Co-occurrence and genetic contexts of NDM-1, KPC-2, IMP-1, and AFM-1 carbapenemase genes in a critically ill patient

Background Carbapenem-resistant organisms are increasingly reported in clinical settings, yet the simultaneous detection of multiple carbapenemase genes within a single specimen remains rare. Methods Metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) were performed on a bronchoalveolar lavage fluid (BALF) sample from a patient with severe pneumonia. Results Four carbapenemase genes— bla AFM-1 , bla NDM-1 , bla IMP-1 , and bla KPC-2 —were simultaneously detected in a single specimen. Three carbapenem-resistant isolates were recovered: an ST11 K. pneumoniae carrying bla KPC-2 and virulence-associated genes, an S. algae strain with an assembly-based tandem chromosomal bla NDM-1 arrangement, and a P. stutzeri strain co-harboring bla AFM-1 and bla IMP-1 . Genomic analysis revealed complex mobile genetic contexts associated with these resistance determinants. Conclusion The coexistence of four carbapenemase genes within one clinical sample highlights the complexity of polymicrobial carbapenem resistance and underscores the importance of genomic surveillance.