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.

Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient

“…Due to its multidrug resistance, adaptability to nutrient-poor environments and a variety of ecological niches and limited therapy choices, E. faecalis was one of the main causes of hospitalacquired infections and saw dramatic increase in prevalence [9][10][11][12][13]. The presence of genes and alleles involved in antimicrobial resistance observed in the isolate IRMC827A were reported earlier from various bacterial organisms, such as multidrug-resistant Moraxella catarrhalis [79], a heavy-metal-resistant bacterium Cupriavidus campinensis S14E4C [80], Bacillus cereus isolated from eye shadow cosmetic products [81], Brucella abortus isolated from aborted fetal sheep [82], Bacillus velezensis CMU008 [83], multidrug-resistant Clostridium perfringens [45], a high-lead-resistance bacterium Raoultella planticola [84], a human pathogenic strain from Malaysia Chromobacterium violaceum [85], and multidrug-resistant Salmonella enterica [86], including E. faecalis [87].…”

“…Thermo Scientific's Nanodrop 2000 (Waltham, MA, USA) was used to evaluate the purity, quality, and amount of genomic DNA in accordance with the manufacturer's recommendations. The isolate was PCR amplified, and the 16S rRNA gene was sequenced (GenBank Accession No: OR533998) and analysed as we described earlier to confirm the strain as bacteria [45,49].…”

“…Raw reads of low quality from paired-end sequencing were discarded and other reads were assembled using SOAPdenovo v1.05 software. The paired readings were put together and annotated as previously described [45,50] using the RAST tool kit (RASTtk 1.3.0) [51] and PATRIC (BV-BRC 3.28.5) [52]. We determined the taxonomy of the IRMC827A's genome and estimated the average G + C content and contig count using the predictions for the proteins and their roles in gene ontology (GO) [53], enzyme commission (EC) [54], pathways [55], subsystems of protein complexes [56] and protein family types [57].…”

“…Various studies including a recent systematic review were conducted to give prominence to the prevalence and emergence of multidrug-resistant bacteria and fungi from the Arabian Peninsula, including Saudi Arabia [43][44][45][46]. Around 80 species of bacteria and fungi were reported in a recent systematic review from the Arabian region [46].…”

Foodborne Clostridioides Species: Pathogenicity, Virulence and Biocontrol Options

“…C. perfringens toxins are classified into pore-forming toxins, membrane-damaging and hydrolytic enzymes, and intracellular toxins and are carried on large plasmids [59]. The chromosomally located alpha toxin phospholipase C (plc) is the main virulent factor in all strains of C. perfringens associated diseases [60]. The poreforming, cytotoxic CPE toxin is the main toxin causative of C. perfringens food poisoning and non-foodborne diarrhoea, and can result in the necrotising of the human ileal and colonic epithelium cells associated with colitis present in clinical strains [43].…”