Cefiderocol resistance in a clinical ST11-KL64 hypervirulent Klebsiella pneumoniae isolate mediated by a novel CirA truncation and SHV-12 β-lactamase

BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections have emerged as a major global public health threat. Cefiderocol is a novel siderophore-conjugated cephalosporin with potent activity to treat severe infections caused by CRKP. In this study, we investigated the underlying mechanisms leading to cefiderocol resistance in an ST11-KL64 hypervirulent K. pneumoniae FK3023 isolated from a patient with infective fever and chronic kidney disease in China. METHODS: Whole genome sequencing (WGS), amino acid sequences alignment, cirA gene complementation and lactamases genes cloning assays were performed to elucidate the molecular basis of cefiderocol resistance. Pathogenicity was evaluated by quantitative siderophore production, string test, capsule quantification, and a Galleria mellonella infection model. RESULTS: This strain carried a hybrid plasmid that contained both virulence and resistance determinants, including key virulence factors (iutA-iucABCD operon and rmpA gene) and β-lactamases genes (blaKPC−2, blaTEM−1B, blaCTX−M−3, blaCTX−M−65). Compared to the wild-type siderophore receptor CirA, K. pneumoniae FK3023 carried 119 nucleotide deletion (c.1830_1948del), leading to a frameshift, followed by a premature stop codon (Val611TyrfsTer32), resulting in a novel mutation in CirA. K. pneumoniae FK3023 complemented with the wild-type cirA showed a substantial decrease in cefiderocol MIC, further confirming the function of CirA. Each of the six identified β-lactamases genes in K. pneumoniae FK3023 was cloned into a pUC vector, and then expressed in Escherichia coli cells. The E. coli strains carrying blaSHV−12 showed an increase in cefiderocol MIC compared to the E. coli strains carrying empty vectors. CONCLUSIONS: In conclusion, we described a clinical ST11-KL64 hypervirulent K. pneumoniae isolate exhibiting cefiderocol resistance likely mediated by a novel CirA truncation and blaSHV−12. K. pneumoniae FK3023 also carried the hybrid plasmid and two additional resistance plasmids, highlighting the convergence of hypervirulence and multidrug resistance and underscoring the challenges for clinical management.