Evolution of cefiderocol resistance in Stenotrophomonas maltophilia using in vitro serial passage techniques

Abstract

Objectives Cefiderocol is a siderophore cephalosporin active against MDR Gram-negatives including Stenotrophomonas maltophilia. Cefiderocol resistance remains uncommon and incompletely understood. We selected for cefiderocol-resistant S. maltophilia in vitro and characterized the genetic mechanisms and potential for cross-resistance to other antimicrobials. Methods We selected cefiderocol resistance in three clinical strains of S. maltophilia by serial passage in escalating concentrations of cefiderocol. Emergent cefiderocol-resistant isolates were subjected to repeat susceptibility testing against a panel of relevant antimicrobials. Isolates with confirmed MIC changes were whole genome sequenced. Results Each parent strain was initially susceptible to cefiderocol (MICs of 0.03125, 0.03125 and 0.125 mg/L), and one initially tested susceptible to ceftazidime/avibactam (MIC 4 mg/L). We recovered evolved isolates achieving cefiderocol resistance at MICs of 8–32 mg/L from each parental strain. Some cefiderocol resistant isolates reverted following one to four drug-free passages. Ceftazidime/avibactam MICs of passaged isolates repeatedly increased to ≥256 mg/L, and while other MICs were largely unchanged, trimethoprim/sulfamethoxazole MICs declined 4-fold in two strains. WGS revealed one evolved isolate carrying six coding mutations, while four were isogenic mutants of tonB, tolQ, smf-1 and the smeT promoter. Mutation of the smeT promoter downregulated the smeDEF efflux pump and reduced susceptibility to penicillins but increased susceptibility to several other classes including sulphonamides. Other mutations occurred in genes putatively involved in iron metabolism including smlt1148 and cirA. Conclusions S. maltophilia strains evolved cefiderocol resistance through different genetic pathways, but often involved iron transport. Future work is required to fully understand the role(s) of other genes in cefiderocol resistance.

Cefiderocol: Systematic Review of Mechanisms of Resistance, Heteroresistance and In Vivo Emergence of Resistance

“…The study flow chart is depicted in Figure 1 . A total of n = 52 relevant studies were reviewed [ 12 , 14 , 15 , 16 , 17 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ]. All studies were published after 2018; n = 17 (33%) in 2022, n = 18 (35%) in 2021, n = 12 (23%) in 2020, n = 1 (2%) in 2019, and n = 4 (8%) in 2018.…”

“…All studies were published after 2018; n = 17 (33%) in 2022, n = 18 (35%) in 2021, n = 12 (23%) in 2020, n = 1 (2%) in 2019, and n = 4 (8%) in 2018. Evaluation of mechanisms of resistance was based on: n = 13 group 1 studies [ 14 , 17 , 27 , 29 , 30 , 37 , 45 , 52 , 53 , 54 , 61 , 63 , 64 ], n = 4 group 2 studies [ 12 , 15 , 19 , 62 ], n = 11 group 3 studies [ 14 , 16 , 21 , 24 , 25 , 32 , 42 , 43 , 44 , 55 , 59 ], n = 7 group 4 studies [ 28 , 31 , 40 , 46 , 57 , 58 , 60 ], and n = 13 group 5 studies [ 29 , 31 , 41 , 47 , 48 , 49 , 50 , 51 , 54 , 55 , 56 , 57 , 64 ] (see Section 4.2 for grouping of studies). Data about the prevalence of heteroresistance were available in only two studies […”

“…Differences in the degree of resistance caused by mutations in specific siderophore receptors may be due to the relative contribution of each iron acquisition system in a given strain [ 57 ]. Mutations affecting iron transport have also been detected in in vitro derived (after serial passaging) cefiderocol-resistant S. maltophilia [ 58 , 60 ]. Mutations affecting the aforementioned genes have also been detected in clinical cefiderocol-resistant isolates, including P. aeruginosa ( piuD and pirR ) [ 44 ], A. baumannii ( pirA and piuA ) [ 52 ], and K. pneumoniae ( cirA ) [ 24 ].…”

“…Efflux pumps may contribute to cefiderocol resistance based on transformed isogenic mutants or in vitro derived cefiderocol-resistant mutants in K. pneumoniae (sugE and chrA) [ 37 ], P. aeruginosa (MexAB–OprM efflux pump) [ 47 ], and S. maltophilia (smeDEF efflux pump) [ 60 ]. Furthermore, overexpression of AxyABM efflux pump in Achromobacter xylosoxidans was associated with a threefold higher cefiderocol MIC [ 51 ].…”

“…Mutations identified by in vitro selection of mutants following exposure to cefiderocol may not be relevant to in vivo observed mutations, as has been described previously for colistin [ 68 , 69 ]. Mutations observed in vitro, especially those affecting iron transport [ 58 , 60 ], may be associated with fitness cost [ 40 , 58 ] and can be unstable or reversible in the absence of continued cefiderocol exposure [ 58 , 60 ]. This is further supported by the fact that resistance emerging in vivo in animal models [ 58 , 67 ] or clinical studies [ 21 , 22 , 23 , 75 ] is much less frequent than heteroresistance [ 20 ] and much less frequent than resistance emerging in vitro after exposure to cefiderocol.…”