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Osbelt L, Almási ÉDH, Wende M, Kienesberger S, Voltz A, Lesker TR, Muthukumarasamy U, Knischewski N, Nordmann E, Bielecka AA, Giralt-Zúñiga M, Kaganovitch E, Kühne C, Baier C, Pietsch M, Müsken M, Greweling-Pils MC, Breinbauer R, Flieger A, Schlüter D, Müller R, Erhardt M, Zechner EL, Strowig T. Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms. Nat Microbiol 2024; 9:1792-1811. [PMID: 38862602 PMCID: PMC11222139 DOI: 10.1038/s41564-024-01710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
The Klebsiella oxytoca species complex is part of the human microbiome, especially during infancy and childhood. K. oxytoca species complex strains can produce enterotoxins, namely, tilimycin and tilivalline, while also contributing to colonization resistance (CR). The relationship between these seemingly contradictory roles is not well understood. Here, by coupling ex vivo assays with CRISPR-mutagenesis and various mouse models, we show that K. oxytoca provides CR against Salmonella Typhimurium. In vitro, the antimicrobial activity against various Salmonella strains depended on tilimycin production and was induced by various simple carbohydrates. In vivo, CR against Salmonella depended on toxin production in germ-free mice, while it was largely toxin-independent in mice with residual microbiota. This was linked to the relative levels of toxin-inducing carbohydrates in vivo. Finally, dulcitol utilization was essential for toxin-independent CR in gnotobiotic mice. Together, this demonstrates that nutrient availability is key to both toxin-dependent and substrate-driven competition between K. oxytoca and Salmonella.
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Affiliation(s)
- Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Éva D H Almási
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Alexander Voltz
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Nele Knischewski
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Elke Nordmann
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Agata A Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - María Giralt-Zúñiga
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eugen Kaganovitch
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Kühne
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claas Baier
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Pietsch
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Rolf Breinbauer
- BioTechMed-Graz, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Schlüter
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Marc Erhardt
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany.
- Center for Individualized Infection Medicine, Hannover, Germany.
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2
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Zhou C, Pawline MB, Pironti A, Morales SM, Perault AI, Ulrich RJ, Podkowik M, Lejeune A, DuMont A, Stubbe FX, Korman A, Jones DR, Schluter J, Richardson AR, Fey PD, Drlica K, Cadwell K, Torres VJ, Shopsin B. Microbiota and metabolic adaptation shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593044. [PMID: 38766195 PMCID: PMC11100824 DOI: 10.1101/2024.05.11.593044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Depletion of microbiota increases susceptibility to gastrointestinal colonization and subsequent infection by opportunistic pathogens such as methicillin-resistant Staphylococcus aureus (MRSA). How the absence of gut microbiota impacts the evolution of MRSA is unknown. The present report used germ-free mice to investigate the evolutionary dynamics of MRSA in the absence of gut microbiota. Through genomic analyses and competition assays, we found that MRSA adapts to the microbiota-free gut through sequential genetic mutations and structural changes that enhance fitness. Initially, these adaptations increase carbohydrate transport; subsequently, evolutionary pathways largely diverge to enhance either arginine metabolism or cell wall biosynthesis. Increased fitness in arginine pathway mutants depended on arginine catabolic genes, especially nos and arcC, which promote microaerobic respiration and ATP generation, respectively. Thus, arginine adaptation likely improves redox balance and energy production in the oxygen-limited gut environment. Findings were supported by human gut metagenomic analyses, which suggest the influence of arginine metabolism on colonization. Surprisingly, these adaptive genetic changes often reduced MRSA's antimicrobial resistance and virulence. Furthermore, resistance mutation, typically associated with decreased virulence, also reduced colonization fitness, indicating evolutionary trade-offs among these traits. The presence of normal microbiota inhibited these adaptations, preserving MRSA's wild-type characteristics that effectively balance virulence, resistance, and colonization fitness. The results highlight the protective role of gut microbiota in preserving a balance of key MRSA traits for long-term ecological success in commensal populations, underscoring the potential consequences on MRSA's survival and fitness during and after host hospitalization and antimicrobial treatment.
