Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota

Nature Medicine volume 18, pages 799–806 (2012)Cite this article

Subjects

Abstract

The mammalian intestine harbors a complex microbial community that provides numerous benefits to its host. However, the microbiota can also include potentially virulent species, termed pathobiont, which can cause disease when intestinal homeostasis is disrupted. The molecular mechanisms by which pathobionts cause disease remain poorly understood. Here we describe a sepsis-like disease that occurs upon gut injury in antibiotic-treated mice. Sepsis was associated with the systemic spread of a specific multidrug-resistant Escherichia coli pathobiont that expanded markedly in the microbiota of antibiotic-treated mice. Rapid sepsis-like death required a component of the innate immune system, the Naip5-Nlrc4 inflammasome. In accordance with Koch's postulates, we found the E. coli pathobiont was sufficient to activate Naip5-Nlrc4 and cause disease when injected intravenously into unmanipulated mice. These findings reveal how sepsis-like disease can result from recognition of pathobionts by the innate immune system.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Antibiotic treatment plus intestinal injury triggers a sepsis-like syndrome in wild-type mice.
Figure 2: Expansion and extraintestinal colonization of a multidrug-resistant E. coli in response to intestinal injury in dysbiotic mice.
Figure 3: Systemic E. coli O21:H+ infection is pathogenic in wild-type mice.
Figure 4: Naip5-Nlrc4 mediates the pathogenesis of a sepsis-like syndrome in response to intestinal injury in dysbiotic mice.
Figure 5: E. coli O21:H+ activates the Naip5-Nlrc4 inflammasome.
Figure 6: The Naip5-Nlrc4 inflammasome reduces host tolerance of a systemic E. coli infection.

Similar content being viewed by others

References

  1. Round, J.L. & Mazmanian, S.K. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9, 313–323 (2009).

    Article  CAS  Google Scholar 

  2. Chow, J. & Mazmanian, S.K. A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe 7, 265–276 (2010).

    Article  CAS  Google Scholar 

  3. Voth, D.E. & Ballard, J.D. Clostridium difficile toxins: mechanism of action and role in disease. Clin. Microbiol. Rev. 18, 247–263 (2005).

    Article  CAS  Google Scholar 

  4. Oteo, J., Perez-Vazquez, M. & Campos, J. Extended-spectrum β-lactamase producing Escherichia coli: changing epidemiology and clinical impact. Curr. Opin. Infect. Dis. 23, 320–326 (2010).

    Article  CAS  Google Scholar 

  5. Russell, D.A. & Thompson, R.C. Targets for sepsis therapies: tumor necrosis factor versus interleukin-1. Curr. Opin. Biotechnol. 4, 714–721 (1993).

    Article  CAS  Google Scholar 

  6. Salyers, A.A., Gupta, A. & Wang, Y. Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol. 12, 412–416 (2004).

    Article  CAS  Google Scholar 

  7. Penders, J., Stobberingh, E.E., van den Brandt, P.A. & Thijs, C. The role of the intestinal microbiota in the development of atopic disorders. Allergy 62, 1223–1236 (2007).

    Article  CAS  Google Scholar 

  8. Lakhan, S.E. & Kirchgessner, A. Gut inflammation in chronic fatigue syndrome. Nutr. Metab. (Lond) 7, 79 (2010).

    Article  Google Scholar 

  9. Wu, H.J. et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 32, 815–827 (2010).

    Article  CAS  Google Scholar 

  10. Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228–231 (2010).

    Article  CAS  Google Scholar 

  11. Turnbaugh, P.J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).

    Article  Google Scholar 

  12. Cadwell, K. et al. Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell 141, 1135–1145 (2010).

    Article  CAS  Google Scholar 

  13. Elinav, E. et al. NLRP6 Inflammasome regulates colonic microbial ecology and risk for colitis. Cell 745–757 (2011).

  14. Garrett, W.S. et al. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131, 33–45 (2007).

    Article  CAS  Google Scholar 

  15. Bloom, S.M. et al. Commensal bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host Microbe 9, 390–403 (2011).

    Article  CAS  Google Scholar 

  16. Schroder, K. & Tschopp, J. The inflammasomes. Cell 140, 821–832 (2010).

    Article  CAS  Google Scholar 

  17. Kofoed, E.M. & Vance, R.E. Innate immune recognition of bacterial ligands by NAIPs determines inflammasome specificity. Nature 477, 592–595 (2011).

