A deeply divergent TcdB-like toxin in a cryptic clade C-III Clostridioides strain from a One Health genomic survey in Japan

ABSTRACT In a recent One Health genomic survey of community-associated Clostridioides difficile in Japan, S. Yoshizawa, K. Komori, K. Aoki, T. Sawa, et al. (Appl Environ Microbiol 92:e00397-26, 2026, https://doi.org/10.1128/aem.00397-26 ) deposited the genome of strain TUM20227, a human tcdA − / tcdB + isolate assigned to the novel sequence type ST919. Reanalysis of its publicly available genome shows that TUM20227 belongs to cryptic clade C-III and carries a chromosomally encoded, monotoxin PaLoc-like locus encoding a 2,367-amino acid TcdB-family protein. This TcdB-like protein shares less than 83% amino acid identity with all recognized TcdB subtypes (B1–B12) and forms a deeply divergent branch in both full-length and domain-resolved phylogenies, with heterogeneous nearest neighbors across domains and an atypical predicted receptor-binding profile. TcdB TUM20227 should therefore be regarded as representative of a previously unrecognized, deeply divergent TcdB lineage. IMPORTANCE Clostridioides difficile is a leading cause of diarrhea, and its principal virulence factor, the toxin TcdB, is both a diagnostic target and a template for therapeutics. The recognized diversity of TcdB is captured in a scheme composed of 12 subtypes largely built from strains of the five C. difficile clades, whereas the Clostridioides cryptic clades and their toxins remain comparatively underexplored, even though they can encode divergent toxins with altered receptor use and antigenicity. Here, reanalysis of a single, previously unremarked genome from a One Health survey uncovers a deeply divergent and apparently complete and intact TcdB-family toxin gene whose product falls outside the established subtype framework. This finding shows that systematic data mining of animal, human, and environmental strains can unearth novel toxin genes and provide critical insight into the evolution, receptor specificity, and subtype boundaries of the toxin genes of this important human pathogen.