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Affiliation(s)
- Chunyi Zhou
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Miranda B. Pawline
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Microbial Computational Genomic Core Lab, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sabrina M. Morales
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew I. Perault
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J. Ulrich
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ashley DuMont
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Aryeh Korman
- Metabolomics Core Resource Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Drew R. Jones
- Metabolomics Core Resource Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jonas Schluter
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony R. Richardson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07102, USA
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07102, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
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3
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Lehmann CJ, Dylla NP, Odenwald M, Nayak R, Khalid M, Boissiere J, Cantoral J, Adler E, Stutz MR, Dela Cruz M, Moran A, Lin H, Ramaswamy R, Sundararajan A, Sidebottom AM, Little J, Pamer EG, Aronsohn A, Fung J, Baker TB, Kacha A. Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection. Cell Host Microbe 2024; 32:117-130.e4. [PMID: 38103544 DOI: 10.1016/j.chom.2023.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/06/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Metabolites produced by the intestinal microbiome modulate mucosal immune defenses and optimize epithelial barrier function. Intestinal dysbiosis, including loss of intestinal microbiome diversity and expansion of antibiotic-resistant pathobionts, is accompanied by changes in fecal metabolite concentrations and increased incidence of systemic infection. Laboratory tests that quantify intestinal dysbiosis, however, have yet to be incorporated into clinical practice. We quantified fecal metabolites in 107 patients undergoing liver transplantation (LT) and correlated these with fecal microbiome compositions, pathobiont expansion, and postoperative infections. Consistent with experimental studies implicating microbiome-derived metabolites with host-mediated antimicrobial defenses, reduced fecal concentrations of short- and branched-chain fatty acids, secondary bile acids, and tryptophan metabolites correlate with compositional microbiome dysbiosis in LT patients and the relative risk of postoperative infection. Our findings demonstrate that fecal metabolite profiling can identify LT patients at increased risk of postoperative infection and may provide guideposts for microbiome-targeted therapies.
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Affiliation(s)
- Christopher J Lehmann
- Department of Medicine, Section of Infectious Disease and Global Health, University of Chicago Medicine, 5841 S. Maryland Ave., Chicago, IL 60637, USA; Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Chicago Medicine, 5841 S. Maryland Ave., Chicago, IL 60637, USA.
| | - Nicholas P Dylla
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Matthew Odenwald
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA; Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - Ravi Nayak
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Maryam Khalid
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Jaye Boissiere
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Jackelyn Cantoral
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Emerald Adler
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Matthew R Stutz
- Department of Pulmonary and Critical Care Medicine, Cook County Health, 1950 W. Polk St, Chicago, IL 60612, USA
| | - Mark Dela Cruz
- Department of Cardiology, Advocate Health Care Systems, 4400 W. 95(th) St, Oak Lawn, IL 60453, USA
| | - Angelica Moran
- Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Jessica Little
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Eric G Pamer
- Department of Medicine, Section of Infectious Disease and Global Health, University of Chicago Medicine, 5841 S. Maryland Ave., Chicago, IL 60637, USA; Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA.
| | - Andrew Aronsohn
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - John Fung
- Department of Surgery, Section of Transplant Surgery, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - Talia B Baker
- Department of Surgery, Division of Transplantation and Advanced Hepatobiliary Surgery, University of Utah Health, 30 N. 1900 East, Salt Lake City, UT 84132, USA
| | - Aalok Kacha
- Department of Anesthesia and Critical Care, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA.
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4
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Odenwald MA, Lin H, Lehmann C, Dylla NP, Cole CG, Mostad JD, Pappas TE, Ramaswamy R, Moran A, Hutchison AL, Stutz MR, Dela Cruz M, Adler E, Boissiere J, Khalid M, Cantoral J, Haro F, Oliveira RA, Waligurski E, Cotter TG, Light SH, Beavis KG, Sundararajan A, Sidebottom AM, Reddy KG, Paul S, Pillai A, Te HS, Rinella ME, Charlton MR, Pamer EG, Aronsohn AI. Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease. Nat Microbiol 2023; 8:2033-2049. [PMID: 37845315 PMCID: PMC11059310 DOI: 10.1038/s41564-023-01493-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023]
Abstract
Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.
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Affiliation(s)
- Matthew A Odenwald
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA.
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Christopher Lehmann
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, USA
| | - Nicholas P Dylla
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Cody G Cole
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Jake D Mostad
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Téa E Pappas
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - Angelica Moran
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Alan L Hutchison
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Matthew R Stutz
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cook County Health, Chicago, IL, USA
| | - Mark Dela Cruz
- Section of Cardiology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Emerald Adler
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jaye Boissiere
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Maryam Khalid
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jackelyn Cantoral
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita A Oliveira
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Thomas G Cotter
- Division of Digestive and Liver Diseases, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | | | | | - K Gautham Reddy
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Sonali Paul
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Anjana Pillai
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Helen S Te
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Mary E Rinella
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Michael R Charlton
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Andrew I Aronsohn
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
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