First report of New Delhi metallo-β-lactamase-6 (blaNDM-6) gene in Africa identified in a carbapenem-resistant Acinetobacter baumannii clinical isolate.

OBJECTIVES

We report the first detection of blaNDM-6 gene in Africa carried in a carbapenem-resistance Acinetobacter baumanii clinical isolate.

METHODS

In this study, an Acinetobacter baumannii isolate cultured from a purulent open septic ulcer on the right breast in a 58-year-old female patient in Kenya was characterized. Bacterial identification and antimicrobial susceptibility testing were conducted using the VITEK 2 system with minimum inhibitory concentrations (MICs) interpreted according to CLSI guidelines 32nd Edition. Whole genome sequencing was performed using Illumina and Oxford Nanopore Technology. Genome assembly was performed from long reads using Autocycler and polished with short reads using Polypolish. This was followed by strain typing with multilocus sequence typing, plasmid replicon typing with using BLASTn against AcinetobacterPlasmidTyping database, screening of antibiotic resistance gene (ARGs) using AbritAMR, comparative plasmid analysis with Proksee and functional annotation with Bakta.

RESULTS

The isolate exhibited resistance to meropenem and displayed a multidrug resistant (MDR) phenotype showing additional resistance to piperacillin, ticarcillin-clavulanic acid, cefepime, ceftriaxone and levofloxacin. It belongs to sequence type ST52, a rare sequence type globally. The isolate carried four plasmids, two of which are resistance plasmids. The isolate also harbored chromosomal intrinsic resistance genes typical within this lineage, however, additional plasmid-encoded ARGs conferring resistance to multiple antibiotic classes including carbapenem were identified, making it multidrug-resistant. The blaNDM-6 was identified in one of the plasmids with r3-T3 replicon type. Genomic analysis revealed blaNDM-6 was embedded within a Tn125-like structure flanked by ISAba125 elements, consistent with previously described genetic contexts for blaNDM variants in A. baumannii and blaNDM-6 genes in all host species.

CONCLUSION

This study presents the first report of blaNDM-6 in Africa. The detection in a rare lineage suggests an independent acquisition via plasmids. Further, it highlights an ongoing evolution of historically susceptible A. baumannii lineages into multidrug-resistant threats. This emphasizes the need for enhanced genomic surveillance in LMICs to monitor the emergence and dissemination of resistance determinants.