    Article  CAS  Google Scholar 

  18. Zhao, Y. et al. The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus. Nature 477, 596–600 (2011).

    Article  CAS  Google Scholar 

  19. Allen, I.C. et al. The NLRP3 inflammasome functions as a negative regulator of tumorigenesis during colitis-associated cancer. J. Exp. Med. 207, 1045–1056 (2010).

    Article  CAS  Google Scholar 

  20. Dupaul-Chicoine, J. et al. Control of intestinal homeostasis, colitis and colitis-associated colorectal cancer by the inflammatory caspases. Immunity 32, 367–378 (2010).

    Article  CAS  Google Scholar 

  21. Zaki, M.H. et al. The NLRP3 inflammasome protects against loss of epithelial integrity and mortality during experimental colitis. Immunity 32, 379–391 (2010).

    Article  CAS  Google Scholar 

  22. Hu, B. et al. Inflammation-induced tumorigenesis in the colon is regulated by caspase-1 and NLRC4. Proc. Natl. Acad. Sci. USA 21635–21640 (2010).

    Article  Google Scholar 

  23. Okayasu, I. et al. A Novel method in the induction of reliable experimental acute and chronic ulcerative-colitis in mice. Gastroenterology 98, 694–702 (1990).

    Article  CAS  Google Scholar 

  24. Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. & Medzhitov, R. Recognition of commensal microflora by Toll-like receptors is required for intestinal homeostasis. Cell 118, 229–241 (2004).

    Article  CAS  Google Scholar 

  25. Sherwood, E.R., Enoh, V.T., Murphey, E.D. & Lin, C.Y. Mice depleted of CD8+ T and NK cells are resistant to injury caused by cecal ligation and puncture. Lab. Invest. 84, 1655–1665 (2004).

    Article  Google Scholar 

  26. Larsen, R. et al. A central role for free heme in the pathogenesis of severe sepsis. Sci. Transl. Med. 2, 51ra71 (2010).

    Article  Google Scholar 

  27. 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).

    Article  CAS  Google Scholar 

  28. Ren, Y. et al. Characterization of Escherichia coli O3 and O21 O antigen gene clusters and development of serogroup-specific PCR assays. J. Microbiol. Methods 75, 329–334 (2008).

    Article  CAS  Google Scholar 

  29. Evans, D.J. Jr., Evans, D.G., Young, L.S. & Pitt, J. Hemagglutination typing of Escherichia coli: definition of seven hemagglutination types. J. Clin. Microbiol. 12, 235–242 (1980).

    Google Scholar 

  30. Stevens, P., Young, L.S. & Adamu, S. Opsonization of various capsular (K) E. coli by the alternative complement pathway. Immunology 50, 497–502 (1983).

    CAS  Google Scholar 

  31. Evans, D.J. Jr. et al. Hemolysin and K antigens in relation to serotype and hemagglutination type of Escherichia coli isolated from extraintestinal infections. J. Clin. Microbiol. 13, 171–178 (1981).

    Google Scholar 

  32. Orskov, I. & Orskov, F. Escherichia coli in extra-intestinal infections. J. Hyg. (Lond.) 95, 551–575 (1985).

    Article  CAS  Google Scholar 

  33. Sander, L.E. et al. Detection of prokaryotic mRNA signifies microbial viability and promotes immunity. Nature 474, 385–389 (2011).

