Small colony variants and cefiderocol resistance in clinical Escherichia coli: an in vitro mechanistic study

The emergence of cefiderocol resistance in Escherichia coli poses a threat to this last line antibiotic against carbapenem-resistant infections. This study aimed to induce and characterize the mechanisms of cefiderocol resistance in vitro.

Cefiderocol resistance was induced in four clinical E. coli strains (carrying bla _NDM-5, bla _KPC-2, bla _OXA-48, bla _IMP-4) and ATCC 25922 via serial passaging in increasing drug concentrations. Resistant strains were subjected to whole-genome sequencing (WGS) and RNA sequencing (RNA-Seq) to identify genetic determinants. Phenotypic changes were assessed through growth kinetics, biofilm formation assays, and transmission electron microscopy (TEM).

Resistance developed in all strains within 4-59 days. Small-colony-variant (SCV) emerged in all strains except K66460L (carrying bla _NDM-5), which developed resistance within only 4 days. The resistant strains showed reduced biofilm production and impaired growth kinetics. WGS revealed mutations in genes related to iron transport, membrane function, and metabolic pathways. RNA-Seq confirmed altered expression of iron transport genes. TEM showed that resistant strains had an increased cell wall diameter. In addition, results of our study confirm the role of serine and metallo-beta-lactamase enzymes in cefiderocol resistance.

Cefiderocol resistance can be rapidly selected in E. coli through diverse mechanisms, including mutations affecting iron transport and cell wall biosynthesis, leading to significant phenotypic adaptations like the SCV phenotype. Continuous global surveillance is crucial to monitor the emergence of such resistance.