Genomic Insights into Virulence Factors and Multi-Drug Resistance in Clostridium perfringens IRMC2505A

Abstract

Clostridium perfringens is a spore-forming, Gram-positive anaerobic pathogen that causes several disorders in humans and animals. A multidrug-resistant Clostridium strain was isolated from the fecal sample of a patient who was clinically suspected of gastrointestinal infection and had a recent history of antibiotic exposure and diarrhea. The strain was identified by 16s rRNA sequencing as Clostridium perfringens. The strain's pathogenesis was analyzed through its complete genome, specifically antimicrobial resistance-related genes. The Clostridium perfringens IRMC2505A genome contains 19 (Alr, Ddl, dxr, EF-G, EF-Tu, folA, Dfr, folP, gyrA, gyrB, Iso-tRNA, kasA, MurA, rho, rpoB, rpoC, S10p, and S12p) antibiotic-susceptible genetic species according to the k-mer-based detection of antimicrobial resistance genes. Genome mapping using CARD and VFDB databases revealed significant (p-value = 1 × 10^-26) genes with aligned reads against antibiotic-resistant genes or virulence factors, including phospholipase C, perfringolysin O, collagenase, hyaluronidase, alpha-clostripain, exo-alpha-sialidase, and sialidase activity. In conclusion, this is the first report on C. perfringens from Saudi Arabia that conducted whole genome sequencing of IRMC2505A and confirmed the strain as an MDR bacterium with several virulence factors. Developing control strategies requires a detailed understanding of the epidemiology of C. perfringens, its virulence factors, and regional antimicrobial resistance patterns.

Keywords: Clostridium; anaerobic pathogen; genome mapping; multi-drug resistant; resistance genes; virulence.

Figure 1

A circular graphic of the distribution of genome annotations in IRMC2505A. From the outer to inner rings, this includes the contigs, CDS on the forward strand, CDS on the reverse strand, RNA genes, CDS with homology to known antimicrobial resistance genes, CDS with homology to known virulence factors, GC content, and GC skew. The colors of the CDS on the forward and reverse strands indicate the subsystem these genes belong to (see subsystems below).

Figure 2

(A): Phylogenetic tree of the IRMC2505A genome. The blue arrow indicates the IRMC2505A genome. Tree Analysis Statistics: Requested genomes—22; Genomes with data—22; Max allowed deletions—0; Max allowed duplications—0; Single-copy genes requested—100; Single-copy genes found—100; Num protein alignments—100; Alignment program—mafft; Protein alignment time—189.9 s; Num aligned amino acids—46380; Num CDS alignments—100; Num aligned nucleotides—139140; Best protein model found by RAxML—LG; Branch support method—RAxML Fast Bootstrapping; RAxML likelihood—2571915.6763; RAxML version—8.2.11; RAxML time—3978.6 s. A list of genes used for tree analysis statistics is listed in Supplementary Table S4. (B): Genome comparison represents homologous regions between Clostridium perfringens IRMC2505A and ATCC 13124 195103.10. Alignable sequence blocks are common between the present study’s clinical isolate (lower) and the reference (upper) C. perfringens ATCC 13124 195103.10. Homologous locally collinear blocks between IRMC2505A and ATCC 13124 195103.10 are identified by the same color and connected with a line. (C): Number of specialty genes and the specific source database where homology was found.

Figure 3

Regional view comparison of resistant genes identified in the IRMC2505A genome using the PATRIC cross-genus families (PGfams) method with reference genomes in the 10,000 bp region around the selected gene. Label 1 indicates the gene of interest. The forward and reverse orientations of genes in regions around the selected gene are indicated by arrows. Genes displaying identical colors indicate similar homology. (A): putative membrane protein (Classification: antibiotic target modifying enzyme, peptide antibiotic resistance gene), E-value = 0. (B): tetracycline-resistant MFS efflux pump ≥ TetA(P) (classification: efflux pump conferring antibiotic resistance), E-value: 1 × 10⁻²³⁴. (C): Tetracycline-resistant ribosomal protection type ≥ TetB(P) (classification: antibiotic target protection protein, tetracycline-resistant gene), E-value: 5 × 10⁻⁴⁰.