Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America reveal close similarities

Abstract

Clostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), isolated in Brazil, and NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica. C. difficile isolates were cultured and extracellular proteins were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Genomic analysis revealed that these isolates shared most of the gene composition. Only 83 and 290 NAP1/027 genes were considered singletons in ICC-45 and NAP1/027, respectively. Exoproteome analysis revealed 197 proteins, of which 192 were similar in both strains. Only five proteins were exclusive to the ICC-45 strain. These proteins were involved with catalytic and binding functions and indirectly interacted with proteins related to pathogenicity. Most proteins, including TcdA, TcdB, flagellin subunit, and cell surface protein, were overrepresented in the ICC-45 strain; 14 proteins, including mature S-layer protein, were present in higher proportions in LIBA5756. Data are available via ProteomeXchange with identifier PXD026218. These data show close similarity between the genome and proteins in the supernatant of two strains with hypervirulent features isolated in Latin America and underscore the importance of epidemiological surveillance of the transmission and emergence of new strains.

Figure 1

Homology analysis of Clostridioides difficile (formerly Clostridium difficile) ICC-45 and NAP1/027 (LIBA5756) strains. A total of 3715 orthologous groups (OG) were found between the two strains: 3729 proteins from C. difficile ICC-45 and 3720 from C. difficile NAP1/027 (LIBA5756). C. difficile ICC-45 has 3840 identified proteins, five paralogous groups (PG) with 28 proteins, and 83 singletons (S). C. difficile NAP1/027 (LIBA5756) has 4012 identified proteins, one paralogous group (PG) with two proteins, and 290 singletons (S). Numbers inside the parentheses “( )” represents the total number of proteins.

Figure 2

Distribution of proteins according to biological processes, molecular function, and cellular localization. (A) Distribution of the exclusive proteins of the ICC-45 strain. (B) Distribution of the proteins shared between strains ICC-45 and NAP1/027 (LIBA5756). These C. difficile proteins were identified based on the annotations of the ontology gene (GO annotations).