UMass Chan Medical School Faculty Publications

UMMS Affiliation

Department of Emergency Medicine; Department of Microbiology and Physiological Systems; Program in Microbiome Dynamics; Graduate School of Biomedical Sciences

Publication Date


Document Type



Bacteria | Bacterial Infections and Mycoses | Digestive System | Geriatrics | Microbiology


Clostridioides difficile disproportionally affects the elderly living in nursing homes (NHs). Our objective was to explore the prevalence of C. difficile in NH elders, over time and to determine whether the microbiome or other clinical factors are associated with C. difficile colonization. We collected serial stool samples from NH residents. C. difficile prevalence was determined by quantitative polymerase-chain reaction detection of Toxin genes tcdA and tcdB; microbiome composition was determined by shotgun metagenomic sequencing. We used mixed-effect random forest modeling machine to determine bacterial taxa whose abundance is associated with C. difficile prevalence while controlling for clinical covariates including demographics, medications, and past medical history. We enrolled 167 NH elders who contributed 506 stool samples. Of the 123 elders providing multiple samples, 30 (24.4%) elders yielded multiple samples in which C. difficile was detected and 78 (46.7%) had at least one C. difficile positive sample. Elders with C. difficile positive samples were characterized by increased abundances of pathogenic or inflammatory-associated bacterial taxa and by lower abundances of taxa with anti-inflammatory or symbiotic properties. Proton pump inhibitor (PPI) use is associated with lower prevalence of C. difficile (Odds Ratio 0.46; 95%CI, 0.22-0.99) and the abundance of bacterial species with known beneficial effects was higher in PPI users and markedly lower in elders with high C. difficile prevalence.C. difficile is prevalent among NH elders and a dysbiotic gut microbiome associates with C. difficile colonization status. Manipulating the gut microbiome may prove to be a key strategy in the reduction of C. difficile in the NH.


Clostridioides difficile colonization, bile acids, dysbiosis, gut microbiome, nursing home elders, proton pump inhibitor

Rights and Permissions

Copyright © 2021 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

DOI of Published Version



Haran JP, Ward DV, Bhattarai SK, Loew E, Dutta P, Higgins A, McCormick BA, Bucci V. The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome. Gut Microbes. 2021 Jan-Dec;13(1):1-15. doi: 10.1080/19490976.2021.1897209. PMID: 33764826; PMCID: PMC8007149. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Gut microbes

PubMed ID


Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.