Determination of multidrug resistance mechanisms in Clostridium perfringens type A isolates using RNA sequencing and 2D-electrophoresis

Abstract

In this study, we screened differentially expressed genes in a multidrug-resistant isolate strain of Clostridium perfringens by RNA sequencing. We also separated and identified differentially expressed proteins (DEPs) in the isolate strain by two-dimensional electrophoresis (2-DE) and mass spectrometry (MS). The RNA sequencing results showed that, compared with the control strain, 1128 genes were differentially expressed in the isolate strain, and these included 227 up-regulated genes and 901 down-regulated genes. Bioinformatics analysis identified the following genes and gene categories that are potentially involved in multidrug resistance (MDR) in the isolate strain: drug transport, drug response, hydrolase activity, transmembrane transporter, transferase activity, amidase transmembrane transporter, efflux transmembrane transporter, bacterial chemotaxis, ABC transporter, and others. The results of the 2-DE showed that 70 proteins were differentially expressed in the isolate strain, 45 of which were up-regulated and 25 down-regulated. Twenty-seven DEPs were identified by MS and these included the following protein categories: ribosome, antimicrobial peptide resistance, and ABC transporter, all of which may be involved in MDR in the isolate strain of C. perfringens. The results provide reference data for further investigations on the drug resistant molecular mechanisms of C. perfringens.

Figure 1.. Differentially expressed genes (DEGs) in the multidrug resistance (MDR) isolate strain of C. perfringens. The red color represents up-regulated tags, the green color represents down-regulated tags (fold change) and the blue color represents no significant DEGs. FDR: false discovery rate.

Figure 2.. KEGG enrichment pathway of differentially expressed genes (DEGs) in the multidrug resistance isolate strain of C. perfringens. The top 20 enriched pathways are shown in the graph, different color means different Q-value, and the size of the bubble represents the number of DEGs.

Figure 3.. Comparative analysis of proteins of C. perfringens by 2D- electrophoresis. The image shows the differential expression of protein spots from the proteins extracted from (left) multidrug resistance isolate strain of C. perfringens, and (right) control strain. Proteins whose fold change were higher than 2 or less than 0.5 were selected for further analysis. The arrows refer to the differentially expressed protein spots.

Figure 4.. KEGG pathway enrichment analysis of differentially expressed proteins in the multidrug resistance isolate strain of C. perfringens. Differentially expressed proteins were categorized according to their gene ontology terms and in each category the number of proteins and their P-values are shown in the graph. The X-axis shows the percentage of differentially enriched proteins.