Emergence of High-Level Cefiderocol Resistance in Carbapenem-Resistant Klebsiella pneumoniae from Bloodstream Infections in Patients with Hematologic Malignancies in China

Abstract

Cefiderocol is a novel siderophore cephalosporin exhibiting potent antimicrobial activities. Although cefiderocol has not been approved in China, resistance is emerging. A multicenter study was performed to evaluate the cefiderocol resistance in carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from bloodstream infections in patients with hematologic malignancies in China. Clinical data analysis and whole-genome sequencing were conducted for collected cefiderocol-resistant CRKP strains. CRISPR-Cas9 system was employed to construct site-specific mutagenesis for gene cirA. Plasmid curing and cloning were performed to assess the effect of β-lactamases on cefiderocol resistance. Total 86 CRKP strains were collected. The MICs of cefiderocol ranged from 0.06 to >256 mg/L. Among four cefiderocol-nonsusceptible strains (4/86, 4.7%), two cefiderocol-resistant strains AR8538 (MIC = 32 mg/L) and AR8416 (MIC > 256 mg/L) were isolated from two patients with acute lymphocytic leukemia (frequency of resistance, 2/86, 2.3%). Metallo- and serine-β-lactamase inhibitors addition would decrease the MIC of cefiderocol from 32 to 1 mg/L in AR8538, which harbors bla_SHV-12, bla_DHA-1, and two copies of bla_NDM-1 in different plasmids. Avibactam did not impact cefiderocol susceptibility of AR8416, which produces NDM-5. However, we found a deficient CirA in AR8416. Using the same K serotype strain D3, we proved CirA deficiency or carrying NDM individually reduced cefiderocol susceptibility, but their simultaneously existence rendered a high-level cefiderocol resistance. In summary, the resistance of CRKP against cefiderocol is mediated by multiple factors, including the deficiency of CirA, metallo- or serine-β-lactamases, while a high-level cefiderocol resistance could be rendered by the combined effect of NDM expression and CirA deficiency. IMPORTANCE Cefiderocol-resistant CRKP strains are emerging in bloodstream infections in Chinese patients with hematologic malignancies, although cefiderocol has not been approved for clinical use in China. Our study proved that the resistance of CRKP against cefiderocol is mediated by multiple factors, including the deficiency of CirA, metallo- or serine-β-lactamases, while a high-level cefiderocol resistance could be rendered by the combined effect of NDM expression and CirA deficiency. As NDM production is one of the most critical mechanisms resulting in carbapenem resistance, it would pose great challenges on the clinical efficacy of cefiderocol in future.

Keywords: CRKP; CirA; NDM; bloodstream infections; cefiderocol.

FIG 1

Susceptibility profile of 86 CRKP strains from bloodstream infections in hematological patients in China.

FIG 2

Synteny plot of plasmid pAR8538_3 and pAR8538_4. Direct comparisons are colored with red hues while reverse comparisons are colored with blue hues. Boxes on top depict CDS on the forward strand, and those at the bottom depict CDS on the reverse strand. Genes encoding β-lactamases were indicated with red, insert sequences with green and genetic context of bla_NDM with blue.

FIG 3

CirA deficiency and bla_NDM-5-bearing plasmid in strain AR8416. (A) Alignment of intact cirA sequence and mutant cirA sequence in AR8416. The base deletion and resulting early stop codon are indicated with pink hues. (B) Synteny plot of plasmid pAR8416-NDM5 with plasmids pABC369-NDM-5 (MK372393) and pNDM5-SCNJ1 (MK715437).

FIG 4

Resistance mechanism schema for high-level cefiderocol resistance. In a NDM-producing CRKP, while CirA functioning normally, plenty of cefiderocol molecules have access to periplasmic space, and thus NDM is insufficient to hydrolyze cefiderocol (left). While the CirA was inactivated (right), the important gateway for cefiderocol entry is switched off. Periplasmic drug concentration then dramatically decreases, making NDM sufficient to hydrolyze cefiderocol.