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Beyond perfringens: Exploring the pathology of less prominent Clostridium species in infection

There are approximately 200 validly described species in the genus Clostridium. Among them are multiple human and animal pathogens such as C. botulinum, C. tetani, C. perfringens and C. difficile (recently re-classified as Clostridioides difficile). Naturally, the genus also contains species whose pathogenic potential and clinical significance remains understudied. In 2017, Kiu et al. described five such strains isolated during a study of the microbiota of preterm infants and identified as one C. tertium strain, one C. cadaveris and three C. paraputrificium strains using their 16S rRNA gene sequences and whole-genome sequencing (WGS) based methods. 

These species have between them been described as being infrequently isolated from human infections such as pneumonia, bacteraemia and adult necrotizing enterocolitis. Despite this and the increasing use of genome sequencing in microbiology and biomedical research, extremely limited publicly accessible genomic sequence data existed for these species prior to the publication of Kiu et al in 2017. With the aim of improving the resources available to researchers wanting to further investigate the role of these species in infection, the annotated whole genome sequences were deposited into the European Nucleotide Archive under the project accession number PRJEB22142, alongside pure cultures of all five strains into the National Collection of Type Cultures (NCTC) as NCTC 14034-14038 detailed in the below.


NCTC / Kiu et al. Strain No.


ENA WGS Accession

NCTC 14034 / LH009

Clostridium tertium


NCTC 14035 / LH025

Clostridium paraputrificum


NCTC 14036 / LH052

Clostridium cadaveris


 NCTC 14037 / LH058

Clostridium paraputrificum


NCTC 14038 / LH141

Clostridium paraputrificum


A concise search of the annotated genomes revealed antibiotic resistance genes such as vanW (associated with vancomycin resistance) and known virulence genes such as toxA which encodes C. difficile-associated Toxin A; a major virulence factor. Interestingly, over 40% of the genes in each genome were of unknown function. This perhaps highlights the limitations of the understanding of specific virulence factors of these species, or the suitability current bioinformatic databases used to annotate them.

The addition of these five strains to the NCTC builds on its legacy of providing authentic cultures of anaerobes; some of the collection’s first accessions were cultures of Clostridium sp. from wounds. Numerous reference strains of anaerobic bacterial species are available from the NCTC including many strains from clinical sources, and 57 type strains of anaerobic species which are listed on the NCTC anaerobe type strains page. More than 15 additional type strains of anaerobic species not currently represented in the collection are currently being accessioned and will be made available throughout 2019.

The National Collection of Type Cultures would like to thank Raymond Kiu and Lindsay Hall for depositing these strains, and the authors of Kiu et al for their work in characterising them.  



Kiu, R., et al. (2017). "Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights." Genome biology and evolution 9(10): 2707-2714.

Image Source: Wellcome Images. Credit: Annie Cavanagh. Used under Creative Commons Attribution Non-Commercial (CC BY-NC 4.0) terms and conditions.

January 2020