Clostridioides difficile in calves, cattle and humans from Dutch dairy farms: Predominance of PCR ribotype 695 (clade 5, sequence type 11) in cattle

Tryntsje Cuperus; Ben Wit; Greetje Castelijn; Paul Hengeveld; Marieke Opsteegh; Joke van der Giessen; Céline Harmanus; Joffrey van Prehn; Ed J Kuijper; Wiep Klaas Smits

doi:10.1016/j.onehlt.2024.100739

Clostridioides difficile in calves, cattle and humans from Dutch dairy farms: Predominance of PCR ribotype 695 (clade 5, sequence type 11) in cattle

One Health. 2024 Apr 24:18:100739. doi: 10.1016/j.onehlt.2024.100739. eCollection 2024 Jun.

Authors

Tryntsje Cuperus¹, Ben Wit², Greetje Castelijn³, Paul Hengeveld¹, Marieke Opsteegh¹, Joke van der Giessen¹, Céline Harmanus⁴, Joffrey van Prehn^{4

5}, Ed J Kuijper^{4

5}, Wiep Klaas Smits^{4

5}

Affiliations

¹ Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
² Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands.
³ Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen, the Netherlands.
⁴ Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center (LUMC), Leiden, the Netherlands.
⁵ National Expertise Centre for Clostridiodes difficile infections at Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Centre (LUMC), Leiden, the Netherlands and Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.

Abstract

Background: Clostridioides difficile is a leading cause of infectious diarrhea in both humans and livestock. In particular, C. difficile strains belonging to sequence type (ST) 11 are common enteropathogens. The aim of this study was to determine the presence and genetic relatedness of C. difficile types in dairy cattle and calves.

Method: Dutch dairy farms were visited between February and December 2021. Feces was collected from adult dairy cattle and calves of two age categories (<4 weeks and 4 weeks-4 months). Fecal samples were also requested from dairy farmers, family members and employees. Fecal samples were cultured in an enrichment medium for 10-15 days and subcultured on solid media for capillary PCR ribotyping and whole genome sequencing.

Results: C. difficile was detected on 31 out of 157 (19.8%) dairy farms. The highest prevalence was found in calves <4 weeks (17.5%). None of the 99 human samples collected were positive. Thirty-seven cultured isolates belonged to 11 different PCR ribotypes (RT) of which RT695 (56.8%) and RT078/126 (16.2%) were most abundant. In the database of the Netherlands National Expertise Centre for C. difficile infections (CDI, >10.000 patient isolates), RT695 was found in only two patients with hospital-onset CDI, diagnosed in 2020 and 2021. Sequence analysis of 21C. difficile RT695 from cattle revealed that all isolates belonged to clade 5, ST11 and contained genes encoding toxin A, toxin B and binary toxin. RT695 strains carried antimicrobial resistance genes typically found in clade 5C. difficile. Groups of genetically related RT695 isolates were found between dairy farms, whereas identical strains were only present in individual farms.

Conclusions: C. difficile was found in ∼20% of dairy farms with a predominance of the relatively unknown RT695. Isolates of RT695 belonged to the same clade and sequence type as RT078/126, which is recognized as an important zoonotic type.

Keywords: Calves; Clostridioides (Clostridium) difficile; Dairy cattle; Zoonosis.