Enterococci enhance Clostridioides difficile pathogenesis

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  • Abbas, A. & Zackular, J. P. Microbe–microbe interactions during Clostridioides difficile infection. Curr. Opin. Microbiol. 53, 19–25 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Lessa, F. C., Winston, L. G. & McDonald, L. C., Team, E. I. P. C. d. S. Burden of Clostridium difficile infection in the United States. N. Engl. J. Med. 372, 2369–2370 (2015).

    PubMed 

    Google Scholar 

  • Schubert, A. M. et al. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. mBio 5, e01021–01014 (2014).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Auchtung, J. M., Preisner, E. C., Collins, J., Lerma, A. I. & Britton, R. A. Identification of simplified microbial communities that inhibit Clostridioides difficile infection through dilution/extinction. mSphere 5, e00387–20 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zackular, J. P. et al. Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection. Nat. Med. 22, 1330–1334 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tomkovich, S., Stough, J. M. A., Bishop, L. & Schloss, P. D. The initial gut microbiota and response to antibiotic perturbation influence Clostridioides difficile clearance in mice. mSphere 5, e00869–20 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Berkell, M. et al. Microbiota-based markers predictive of development of Clostridioides difficile infection. Nat. Commun. 12, 2241 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Antharam, V. C. et al. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J. Clin. Microbiol. 51, 2884–2892 (2013).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Poduval, R. D., Kamath, R. P., Corpuz, M., Norkus, E. P. & Pitchumoni, C. S. Clostridium difficile and vancomycin-resistant Enterococcus: the new nosocomial alliance. Am. J. Gastroenterol. 95, 3513–3515 (2000).

    CAS 
    PubMed 

    Google Scholar 

  • Ubeda, C. et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J. Clin. Invest. 120, 4332–4341 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Taur, Y. et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin. Infect. Dis. 55, 905–914 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Willett, J. L. E. et al. Comparative biofilm assays using Enterococcus faecalis OG1RF identify new determinants of biofilm formation. mBio 12, e0101121 (2021).

    PubMed 

    Google Scholar 

  • Willett, J. L. E., Robertson, E. B. & Dunny, G. M. The phosphatase Bph and peptidyl–prolyl isomerase PrsA are required for gelatinase expression and activity in Enterococcus faecalis. J. Bacteriol. 204, e0012922 (2022).

    PubMed 

    Google Scholar 

  • Lee, I. P. A., Eldakar, O. T., Gogarten, J. P. & Andam, C. P. Bacterial cooperation through horizontal gene transfer. Trends Ecol. Evol. 37, 223–232 (2021).

    PubMed 

    Google Scholar 

  • Roberts, A. P. & Mullany, P. Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. FEMS Microbiol. Rev. 35, 856–871 (2011).

    CAS 
    PubMed 

    Google Scholar 

  • Chambers, C. J., Roberts, A. K., Shone, C. C. & Acharya, K. R. Structure and function of a Clostridium difficile sortase enzyme. Sci. Rep. 5, 9449 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jenior, M. L. et al. Novel drivers of virulence in Clostridioides difficile identified via context-specific metabolic network analysis. mSystems 6, e0091921 (2021).

    PubMed 

    Google Scholar 

  • Fang, X., Lloyd, C. J. & Palsson, B. O. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nat. Rev. Microbiol. 18, 731–743 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jenior, M. L., Moutinho, T. J., Dougherty, B. V. & Papin, J. A. Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS Comput. Biol. 16, e1007099 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pruss, K. M. et al. Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization. Nat Metab 4, 19–28 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Barker, H. A. Amino acid degradation by anaerobic bacteria. Annu. Rev. Biochem. 50, 23–40 (1981).

    CAS 
    PubMed 

    Google Scholar 

  • Matthews, M. L. et al. Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat. Chem. 9, 234–243 (2017).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Keogh, D. et al. Enterococcal metabolite cues facilitate interspecies niche modulation and polymicrobial infection. Cell Host Microbe 20, 493–503 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sundermann, A. J. et al. Whole genome sequencing surveillance and machine learning of the electronic health record for enhanced healthcare outbreak detection. Clin. Infect. Dis. 75, 476–482 (2021).

    Google Scholar 

  • Bryan, N. C. et al. Genomic and functional characterization of Enterococcus faecalis isolates recovered from the International Space Station and their potential for pathogenicity. Front. Microbiol. 11, 515319 (2020).

    PubMed 

    Google Scholar 

  • Deibel, R. H. Utilization of arginine as an energy source for the growth of Streptococcus faecalis. J. Bacteriol. 87, 988–992 (1964).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fishbein, S. R. et al. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. eLife 11, e72801 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Karasawa, T., Maegawa, T., Nojiri, T., Yamakawa, K. & Nakamura, S. Effect of arginine on toxin production by Clostridium difficile in defined medium. Microbiol. Immunol. 41, 581–585 (1997).

