Occurrence of High Levels of Cefiderocol Resistance in Carbapenem-Resistant Escherichia coli before Its Approval in China: a Report from China CRE-Network

Abstract

Cefiderocol has been approved in the United States and Europe but not in China. We aim to evaluate carbapenem-resistant <i>Enterobacterales</i> (CRE) susceptibility to cefiderocol to provide baseline data and investigate the resistance mechanism. From 2018 to 2019, 1,158 CRE isolates were collected from 23 provinces and municipalities across China. The MICs of antimicrobials were determined via the agar dilution and broth microdilution methods. Whole-genome sequencing was performed for 26 cefiderocol-resistant Escherichia coli isolates to investigate the resistance mechanism. Clone transformations were used to explore the function of <i>cirA</i>, <i>pbp3</i>, and <i>bla</i>_NDM-5 in resistance. Among the 21 antimicrobials tested, aztreonam-avibactam had the highest antibacterial activity (98.3%), followed by cefiderocol (97.3%) and colistin (95.3%). A total of 26 E. coli isolates harboring New Delhi metallo-beta-lactamase 5 (NDM-5) showed high levels of cefiderocol resistance, of which sequence type 167 (ST167) accounted for 76.9% (20/26). We found 4 amino-acid insertions (YRIN/YRIK) at position 333 of penicillin-binding protein 3 (PBP3) in the 26 E. coli isolates, and 22 isolates had a siderophore receptor <i>cirA</i> premature stop codon. After obtaining the wild-type <i>cirA</i> supplementation, the MIC of the transformants decreased by 8 to 16 times in two cefiderocol-resistant isolates. A cefiderocol-susceptible isolate harboring NDM-5 has an MIC increased from 1 μg/mL to 64 μg/mL after <i>cirA</i> deletion, and the MIC decreased from 64 μg/mL to 0.5 μg/mL after <i>bla</i>_NDM-5 deletion. The MIC of the E. coli DH5α, from which the <i>pbp3</i> mutant was obtained, increased from 0.064 μg/mL to 0.25 μg/mL. Cefiderocol showed activity against most CRE in China. The resistance of ST167 E. coli to cefiderocol is a combination of the premature stop codon of <i>cirA</i>, <i>pbp3</i> mutation, and <i>bla</i>_NDM-5 existence. <b>IMPORTANCE</b> Cefiderocol, a new siderophore cephalosporin, has been approved in the United States and Europe but not in China. At present, there are almost no antimicrobial susceptibility evaluation data on cefiderocol in China. We evaluated the <i>in vitro</i> susceptibility of 1,158 strains of carbapenem-resistant <i>Enterobacterales</i> to cefiderocol and other antibiotics. We found that a high proportion of Escherichia coli showed high-level resistance to cefiderocol. Whole-genome sequencing (WGS) and molecular cloning experiments confirmed that the synergistic effect of the <i>cirA</i> gene premature stop codon, <i>bla</i>_NDM-5 existence, and the <i>pbp3</i> mutation is associated with high levels of cefiderocol resistance.