Combined resistance mechanisms leading to high-level of cefiderocol resistance among NDM-like producing E. coli ST167 clinical isolates.

Purpose: A series of NDM-producing Escherichia coli ST167 clinical isolates exhibiting resistance to cefiderocol (FDC), with no previous exposure to this antibiotic, were analyzed in this study.

Methods: The antimicrobial susceptibility testing and phenotypic detection of resistance patterns (Rapid Cefiderocol NP test and MIC determination) were performed for all tested isolates. Their entire genomes were sequenced by using the Illumina MiSeq platform and high-quality reads were de-novo assembled using the CLC Genomic Workbench. Genome-sequence based characteristics were analyzed using bioinformatics tools.

Results: All NDM-producing E. coli ST167 isolates showed a high level of resistance to FDC (MICs being 64 or > 64 mg/L). The chromosomally located cirA gene, encoding a catecholate siderophore receptor in E. coli, was truncated in all FDC-resistant isolates due to a frameshift mutation (S90Y), leading to CirA-deficient isolates. A four amino acid insertion (YRIN) was also identified after residue 333 in the PBP3 protein sequence of all E. coli isolates. Among them, a single FDC-resistant NDM-5-producing E. coli isolate (1006) was additionally resistant to aztreonam/avibactam (AZA MIC of 8 mg/L). When analyzed against the genome of another FDC resistant NDM-5 producing E. coli ST167 containing a YRIN insertion in the PBP3, and exhibiting decreased susceptibility to AZA, the broad-spectrum ß-lactamase CMY-42 was identified.

Conclusion: We identified a variety of NDM-producing E. coli isolates exhibiting high level of resistance to FDC as a result of the combined effect of CirA deficiency, along with production of NDM-type enzymes. The spread of such resistance phenotype across Europe poses great concern on the clinical efficacy of this novel drug. Additionally, the identification of an FDC- and AZA-resistant NDM-5 producing E. coli isolate represents one of the ultimate evolutions with a possible step towards pan-resistance.