Genomic epidemiology and molecular characteristics of bla_NDM-1-positive carbapenem-resistant Pseudomonas aeruginosa belonging to international high-risk clone ST773 in the Gauteng region, South Africa

Purpose The emergence of carbapenem-resistant P. aeruginosa (CRPA) harbouring acquired carbapenemase genes (bla(VIM), bla(IMP) and bla(NDM)) has become a global public health threat. Three CRPA isolates included in the study had an extensively drug-resistant phenotype with susceptibility to colistin only and were positive for the bla(NDM-1) gene. The current study aimed to investigate the genomic epidemiology and molecular characteristics of the bla(NDM-1)-positive CRPA isolates collected from the Gauteng region, South Africa.Methods Short read whole genome sequencing (WGS) was performed to determine sequence types (STs), genetic relatedness, resistome, virulome and the genetic environment of the bla(NDM-1) gene.Results The WGS and phylogenetic analyses revealed that the study isolates belonged to an international high-risk clone ST773 and belonged to the same clade with eight bla(NDM-1)-positive ST773 isolates from Hungary, India, Nigeria, South Korea and USA. The study isolates harboured a wide repertoire of intrinsic and acquired antibiotic resistance genes (ARGs) related with mobile genetic elements, porins and efflux pumps, as well as virulence factor genes. The clade-specific ARGs (bla(NDM-1), floR2/cmlA9, rmtB4, tetG) were found in a putative integrative and conjugative element (ICE) region similar to ICE6660-like.Conclusion As ICE carrying the bla(NDM-1) gene can easily spread to other P. aeruginosa isolates and other Gram-negative bacteria, the findings in this study highlight the need for appropriate management strategies and active surveillance of CRPA isolates in the Gauteng region, South Africa.