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Clostridium perfringenosum sp. nov., a closely related species to Clostridium perfringens and its virulence factors, isolated from a human soft tissue infection

Two Gram-positive, anaerobic bacteria, designated 27733 and 27737, were isolated from a soft tissue infection from a human patient. They were preliminarily identified as Clostridium perfringens through a series of phenotypic tests, including Gram-staining, determination of lipase and hemolytic activities, MALDI-ToF profiling, and a commercial biochemical identification system. In line with these results, genomes obtained for both isolates were ~3.56 Mbp in size, showed a DNA G+C content of ~28.4%, and contained C. perfringens ribosomal markers (i.e. 16S rRNA gene identity >99.0% to C. perfringens ATCC13124T). A closer examination of these sequences; however, revealed low average Nucleotide Identity (~87%) and digital DNA-DNA Hybridization (~35%) values between isolates 27733/27737 and C. perfringens ATCC13124T, as well as substantial differences in gene content to multiple C. perfringens strains, indicating that they represent a novel species within the genus Clostridium. Congruently, Bayesian dating analyses placed the divergence of this new species and C. perfringens from its common ancestor hundreds of thousands of years ago. Isolates 27733/27737 are not genomically identical (34-197 SNPs apart) and carry genes for C. perfringens-like toxins (<94% nucleotide sequence identity), including plc (alpha toxin), pfoA (perfringolysin O, theta-toxin), nagHIJKL (hyalorudinase, mu-toxin), nanHIJ (exo-alpha sialidase), and cloSI (alpha-clostripain). They do not have known antibiotic resistance genes but were catalogued as resistant to clindamycin through phenotypic tests. On the basis of the presented evidence, and due to its resemblance and potential confusion with C. perfringens, we herein propose the species C. perfringenosum sp. nov. and strain 27733 as its type strain.