Emergence of New Delhi Metallo-β-lactamase-9 (blaNDM-9) gene in Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates in Africa

Background Carbapenem-resistant Acinetobacter baumannii (CRAB) are World Health Organization priority pathogens due to their significant role in hospital-acquired infections and multidrug resistance. The main carbapenem resistance mechanism in A. baumannii is the carbapenem-hydrolyzing oxacillinases (OXA-type carbapenemases); however, metallo-β-lactamases (MBLs) confer broader β-lactam drug resistance, threatening the effectiveness of available treatments. Results In this study, A. baumannii clinical isolates in Africa were recovered from patients in three Kenyan hospitals with skin and soft tissue, or throat infections. Bacterial identification and antimicrobial susceptibility testing were performed using the VITEK-2 system, and minimum inhibitory concentrations were interpreted according to CLSI guidelines. Whole-genome sequencing (Oxford Nanopore) and bioinformatics analysis revealed all isolates belonged to high-risk strain type ST2 and exhibited resistance to a range of antibiotics in multiple classes, including carbapenems. Three carbapenemase genes were identified: bla _NDM−9 , bla _OXA−23 , and bla _OXA−66 , all chromosomally encoded, with bla _NDM−9 embedded within a Tn125 transposon flanked by IS Aba125 . Additionally, a biocide resistance gene, qacEΔ1 , was identified on an integron, highlighting the role of mobile genetic elements in driving resistance to both antibiotics and antiseptics. Conclusions This study reports the first identification of New Delhi Metallo-β-lactamase-9 ( NDM-9) producing A. baumannii clinical isolates in Africa. Enhanced surveillance and effective infection control strategies are urgently needed to mitigate the public health impact of highly resistant CRAB strains in Africa.