Abstract
Clostridium perfringens is an opportunistic pathogenic bacterium that infects both animals and humans. Clostridium perfringens genomes encode a diverse array of toxins and virulence proteins, which continues to expand as more genomes are sequenced. In this study, the genomes of 44 C. perfringens strains isolated from intestinal sections of diseased cattle and from broiler chickens from diseased and healthy flocks were sequenced. These newly assembled genomes were compared to 141 publicly available C. perfringens genome assemblies, by aligning known toxin and virulence protein sequences in the assemblies using BLASTp. The genes for alpha toxin, collagenase, a sialidase (nanH), and alpha-clostripain were present in at least 99% of assemblies analyzed. In contrast, beta toxin, epsilon toxin, iota toxin, and binary enterotoxin of toxinotypes B, C, D, and E were present in less than 5% of assemblies analyzed. Additional sequence variants of beta2 toxin were detected, some of which were missing the leader or signal peptide sequences and therefore likely not secreted. Some pore-forming toxins involved in intestinal diseases were host-associated, the netB gene was only found in avian isolates, while netE, netF, and netG were only present in canine and equine isolates. Alveolysin was positively associated with canine and equine strains and only present in a single monophyletic clade. Strains from ruminant were not associated with known virulence factors and, except for the food poisoning associated clade, were present across the phylogenetic diversity identified to date for C. perfringens. Many C. perfringens strains associated with food poisoning lacked the genes for hyaluronidases and sialidases, important for attaching to and digesting complex carbohydrates found in animal tissues. Overall, the diversity of virulence factors in C. perfringens makes these species capable of causing disease in a wide variety of hosts and niches.
Highlights
Clostridium perfringens is a Gram-positive facultative anaerobic bacterium that is a normal inhabitant of the soil as well as the gastrointestinal tracts of healthy animals
All animal facilities were operated under the standards for humane care and treatment for commercial animals set in the Animal Welfare Act (AWA; USDA, 2020) and the National Dairy Farmers Assuring Responsible Management animal care program (National Milk Producers Federation Board of Directors, 2019)
The largest group was of avian strains (n = 61) which were all chicken associated, except for one strain isolated from a turkey, with 49 of these strains from flocks experiencing necrotic enteritis (NE)
Summary
Clostridium perfringens is a Gram-positive facultative anaerobic bacterium that is a normal inhabitant of the soil as well as the gastrointestinal tracts of healthy animals. C. perfringens is an opportunistic pathogen known for its ability to cause gas gangrene/clostridial myonecrosis of the skin (Buboltz and Murphy-Lavoie, 2020) as well as foodpoisoning in humans that costs the United States approximately $343 million annually (ERS-USDA, 2014) In cattle, it can cause hemorrhagic bowel syndrome (HBS), enterotoxaemia, and abomastitis (Nowell et al, 2012; USDA, 2018; Diancourt et al, 2019). The toxinotyping scheme is based on the presence of alpha toxin, beta toxin, epsilon toxin, iota toxin, enterotoxin, and NetB toxin These toxins are used for typing but are not the only factors important to disease as C. perfringens is known to produce multiple additional toxins and virulence factors (Revitt-Mills et al, 2015; Kiu and Hall, 2018)
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