Characterization of the clade 4 non-toxigenic C. difficile isolate L-NTCD03 carrying the cfr(B) gene

Britt Nibbering; Sam Nooij; Céline Harmanus; Ingrid M. J. G. Sanders; Inez M. Miedema; Quinten R. Ducarmon; Rolf H. A. M. Vossen; Susan L. Kloet; Colleen K. Ardis; Robert A. Britton; Farnaz Yousefi; Jenna E. Bayne; Chandrashekhar Charavaryamath; Andy Y. Law; Morgan L. Murphy; Brett Sponseller; Eric Ryan Burrough; Alejandro Ramírez; Shankumar Mooyottu; Tanja Opriessnig; Ed J. Kuijper; Meta Roestenberg; Wiep Klaas Smits

doi:10.1093/femsmc/xtag010

MicrobiologyFEMS MicrobesJan 1, 2026

Peer-reviewed journal article

Characterization of the clade 4 non-toxigenic C. difficile isolate L-NTCD03 carrying the cfr(B) gene

Britt Nibbering iD, Sam Nooij iD, Céline Harmanus iD, Ingrid M. J. G. Sanders, Inez M. Miedema, Quinten R. Ducarmon iD, Rolf H. A. M. Vossen, Susan L. Kloet iD, Colleen K. Ardis iD, Robert A. Britton iD, Farnaz Yousefi, Jenna E. Bayne iD, Chandrashekhar Charavaryamath iD, Andy Y. Law, Morgan L. Murphy, Brett Sponseller, Eric Ryan Burrough iD, Alejandro Ramírez, Shankumar Mooyottu iD, Tanja Opriessnig iD, Ed J. Kuijper iD, Meta Roestenberg iD, Wiep Klaas Smits iD

Abstract

Clostridioides difficile infection (CDI) is a toxin-mediated gastro-intestinal disease. Yet, C. difficile is a phylogenetically diverse species that includes many non-toxigenic strains. In general, these are understudied, despite having significant potential impact for our understanding of the colonization process and as therapeutic modalities. Here, we present an in-depth characterization - including the complete genome sequence - of the non-toxigenic C. difficile strain L-NTCD03. This strain belongs to PCR ribotype 416, clade 4 and multilocus sequence type 39. It is resistant to multiple antimicrobials, but not those used for treatment of CDI. We validated the relevance of the cfr(B) gene from this strain in antimicrobial resistance to clindamycin, linezolid, retapamulin and streptogramin A. We found the L-NTCD03 strain to be non-toxic in various assays. Altogether, L-NTCD03 is a promising candidate for developing into a live biotherapeutic product.

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