Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection

Autoři: Ashley D. Smith aff001;  Elissa D. Foss aff001;  Irma Zhang aff001;  Jessica L. Hastie aff001;  Nicole P. Giordano aff001;  Lusine Gasparyan aff002;  Lam Phuc VinhNguyen aff002;  Alyxandria M. Schubert aff001;  Deepika Prasad aff001;  Hannah L. McMichael aff001;  Jinchun Sun aff003;  Richard D. Beger aff003;  Vahan Simonyan aff002;  Siobhán C. Cowley aff001;  Paul E. Carlson, Jr aff001
Působiště autorů: Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spri aff001;  Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spri aff001;  High-performance Integrated Personal Environment, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America aff002;  Division of Systems Biology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America aff003
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223025


Clostridium difficile (Cd) infection (CDI) typically occurs after antibiotic usage perturbs the gut microbiota. Mucosa-associated invariant T cells (MAIT) are found in the gut and their development is dependent on Major histocompatibility complex-related protein 1 (MR1) and the host microbiome. Here we were interested in determining whether the absence of MR1 impacts resistance to CDI. To this end, wild-type (WT) and MR1-/- mice were treated with antibiotics and then infected with Cd spores. Surprisingly, MR1-/- mice exhibited resistance to Cd colonization. 16S rRNA gene sequencing of feces revealed inherent differences in microbial composition. This colonization resistance was transferred from MR1-/- to WT mice via fecal microbiota transplantation, suggesting that MR1-dependent factors influence the microbiota, leading to CDI susceptibility.

Klíčová slova:

Antibiotic resistance – Antibiotics – Clostridium difficile – Gastrointestinal tract – Microbiome – Mouse models – Sequence databases – Bacterial spores


1. Gherardin NA, Keller AN, Woolley RE, Le Nours J, Ritchie DS, Neeson PJ, et al. Diversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition. Immunity. 2016;44(1):32–45. Epub 2016/01/23. doi: 10.1016/j.immuni.2015.12.005 26795251.

2. Huang S, Martin E, Kim S, Yu L, Soudais C, Fremont DH, et al. MR1 antigen presentation to mucosal-associated invariant T cells was highly conserved in evolution. Proc Natl Acad Sci U S A. 2009;106(20):8290–5. Epub 2009/05/07. doi: 10.1073/pnas.0903196106 19416870

3. Tsukamoto K, Deakin JE, Graves JAM, Hashimoto K. Exceptionally high conservation of the MHC class I-related gene, MR1, among mammals. Immunogenetics. 2013;65(2):115–24. doi: 10.1007/s00251-012-0666-5 23229473

4. Yamaguchi H, Kurosawa Y, Hashimoto K. Expanded Genomic Organization of Conserved Mammalian MHC Class I-Related Genes, HumanMR1and Its Murine Ortholog. Biochemical and Biophysical Research Communications. 1998;250(3):558–64. https://doi.org/10.1006/bbrc.1998.9353 9784382

5. Kjer-Nielsen L, Patel O, Corbett AJ, Le Nours J, Meehan B, Liu L, et al. MR1 presents microbial vitamin B metabolites to MAIT cells. Nature. 2012;491(7426):717–23. http://www.nature.com/nature/journal/v491/n7426/abs/nature11605.html#supplementary-information 23051753

6. Treiner E, Duban L, Bahram S, Radosavljevic M, Wanner V, Tilloy F, et al. Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1. Nature. 2003;422(6928):164–9. Epub 2003/03/14. doi: 10.1038/nature01433 12634786.

7. Cowley SC. MAIT cells and pathogen defense. Cell Mol Life Sci. 2014;71(24):4831–40. Epub 2014/08/29. doi: 10.1007/s00018-014-1708-y 25164578.

8. Le Bourhis L, Dusseaux M, Bohineust A, Bessoles S, Martin E, Premel V, et al. MAIT cells detect and efficiently lyse bacterially-infected epithelial cells. PLoS Pathog. 2013;9(10):e1003681. Epub 2013/10/17. doi: 10.1371/journal.ppat.1003681 24130485

9. Kwon YS, Cho YN, Kim MJ, Jin HM, Jung HJ, Kang JH, et al. Mucosal-associated invariant T cells are numerically and functionally deficient in patients with mycobacterial infection and reflect disease activity. Tuberculosis (Edinb). 2015;95(3):267–74. Epub 2015/04/04. doi: 10.1016/j.tube.2015.03.004 25837440.

