Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

Abstract

Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%). However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling reveals key factors linked to poultry Necrotic Enteritis

“…2B). This analysis suggests a potential widespread reservoir of this C. perfringens lineage given they are genetically highly-similar, and previous studies have indicated this species has a highly divergent genome [20-22].…”

Molecular structure and function of the carboxy‐terminus of the alpha‐toxin from Clostridium perfringens type A

“…All C. perfringens can secrete alpha‐toxin (CPA). As the most important exotoxin of C. perfringens , alpha‐toxin has been regarded as the most important research object by researchers (Chen et al, ; Hosomi et al, ; Kiu, Caim, Alexander, Pachori, & Hall, ). CPA is a multifunctional zinc metalloenzyme with phospholipase C activity at the amino‐terminus.…”

Phylogenomic analysis ofClostridium perfringensidentifies isogenic strains in gastroenteritis outbreaks, and novel virulence-related features

“…Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7%; 50/109), and genes encoding phage proteins were also frequently identified, with additional analysis indicating their contribution to increased virulence determinants within the genomes of gastroenteritis-associated C. perfringens . Overall this large-scale genomic study of gastroenteritis-associated C. perfringens suggested that 3 major sub-types underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid, and (3) strains carrying cpe on transposable element Tn 5565 (usually integrated into chromosome). Our findings indicate that further studies will be required to fully probe this enteric pathogen, particularly in relation to developing intervention and prevention strategies to reduce food poisoning disease burden in vulnerable patients, such as the elderly.…”

“…Clostridium perfringens is an important pathogen known to cause disease in humans and animals (1, 2). Notably, the pathogenesis of C. perfringens -associated infections is largely attributed to the wide array of toxins this species can produce, with >20 toxins currently identified (3, 4). This Gram-positive spore former has been associated with foodborne and non-foodborne diarrhoeal diseases in humans, and preterm-necrotising enterocolitis (5, 6).…”

“…C. perfringens , and associated encoded toxins, have been extensively studied with respect to disease pathogenesis, with a strong focus on animal infections (20–24). Recent studies analysing a range of diverse C. perfringens strains (from both animal and human-associated infections) indicates a plastic and divergent pangenome, with a significant proportion of accessory genes predicted to be involved in virulence mechanisms and metabolisms, linked to enhanced host colonisation and disease initiation (3, 25). However, studies describing human outbreak-associated C. perfringens infections are limited, and to date only one recent study (58 isolates) has utilised Whole Genome Sequencing (WGS) data to probe the genomic epidemiology of associated strains (3, 26).…”