NDM-63: a novel NDM metallo-β-lactamase variant in the L3 loop, from a Klebsiella pneumoniae clinical isolate

NDM-type metallo-beta-lactamases (MBLs) are among the most widespread acquired carbapenemases in carbapenem-resistant Enterobacterales. As with other beta-lactamases, allelic variability occurs among NDM-type MBLs, with almost 100 variants so far reported, differing by single or multiple amino acid substitutions or insertions, which may have implications for enzymatic activity. In this study, we report on a novel NDM variant, NDM-63, identified in a carbapenem-resistant ST147 Klebsiella pneumoniae from a surveillance rectal swab. Compared to NDM-1, NDM-63 features an original array of changes in the L3 loop, including deletion of phenylalanine at position 70 and two amino acid substitutions (G69S and A72H), due to a four-nucleotide deletion plus a nucleotide insertion in the gene region encoding the L3 loop. When expressed in Escherichia coli under isogenic conditions, NDM-63 conferred a resistance profile overall similar to NDM-1, but exhibiting a lower level of resistance to carbapenems and cefepime, while remaining susceptible to inhibition by taniborbactam. Present findings expand current knowledge on the structural plasticity of NDM-type MBLs and highlight that variability in the L3 loop, which contributes to delimitation of the active site, could also tolerate amino acid deletions without loss of enzymatic activity. A virtually identical K. pneumoniae carrying a non-functional blaNDM allele entailing only the nucleotide insertion observed in blaNDM-63 (which might have played a role in the evolution of blaNDM) was also isolated from a bloodstream infection that occurred in the same patient, yielding a misleading result of molecular diagnostic testing due to the lack of enzyme activity despite the presence of the target gene.