    Article  CAS  Google Scholar 

  34. Ren, C.P. et al. The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J. Bacteriol. 186, 3547–3560 (2004).

    Article  CAS  Google Scholar 

  35. Ideses, D. et al. A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis. J. Bacteriol. 187, 8164–8171 (2005).

    Article  CAS  Google Scholar 

  36. Barnhart, M.M. & Chapman, M.R. Curli biogenesis and function. Annu. Rev. Microbiol. 60, 131–147 (2006).

    Article  CAS  Google Scholar 

  37. Wong, W.T., Bettelheim, K.A., Cheng, F.C. & Ong, G.B. Serotypes of Escherichia coli isolated from patients with recurrent pyogenic cholangitis. J. Hyg. (Lond.) 88, 513–517 (1982).

    Article  CAS  Google Scholar 

  38. Sannes, M.R., Kuskowski, M.A., Owens, K., Gajewski, A. & Johnson, J.R. Virulence factor profiles and phylogenetic background of Escherichia coli isolates from veterans with bacteremia and uninfected control subjects. J. Infect. Dis. 190, 2121–2128 (2004).

    Article  Google Scholar 

  39. Mokady, D., Gophna, U. & Ron, E.Z. Virulence factors of septicemic Escherichia coli strains. Int. J. Med. Microbiol. 295, 455–462 (2005).

    Article  CAS  Google Scholar 

  40. Ramos, N.L. et al. Genetic relatedness and virulence gene profiles of Escherichia coli strains isolated from septicaemic and uroseptic patients. Eur. J. Clin. Microbiol. Infect. Dis. 29, 15–23 (2010).

    Article  CAS  Google Scholar 

  41. Korczak, B. et al. Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J. Clin. Microbiol. 43, 1024–1031 (2005).

    Article  CAS  Google Scholar 

  42. Mapes, S., Rhodes, D.M., Wilson, W.D., Leutenegger, C.M. & Pusterla, N. Comparison of five real-time PCR assays for detecting virulence genes in isolates of Escherichia coli from septicaemic neonatal foals. Vet. Rec. 161, 716–718 (2007).

    Article  CAS  Google Scholar 

  43. Henderson, J.P. et al. Quantitative metabolomics reveals an epigenetic blueprint for iron acquisition in uropathogenic Escherichia coli. PLoS Pathog. 5, e1000305 (2009).

    Article  Google Scholar 

  44. Lightfield, K.L. et al. Critical function for Naip5 in inflammasome activation by a conserved carboxy-terminal domain of flagellin. Nat. Immunol. 9, 1171–1178 (2008).

    Article  CAS  Google Scholar 

  45. Miao, E.A. et al. Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc. Natl. Acad. Sci. USA 107, 3076–3080 (2010).

    Article  CAS  Google Scholar 

  46. Lightfield, K.L. et al. Differential requirements for NAIP5 in activation of the NLRC4 inflammasome. Infect. Immun. 79, 1606–1614 (2011).

    Article  CAS  Google Scholar 

  47. Schneider, D.S. & Ayres, J.S. Two ways to survive infection: what resistance and tolerance can teach us about treating infectious diseases. Nat. Rev. Immunol. 8, 889–895 (2008).

    Article  CAS  Google Scholar 

  48. Russell, J.A. Drug therapy: Management of sepsis. N. Engl. J. Med. 355, 1699–1713 (2006).

    Article  CAS  Google Scholar 

  49. Lamkanfi, M. & Dixit, V.M. The inflammasomes. PLoS Pathog. 5, e1000510 (2009).

    Article  Google Scholar 

  50. Sarkar, A. et al. Caspase-1 regulates Escherichia coli sepsis and splenic B cell apoptosis independently of interleukin-1beta and interleukin-18. Am. J. Respir. Crit. Care Med. 174, 1003–1010 (2006).

    Article  CAS  Google Scholar 

  51. Fantuzzi, G. et al. Effect of endotoxin in IL-1 β-deficient mice. J. Immunol. 157, 291–296 (1996).

    CAS  Google Scholar 

  52. O'Reilly, M., Silver, G.M., Davis, J.H., Gamelli, R.L. & Hebert, J.C. Interleukin 1 beta improves survival following cecal ligation and puncture. J. Surg. Res. 52, 518–522 (1992).

    Article  CAS  Google Scholar 

  53. Opal, S.M. et al. Confirmatory interleukin-1 receptor antagonist trial in severe sepsis: A phase III, randomized, double-blind, placebo-controlled, multicenter trial. Crit. Care Med. 25, 1115–1124 (1997).