    CAS 
    PubMed 

    Google Scholar 

  • Fredrick, C. M., Lin, G. & Johnson, E. A. Regulation of botulinum neurotoxin synthesis and toxin complex formation by arginine and glucose in Clostridium botulinum ATCC 3502. Appl. Environ. Microbiol. 83, e00642–17 (2017).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bushman, F. D. et al. Multi-omic analysis of the interaction between Clostridioides difficile infection and pediatric inflammatory bowel disease. Cell Host Microbe 28, 422–433.e7 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Keith, J. W. et al. Impact of antibiotic-resistant bacteria on immune activation and Clostridioides difficile infection in the mouse intestine. Infect. Immun. 88, e00362–19 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Lesniak, N. A. et al. The gut bacterial community potentiates Clostridioides difficile infection severity. mBio 13, e0118322 (2022).

    PubMed 

    Google Scholar 

  • Girinathan, B. P. et al. In vivo commensal control of Clostridioides difficile virulence. Cell Host Microbe 29, 1693–1708.e1697 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Hirose, Y. et al. Streptococcus pyogenes upregulates arginine catabolism to exert its pathogenesis on the skin surface. Cell Rep. 34, 108924 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stabler, R. A. et al. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol. 10, R102 (2009).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Carter, G. P. et al. Defining the roles of TcdA and TcdB in localized gastrointestinal disease, systemic organ damage, and the host response during Clostridium difficile infections. mBio 6, e00551 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hanahan, D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166, 557–580 (1983).

    CAS 
    PubMed 

    Google Scholar 

  • Dale, J. L. et al. Comprehensive functional analysis of the Enterococcus faecalis core genome using an ordered, sequence-defined collection of insertional mutations in strain OG1RF. mSystems 3, e00062–18 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Theriot, C. M. et al. Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains. Gut Microbes 2, 326–334 (2011).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Kumar, L., Cox, C. R. & Sarkar, S. K. Matrix metalloprotease-1 inhibits and disrupts Enterococcus faecalis biofilms. PLoS One 14, e0210218 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bloedt, K., Riecker, M., Poppert, S. & Wellinghausen, N. Evaluation of new selective culture media and a rapid fluorescence in situ hybridization assay for identification of Clostridium difficile from stool samples. J. Med. Microbiol. 58, 874–877 (2009).

    CAS 
    PubMed 

    Google Scholar 

  • Wellinghausen, N., Bartel, M., Essig, A. & Poppert, S. Rapid identification of clinically relevant Enterococcus species by fluorescence in situ hybridization. J. Clin. Microbiol. 45, 3424–3426 (2007).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Knippel, R. J. et al. Heme sensing and detoxification by HatRT contributes to pathogenesis during Clostridium difficile infection. PLoS Pathog. 14, e1007486 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).

    Google Scholar 

  • Calle, M. L., Urrea, V., Boulesteix, A. L. & Malats, N. AUC-RF: a new strategy for genomic profiling with random forest. Hum. Hered. 72, 121–132 (2011).

    CAS 
    PubMed 

    Google Scholar 

  • Hankin, J. A., Barkley, R. M. & Murphy, R. C. Sublimation as a method of matrix application for mass spectrometric imaging. J. Am. Soc. Mass. Spectrom. 18, 1646–1652 (2007).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thomas, A., Charbonneau, J. L., Fournaise, E. & Chaurand, P. Sublimation of new matrix candidates for high spatial resolution imaging mass spectrometry of lipids: enhanced information in both positive and negative polarities after 1,5-diaminonapthalene deposition. Anal. Chem. 84, 2048–2054 (2012).

    CAS 
    PubMed 

    Google Scholar 

  • Yang, J. & Caprioli, R. M. Matrix sublimation/recrystallization for imaging proteins by mass spectrometry at high spatial resolution. Anal. Chem. 83, 5728–5734 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Prentice, B. M. et al. Dynamic range expansion by gas-phase ion fractionation and enrichment for imaging mass spectrometry. Anal. Chem. 92, 13092–13100 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jackson, S., Calos, M., Myers, A. & Self, W. T. Analysis of proline reduction in the nosocomial pathogen Clostridium difficile. J. Bacteriol. 188, 8487–8495 (2006).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Evans, D. R. et al. Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital. eLife 9, e53886 (2020).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

    CAS 
    PubMed 

    Google Scholar 

  • Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bryan, E. M., Bae, T., Kleerebezem, M. & Dunny, G. M. Improved vectors for nisin-controlled expression in Gram-positive bacteria. Plasmid 44, 183–190 (2000).

    CAS 
    PubMed 

    Google Scholar 

  • Chilambi, G. S. et al. Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients. Proc. Natl Acad. Sci. USA 117, 11703–11714 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Obeid, J. S. et al. Procurement of shared data instruments for Research Electronic Data Capture (REDCap). J. Biomed. Inform. 46, 259–265 (2013).

    PubMed 

    Google Scholar 

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