10. Meierovics AI, Cowley SC. MAIT cells promote inflammatory monocyte differentiation into dendritic cells during pulmonary intracellular infection. J Exp Med. 2016;213(12):2793–809. Epub 2016/11/02. doi: 10.1084/jem.20160637 27799620

11. Loh L, Wang Z, Sant S, Koutsakos M, Jegaskanda S, Corbett AJ, et al. Human mucosal-associated invariant T cells contribute to antiviral influenza immunity via IL-18-dependent activation. Proc Natl Acad Sci U S A. 2016;113(36):10133–8. Epub 2016/08/21. doi: 10.1073/pnas.1610750113 27543331

12. Leung DT, Bhuiyan TR, Nishat NS, Hoq MR, Aktar A, Rahman MA, et al. Circulating mucosal associated invariant T cells are activated in Vibrio cholerae O1 infection and associated with lipopolysaccharide antibody responses. PLoS Negl Trop Dis. 2014;8(8):e3076. Epub 2014/08/22. doi: 10.1371/journal.pntd.0003076 25144724

13. Bernal I, Hofmann JD, Bulitta B, Klawonn F, Michel AM, Jahn D, et al. Clostridioides difficile Activates Human Mucosal-Associated Invariant T Cells. Front Microbiol. 2018;9:2532. Epub 2018/11/10. doi: 10.3389/fmicb.2018.02532 30410474

14. Jo J, Tan AT, Ussher JE, Sandalova E, Tang XZ, Tan-Garcia A, et al. Toll-like receptor 8 agonist and bacteria trigger potent activation of innate immune cells in human liver. PLoS Pathog. 2014;10(6):e1004210. Epub 2014/06/27. doi: 10.1371/journal.ppat.1004210 24967632

15. Prevention CfDCa. Antibiotic Resistance Treats in the Unites States, 2013. 2013.

16. Lessa FC, Winston LG, McDonald LC. Burden of Clostridium difficile infection in the United States. N Engl J Med. 2015;372(24):2369–70. Epub 2015/06/11. doi: 10.1056/NEJMc1505190 26061850.

17. Johnson S. Recurrent Clostridium difficile infection: causality and therapeutic approaches. Int J Antimicrob Agents. 2009;33 Suppl 1:S33–6. Epub 2009/07/18. doi: 10.1016/s0924-8579(09)70014-7 19303567.

18. Cohen SH, Gerding DN, Johnson S, Kelly CP, Loo VG, McDonald LC, et al. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA). Infect Control Hosp Epidemiol. 2010;31(5):431–55. Epub 2010/03/24. doi: 10.1086/651706 20307191.

19. Rao K, Young VB. Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection. Infectious disease clinics of North America. 2015;29(1):109–22. doi: 10.1016/j.idc.2014.11.009 25677705

20. Kelly CR, Khoruts A, Staley C, et al. Effect of fecal microbiota transplantation on recurrence in multiply recurrent clostridium difficile infection: A randomized trial. Annals of Internal Medicine. 2016;165(9):609–16. doi: 10.7326/M16-0271 27547925

21. Chen X, Katchar K, Goldsmith JD, Nanthakumar N, Cheknis A, Gerding DN, et al. A mouse model of Clostridium difficile-associated disease. Gastroenterology. 2008;135(6):1984–92. Epub 2008/10/14. doi: 10.1053/j.gastro.2008.09.002 18848941.

22. Theriot CM, Koumpouras CC, Carlson PE, Bergin II, Aronoff DM, Young VB. Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains. Gut Microbes. 2011;2(6):326–34. Epub 2011/12/27. doi: 10.4161/gmic.19142 22198617

23. Collins J, Auchtung JM, Schaefer L, Eaton KA, Britton RA. Humanized microbiota mice as a model of recurrent Clostridium difficile disease. Microbiome. 2015;3:35. Epub 2015/08/21. doi: 10.1186/s40168-015-0097-2 26289776

24. Schubert AM, Sinani H, Schloss PD. Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile. MBio. 2015;6(4):e00974. Epub 2015/07/16. doi: 10.1128/mBio.00974-15 26173701

25. Theriot CM, Koenigsknecht MJ, Carlson PE Jr., Hatton GE, Nelson AM, Li B, et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun. 2014;5:3114. Epub 2014/01/22. doi: 10.1038/ncomms4114 24445449

