Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study

AIMS Microbiology
Marina SantiagoSonia Timberlake

Abstract

The gastrointestinal microbiome is intrinsically linked to the spread of antibiotic resistance. Antibiotic treatment puts patients at risk for colonization by opportunistic pathogens like vancomycin resistant Enterococcus and Clostridioides difficile by destroying the colonization resistance provided by the commensal microbiota. Once colonized, the host is at a much higher risk for infection by that pathogen. Furthermore, we know that microbiome community differences are associated with disease states, but we do not have a good understanding of how we can use these changes to classify different patient populations. To that end, we have performed a multicenter retrospective analysis on patients who received fecal microbiota transplants to treat recurrent Clostridioides difficile infection. We performed 16S rRNA gene sequencing on fecal samples collected as part of this study and used these data to develop a microbiome disruption index. Our microbiome disruption index is a simple index that is predictive across cohorts, indications, and batch effects. We are able to classify pre-fecal transplant vs post-fecal transplant samples in patients with recurrent C. difficile infection, and we are able to predict, using previously-publish...Continue Reading

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Citations

Mar 25, 2021·BMC Research Notes·Marina Santiago, Scott W Olesen
Mar 21, 2021·Applied and Environmental Microbiology·Shaodong WeiTine Rask Licht
Dec 18, 2020·The Journal of Infectious Diseases·Ylaine GerardinZain Kassam

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Methods Mentioned

BETA
prophylactic therapy
PCR
16S sequencing

Software Mentioned

Scikit
house
OpenBiome
Learn
UTAX
QIIME
Bio

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