Table A4.

Other mutations associated with cefiderocol resistance.

Target Gene	Organism(s)	Findings
PBP-3 (=target of cefiderocol)	E. coli , A. baumannii	Based on isogenic E. coli mutants: ○ Introduction of either YRIN or YRIK insertion in PBP-3 resulted in 2-fold higher cefiderocol MIC (0.063→0.125 mg/L) [31]. Based on clinical isolates: ○ In a collection of nine E. coli isolates (all from a single hospital in Turkey) with specific PBP-3 mutations (YRIN insertion after position P333 and I532L substitution), a raised cefiderocol MIC was observed (MIC 5 mg/L in two isolates, 2 mg/L in four isolates, and 4 mg/L in two isolates) [31]. ○ PBP3 mutations (including YRIN insertion at position P33) were also detected in six other cefiderocol-resistant E. coli (in combination with NDM and cirA mutations) [59]. ○ A mutation (predicted to have a moderate likelihood of affecting functionality) in PBP-3 was detected in one of six cefiderocol-resistant A. baumannii clinical isolates in one study [52]. ○ Mutations in PBP-3 were found in four cefiderocol-resistant A. baumannii isolates (in combination with various β-lactamases) [30]. ○ Mutation in PBP-3 (H370Y) was found in a cefiderocol-resistant A. baumannii emerging in vivo after cefiderocol treatment [21,32].
baeS (a sensor of a two-component regulation system)	K. pneumoniae	In three in vitro derived mutants, mutations of baeS were associated with 4- to 32-fold increases in cefiderocol MIC (0.063→2 mg/L, 4→16 mg/L, and 4→32 mg/L) [31]. baeS mutations were identified in all seven cefiderocol-resistant (MIC > 2 mg/L) clinical isolates in a single-centre study [37].
envZ (a sensor of a two-component regulation system) **	K. pneumoniae **, E. coli	In two in vitro derived mutants, mutations of envZ (a sensor of a two-component regulation system) were associated with 4-fold increases in cefiderocol MIC (4→16 mg/L) [31]. In one case, in vivo emerging resistance was described in an E. coli clinical isolate associated with increased copy numbers of NDM-5 in combination with envZ mutations (but the additional role of envZ appeared to be minor).
yicM (putative membrane transport protein)	K. pneumoniae	Mutations in yicM were detected in two of six cefiderocol-resistant K. pneumoniae clinical isolates [37].
tolQ (membrane transporter), smf-1 (affects fimbriae and surface adhesion) **	S. maltophilia **	tolQ and smf-1 mutations were each found in two separate in vitro derived mutants [60].
PmrB, mcr-10		A higher prevalence of colistin resistance (29% vs. 0%) was reported in cefiderocol-resistant than in susceptible K. pneumoniae clinical isolates [37]. Furthermore, PmrB mutations (known to be involved in cefiderocol resistance [69]) were identified in four of seven (57%) cefiderocol-resistant K. pneumoniae isolates, while the mcr-10 gene was identified in half (three of six) of cefiderocol-resistant E. cloacae isolates [37]. A reduction in the net negative charge (associated with cefiderocol resistance) could also affect cefiderocol, but future studies are necessary to confirm this hypothetical mechanism [37].

In bold are mechanisms of resistance of which the role has been confirmed in isogenic mutant experiments (group 5 studies, see “Eligibility criteria” in Methods) and that have been detected in cefiderocol-resistant clinical isolates (group 1–3 studies, see “Eligibility criteria” in Methods). ** Based only on in vitro derived mutants (group 4 studies, see “Eligibility criteria” in Methods).