26. Seekatz AM, Theriot CM, Molloy CT, Wozniak KL, Bergin IL, Young VB. Fecal Microbiota Transplantation Eliminates Clostridium difficile in a Murine Model of Relapsing Disease. Infect Immun. 2015;83(10):3838–46. Epub 2015/07/15. doi: 10.1128/IAI.00459-15 26169276

27. Goulding D, Thompson H, Emerson J, Fairweather NF, Dougan G, Douce GR. Distinctive profiles of infection and pathology in hamsters infected with Clostridium difficile strains 630 and B1. Infect Immun. 2009;77(12):5478–85. Epub 2009/09/16. doi: 10.1128/IAI.00551-09 19752031.

28. Graham ML, Janecek JL, Kittredge JA, Hering BJ, Schuurman HJ. The streptozotocin-induced diabetic nude mouse model: differences between animals from different sources. Comp Med. 2011;61(4):356–60. Epub 2012/02/15. 22330251

29. Olfe J, Domanska G, Schuett C, Kiank C. Different stress-related phenotypes of BALB/c mice from in-house or vendor: alterations of the sympathetic and HPA axis responsiveness. BMC Physiol. 2010;10:2. Epub 2010/03/11. doi: 10.1186/1472-6793-10-2 20214799

30. Bhattarai Y, Kashyap PC. Germ-Free Mice Model for Studying Host-Microbial Interactions. Methods Mol Biol. 2016;1438:123–35. Epub 2016/05/07. doi: 10.1007/978-1-4939-3661-8_8 27150088.

31. Johnson S. Recurrent Clostridium difficile infection: a review of risk factors, treatments, and outcomes. J Infect. 2009;58(6):403–10. Epub 2009/04/28. doi: 10.1016/j.jinf.2009.03.010 19394704.

32. Reeves AE, Koenigsknecht MJ, Bergin IL, Young VB. Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae. Infect Immun. 2012;80(11):3786–94. Epub 2012/08/15. doi: 10.1128/IAI.00647-12 22890996

33. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015;517(7533):205–8. Epub 2014/10/23. doi: 10.1038/nature13828 25337874

34. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336(6086):1268–73. Epub 2012/06/08. doi: 10.1126/science.1223490 22674334.

35. Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, et al. CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. Eur J Immunol. 2017;47(7):1188–99. Epub 2017/05/26. doi: 10.1002/eji.201646792 28543188.

36. Park SJ, Kim JH, Song MY, Sung YC, Lee SW, Park Y. PD-1 deficiency protects experimental colitis via alteration of gut microbiota. BMB Rep. 2017;50(11):578–83. Epub 2017/10/27. doi: 10.5483/BMBRep.2017.50.11.165 29065967.

37. Yoshida K, Murayama MA, Shimizu K, Tang C, Katagiri N, Matsuo K, et al. IL-1R2 deficiency suppresses dextran sodium sulfate-induced colitis in mice via regulation of microbiota. Biochem Biophys Res Commun. 2018;496(3):934–40. Epub 2018/01/26. doi: 10.1016/j.bbrc.2018.01.116 29366788.

38. Rouxel O, Da Silva J, Beaudoin L, Nel I, Tard C, Cagninacci L, et al. Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes. 2017;18(12):1321–31. doi: 10.1038/ni.3854 28991267.

39. Giordano N, Hastie JL, Smith AD, Foss ED, Gutierrez-Munoz DF, Carlson PE Jr. Cysteine desulfurase IscS2 plays a role in oxygen resistance in Clostridium difficile. Infect Immun. 2018. Epub 2018/06/06. doi: 10.1128/iai.00326-18 29866903.

40. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79(17):5112–20. Epub 2013/06/25. doi: 10.1128/AEM.01043-13 23793624.

41. Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S, Golikov A, et al. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database (Oxford). 2016;2016. Epub 2016/03/19. doi: 10.1093/database/baw022 26989153.

42. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41. Epub 2009/10/06. doi: 10.1128/AEM.01541-09 19801464

43. Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. Epub 2016/10/27. doi: 10.7717/peerj.2584 27781170

44. Yue JC, Clayton MK. A Similarity Measure Based on Species Proportions. Communications in Statistics—Theory and Methods. 2005;34(11):2123–31. doi: 10.1080/STA-200066418

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