Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential

Abstract

Clostridium perfringens causes a plethora of devastating infections, with toxin production being the underlying mechanism of pathogenicity in various hosts. Genomic analyses of 206 public-available C. perfringens strains´ sequence data identified a substantial degree of genomic variability in respect to episome content, chromosome size and mobile elements. However, the position and order of the local collinear blocks on the chromosome showed a considerable degree of preservation. The strains were divided into five stable phylogroups (I–V). Phylogroup I contained human food poisoning strains with chromosomal enterotoxin (cpe) and a Darmbrand strain characterized by a high frequency of mobile elements, a relatively small genome size and a marked loss of chromosomal genes, including loss of genes encoding virulence traits. These features might correspond to the adaptation of these strains to a particular habitat, causing human foodborne illnesses. This contrasts strains that belong to phylogroup II where the genome size points to the acquisition of genetic material. Most strains of phylogroup II have been isolated from enteric lesions in horses and dogs. Phylogroups III, IV and V are heterogeneous groups containing a variety of different strains, with phylogroup III being the most abundant (65.5%). In conclusion, C. perfringens displays five stable phylogroups reflecting different disease involvements, prompting further studies on the evolution of this highly important pathogen.

Comparative Genome Analysis and Spore Heat Resistance Assay Reveal a New Component to Population Structure and Genome Epidemiology Within Clostridium perfringens Enterotoxin-Carrying Isolates

“…Lineage III strains had larger genomes ( p -value <0.001, ANOVA), lower GC% ( p -value <0.001, ANOVA), and more CDSs ( p -value <0.01, ANOVA) compared to lineages IV and V. All lineage III strains carried two copies of perfringolysin (PfoA). This variant of pfoA has an 85.7% nucleotide identity to the typical pfoA ( Abdel-Glil et al, 2021 ).…”

“… A minimal spanning tree of Clostridium perfringens strains based on cgMLST (scheme by Abdel-Glil, 2019 ) results annotated with (A) cpe location, (B) lineages I–V ( Feng et al, 2020 ), and (C) isolate category based on their isolation source. Branches with a distance of less than 100 are collapsed.…”

“…To determine the cgMLST target gene set and to create a genome-wide gene-by-gene comparison, ChewBBACA was used ( Silva et al, 2018 ). Both custom-made schema and schema created by Abdel-Glil (2019) available at https://www.cgmlst.org (accessed 10.01.2021) were used. The custom-made schema was created using closed C. perfringens genome ATCC 13124 as a training genome and selected genomes as initial query ( Supplementary Table 1 ).…”

“…Genome sequencing and comparative analysis have shown that C. perfringens has a large accessory genome reflecting the wide variety of caused diseases and produced toxins ( Petit et al, 1999 ; Rood et al, 2018 ). Recently, five phylogenetic lineages (I–V) of C. perfringens have been identified ( Kiu et al, 2017 ; Feng et al, 2020 ; Abdel-Glil et al, 2021 ). There is currently no consensus on naming these lineages, and different nomenclature has been used in previous studies.…”

Measurement over 1 Year of Neutralizing Antibodies in Cattle Immunized with Trivalent Vaccines Recombinant Alpha, Beta and Epsilon of Clostridium perfringens

“…Clostridium perfringens is an aerotolerant, Gram-positive, endospore-forming anaerobic bacillus that is ubiquitous and is commensal in the gastrointestinal tract of humans and other healthy animals [ 5 , 6 ]. This bacterium can produce an average of 20 toxins, which are currently classified into seven toxinotypes (A–G) based on the presence of six main toxins: alpha (CPA), beta (CPB), epsilon (ETX), iota (ITX), enterotoxin (CPE) and NetB [ 6 , 7 , 8 , 9 ]. They cause important myonecrotizing, neurological and enteric conditions in production animals ( Table 1 ) [ 2 , 3 ].…”