    Article  CAS  Google Scholar 

  54. Fisher, C.J. et al. Initial evaluation of human recombinant interleukin-1 receptor antagonist in the treatment of sepsis syndrome—a randomized, open-label, placebo-controlled multicenter Trial. Crit. Care Med. 22, 12–21 (1994).

    Article  Google Scholar 

  55. Råberg, L., Graham, A.L. & Read, A.F. Decomposing health: tolerance and resistance to parasites in animals. Phil. Trans. R. Soc. Lond. B 364, 37–49 (2009).

    Article  Google Scholar 

  56. Roy, B.A. & Kirchner, J.W. Evolutionary dynamics of pathogen resistance and tolerance. Evolution 54, 51–63 (2000).

    Article  CAS  Google Scholar 

  57. Boots, M. Fight or learn to live with the consequences? Trends Ecol. Evol. 23, 248–250 (2008).

    Article  Google Scholar 

  58. Mariathasan, S. et al. Differential activation of the inflammasome by caspase-1 adaptors ASC and Ipaf. Nature 430, 213–218 (2004).

    Article  CAS  Google Scholar 

  59. Li, P. et al. Mice deficient in IL-1 β-converting enzyme are defective in production of mature IL-1 β and resistant to endotoxic shock. Cell 80, 401–411 (1995).

    Article  CAS  Google Scholar 

  60. DeSantis, T.Z. et al. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53, 371–383 (2007).

    Article  CAS  Google Scholar 

  61. Croswell, A., Amir, E., Teggatz, P., Barman, M. & Salzman, N.H. Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection. Infect. Immun. 77, 2741–2753 (2009).

    Article  CAS  Google Scholar 

  62. Fierer, N., Jackson, J.A., Vilgalys, R. & Jackson, R.B. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71, 4117–4120 (2005).

    Article  CAS  Google Scholar 

  63. Dereeper, A. et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36, W465–W469 (2008).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Schapiro and J. LaPan for biochemical characterization of E. coli O21:H+ and S. Brandt for helpful discussions about the isolate; K. Bodi for helpful advice about whole-genome sequencing analysis; G. Barton, D. Portnoy and K. Barry for helpful discussions and critical reading of the manuscript; E. Kofoed (University of California–Berkeley) for the flaA-IRES-GFP construct; K. Sotelo-Troha for technical help and L. Lopez for support in our mouse facility (University of California–Berkeley). Nlrc4−/− mice were from S. Mariathasan and V. Dixit (Genentech). Casp1−/− mice and S. Typhimurium LT2 ΔfliCΔfljB were a gift from A. Van der Velden and M. Starnbach (Harvard Medical School). Il1b−/− mice were from the Zychlinsky lab at Max Planck Institute. This work was supported in part by US National Institutes of Health grants AI063302, AI075039 and AI080749 awarded to R.E.V. and National Institutes of Health Ruth L. Kirschstein National Research Service Award fellowship AI091068 awarded to J.S.A. R.E.V. is an Investigator of the Cancer Research Institute and a Burroughs Wellcome Fund Investigator in the Pathogenesis of Infectious Disease.

Author information

Authors and Affiliations

  1. Department of Molecular & Cell Biology, Division of Immunology & Pathogenesis, University of California, Berkeley, California, USA

    Janelle S Ayres, Norver J Trinidad & Russell E Vance

Authors
  1. Janelle S Ayres
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Norver J Trinidad
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Russell E Vance
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.S.A. and R.E.V. conceived of the study, designed experiments and wrote the manuscript. J.S.A. directed the study and performed all experiments. N.J.T. did all mouse intravenous injections and performed the retroviral lethality assay.

Corresponding authors

Correspondence to Janelle S Ayres or Russell E Vance.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Table 1 (PDF 13588 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ayres, J., Trinidad, N. & Vance, R. Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota. Nat Med 18, 799–806 (2012). https://doi.org/10.1038/nm.2729

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nm.2729

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing