Genotypic-phenotypic discordance for cefiderocol against Enterobacter hormaechei

• Cefiderocol-susceptible Enterobacter hormaechei carried extensive resistance genotypes • Whole-genome sequencing revealed disrupted siderophore uptake and PBP3 variants • Cefiderocol MIC susceptibility contrasted with resistant disk diffusion results • Findings highlight diagnostic uncertainty for cefiderocol at MICs at or close to the breakpoint Cefiderocol-susceptible Enterobacter hormaechei carried extensive resistance genotypes Whole-genome sequencing revealed disrupted siderophore uptake and PBP3 variants Cefiderocol MIC susceptibility contrasted with resistant disk diffusion results Findings highlight diagnostic uncertainty for cefiderocol at MICs at or close to the breakpoint The Enterobacter cloacae complex (ECC) is an emerging global cause of healthcare-associated infections, marked by high mortality and limited treatment options due to extensive antimicrobial resistance. Cefiderocol is increasingly used against carbapenem-resistant pathogens, including metallo-β-lactamase producers. However, reports of treatment failure, particularly in isolates with borderline MICs, indicate uncertainty regarding the relationship between phenotypic susceptibility and underlying genomic resistance mechanisms. The objective of this study was to characterise the genomic resistance landscape of a cefiderocol-susceptible Enterobacter hormaechei isolate and to examine potential genomic-phenotypic discordance relevant to cefiderocol activity. We conducted genomic and phenotypic characterisation of a clinical Enterobacter hormaechei subsp. hoffmannii isolate recovered at Liverpool Clinical Laboratories (Royal Liverpool Hospital, United Kingdom). The isolate exhibited extensive resistance to β-lactams, carbapenems, aztreonam, most aminoglycosides, and multiple ancillary agents, yet remained phenotypically susceptible to cefiderocol (MIC = 2 mg/L; EUCAST susceptible breakpoint). Whole-genome sequencing revealed a multifactorial resistance architecture, including blaNDM-1 and widespread mutations across siderophore-mediated iron uptake pathways ( tonB, fhu, fep, ent, wzz ). Variants in global regulators ( fur, ampR ) suggested altered iron-acquisition and β-lactamase ( blaACT- associated) regulatory networks. Multiple mutations affecting β-lactam targets, including ftsI (PBP3) indicated reduced PBP affinity. Together, these determinants form a complex genomic resistance landscape. This study highlights a genomic-phenotypic discordance in an E. hormaechei isolate with borderline cefiderocol susceptibility. The findings underscore the risk of overestimating cefiderocol activity based solely on MIC values and emphasise the need for genomic resistance assessment in high-risk Enterobacterales.