Fidaxomicin resistance in Clostridioides difficile: a systematic review and predictive modeling with RNA polymerase binding sites

Abstract

Fidaxomicin (FDX), an RNA polymerase (RNAP) inhibitor antibiotic, is a guideline-recommended therapy for Clostridioides difficile infection. Mutations associated with reduced FDX minimum inhibitory concentrations (MICs) have been identified. However, the molecular characterization of these mutations on FDX binding and the development of FDX resistance have not been studied. The purpose of this systematic review was to identify FDX resistance in C. difficile isolates and determine whether single nucleotide polymorphisms associated with increased FDX MIC aligned with the RNAP binding pocket interacting residues. A systematic literature search was done in PubMed (1991-2023) with identified articles and their bibliographies searched for papers that included C. difficile genetic mutations and increased FDX MIC. Visualization of FDX-RNAP interactions was performed on Schrödinger Maestro using the publicly available C. difficile RNAP with fidaxomicin sequence (code 7L7B) on the Protein Data Bank. Seven articles were identified after applying inclusion and exclusion criteria. The most common mutation in clinical and laboratory isolates was at position V1143 of the β subunit, which accounted for approximately 50% of the identified mutations. Most other mutations occurred within the β' subunit of RNAP. Approximately one-third of the identified mutation aligned directly with FDX interacting residues with C. difficile RNAP (7/20) with most of the remainder occurring within 5 Å of the binding residues. C. difficile strains with elevated FDX MIC align closely with the known RNAP binding residues. These data demonstrate the potential to identify genomic methods to identify emerging FDX resistance.

Keywords: RNA polymerase; antimicrobial resistance; macrocyclic antibiotics.

Fig 1

Preferred Reporting Items for Systematic Review and Meta-Analyses flow chart.

Fig 2

Interaction between FDX and RNAP residues. (A) Comparison between FDX-RNAP interaction when ARG89GLY mutation occurred in C. difficile RNAP. ARG89 formed a hydrogen bond (yellow dash) with LYS86 and salt bridge interaction (pink dash) with GLU1139 and ASP237. Mutation to GLY89 resulted in the loss of salt bridge interaction with GLU1139 and ASP237. (B) Comparison between FDX-RNAP interactions when mutation occurred at position VAL1143. At this position, valine formed hydrogen bonds with GLU1139, SER1140, and GLU1147. Mutation to PHE1143 resulted in steric clashes and bad/ugly contacts (orange/red dash) with FDX and ARG326. Mutation to ASP1143 resulted in the formation of salt bridge interaction between the oxygen of ASP1143 and nitrogen of ARG326.

Fig 3

Total predicted change in stability upon mutation in rpoB (ΔΔG_pred). (A) Scanning for (de)stabilizing mutations at FDX-RNAP key binding residues in rpoB (L1071, V1072, T1073, Q1074, D1114, V1116, V1117, V1120, R1121, E1139, and S1140) and commonly identified mutation V1143. (B) Scanning for de(stabilizing) mutations at FDX-RNAP key binding residues in rpoC (K84, S85, K86, R89, D237, L238, P240, S252, K314, M319, and R326). ΔΔG_pred < 0.0 indicated a stabilizing mutation.