin and amikacin. Multidrug resistance was observed in 65 (61.9%) isolates, which was significantly more common in human samples (p < 0.05). Carbapenemase production was detected in 9.2% of MDR isolates, predominantly in human samples. The OXA-48, VIM , and KPC genes were identified in Carbapenemase-producing K. pneumoniae . Whole-genome sequencing of K. pneumoniae isolates NGEK23 and NGEK25 revealed distinct resistomes and mobile genetic elements between the two isolates, suggesting distinct origins and differing diversity of resistance genes. Conclusion The high frequency of multidrug resistance and the presence of carbapenemase-producing K. pneumoniae across human, animal, and environmental sources in the study samples highlight an urgent need for robust infection control and antibiotic stewardship programmes.