Proteomic analysis of a NAP1 Clostridium difficile clinical isolate resistant to metronidazole

Abstract

Background: Clostridium difficile is an anaerobic, Gram-positive bacterium that has been implicated as the leading cause of antibiotic-associated diarrhea. Metronidazole is currently the first-line treatment for mild to moderate C. difficile infections. Our laboratory isolated a strain of C. difficile with a stable resistance phenotype to metronidazole. A shotgun proteomics approach was used to compare differences in the proteomes of metronidazole-resistant and -susceptible isolates.

Methodology/principal findings: NAP1 C. difficile strains CD26A54_R (Met-resistant), CD26A54_S (reduced- susceptibility), and VLOO13 (Met-susceptible) were grown to mid-log phase, and spiked with metronidazole at concentrations 2 doubling dilutions below the MIC. Peptides from each sample were labeled with iTRAQ and subjected to 2D-LC-MS/MS analysis. In the absence of metronidazole, higher expression was observed of some proteins in C. difficile strains CD26A54_S and CD26A54_R that may be involved with reduced susceptibility or resistance to metronidazole, including DNA repair proteins, putative nitroreductases, and the ferric uptake regulator (Fur). After treatment with metronidazole, moderate increases were seen in the expression of stress-related proteins in all strains. A moderate increase was also observed in the expression of the DNA repair protein RecA in CD26A54_R.

Conclusions/significance: This study provided an in-depth proteomic analysis of a stable, metronidazole-resistant C. difficile isolate. The results suggested that a multi-factorial response may be associated with high level metronidazole-resistance in C. difficile, including the possible roles of altered iron metabolism and/or DNA repair.

Figure 1. Work flow for digestion and analysis of iTRAQ-labeled peptides from NAP1 C. difficile strains.

Met, metronidazole. See text for details.

Figure 2. Hierarchical clustering analysis of protein expression using Perseus (Max Quant, v1.1.1.34). V

(VLOO13). VM (VLOO13+Met). R (CD26A54_R). RM (CD26A54_R+Met). S (CD26A54_S). SM (CD26A54_S+Met). Green, reduced expression relative to VLOO13. Red, increased expression relative to VLOO13. Black, no difference in expression. White, no data. Number refers to experiment #. a, CD26A54_S set. b, CD26A54_R set.