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Abstract
Antibiotics have benefitted human health since their introduction nearly a century ago. However, the rise of antibiotic resistance may portend the dawn of the "post-antibiotic age." With the narrow pipeline for novel antimicrobials, we need new approaches to deal with the rise of multidrug resistant organisms. In the last 2 decades, the role of the intestinal microbiota in human health has been acknowledged and studied widely. Of the various activities carried out by the gut microbiota, colonization resistance is a key function that helps maintain homeostasis. Therefore, re-establishing a healthy microbiota is a novel strategy for treating drug resistance organisms. Preliminary studies suggest that this is a viable approach. However, the extent of their success still needs to be examined. Herein, we will review work in this area and suggest where future studies can further investigate this method for dealing with the threat of antibiotic resistance.
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Affiliation(s)
- Nguyen T Q Nhu
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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2
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Ötleş E, Balczewski EA, Keidan M, Oh J, Patel A, Young VB, Rao K, Wiens J. Clostridioides difficile infection surveillance in intensive care units and oncology wards using machine learning. Infect Control Hosp Epidemiol 2023; 44:1776-1781. [PMID: 37088695 PMCID: PMC10665879 DOI: 10.1017/ice.2023.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 04/25/2023]
Abstract
OBJECTIVE Screening individuals admitted to the hospital for Clostridioides difficile presents opportunities to limit transmission and hospital-onset C. difficile infection (HO-CDI). However, detection from rectal swabs is resource intensive. In contrast, machine learning (ML) models may accurately assess patient risk without significant resource usage. In this study, we compared the effectiveness of swab surveillance to daily risk estimates produced by an ML model to identify patients who will likely develop HO-CDI in the intensive care unit (ICU) setting. DESIGN A prospective cohort study was conducted with patient carriage of toxigenic C. difficile identified by rectal swabs analyzed by anaerobic culture and polymerase chain reaction (PCR). A previously validated ML model using electronic health record data generated daily risk of HO-CDI for every patient. Swab results and risk predictions were compared to the eventual HO-CDI status. PATIENTS Adult inpatient admissions taking place in University of Michigan Hospitals' medical and surgical intensive care units and oncology wards between June 6th and October 8th, 2020. RESULTS In total, 2,979 admissions, representing 2,044 patients, were observed over the course of the study period, with 39 admissions developing HO-CDIs. Swab surveillance identified 9 true-positive and 87 false-positive HO-CDIs. The ML model identified 9 true-positive and 226 false-positive HO-CDIs; 8 of the true-positives identified by the model differed from those identified by the swab surveillance. CONCLUSION With limited resources, an ML model identified the same number of HO-CDI admissions as swab-based surveillance, though it generated more false-positives. The patients identified by the ML model were not yet colonized with C. difficile. Additionally, the ML model identifies at-risk admissions before disease onset, providing opportunities for prevention.
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Affiliation(s)
- Erkin Ötleş
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Industrial & Operations Engineering, College of Engineering, University of Michigan, Ann Arbor, Michigan
| | - Emily A. Balczewski
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Micah Keidan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jeeheh Oh
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, Michigan
| | - Alieysa Patel
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jenna Wiens
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, Michigan
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Kamineni M, Ötleş E, Oh J, Rao K, Young VB, Li BY, West LR, Hooper DC, Shenoy ES, Guttag JG, Wiens J, Makar M. Prospective evaluation of data-driven models to predict daily risk of Clostridioides difficile infection at 2 large academic health centers - ERRATUM. Infect Control Hosp Epidemiol 2023; 44:1705. [PMID: 36533309 DOI: 10.1017/ice.2022.250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Bloom PP, Rao K, Bassis C, Nojkov B, Young VB, Lok ASF. Regional changes in intestinal permeability in cirrhosis are associated with mucosal bacteria. Hepatol Commun 2023; 7:e0221. [PMID: 37756036 PMCID: PMC10531369 DOI: 10.1097/hc9.0000000000000221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Several complications of cirrhosis are theorized to result from the translocation of bacteria or their products across the intestinal epithelium. We aimed to assess epithelial permeability and associations with mucosal bacteria in patients with cirrhosis. APPROACH AND RESULTS We collected 247 duodenum, ileum, and colon biopsies from 58 consecutive patients with cirrhosis and 33 controls during clinically indicated endoscopies. Patients with cirrhosis were similarly aged to controls (60 vs. 58 y) and had a median Model for End-stage Liver Disease of 8 (interquartile range 7, 10). Biopsies underwent 16S rRNA-encoding gene amplicon sequencing to determine mucosal bacteria composition and transepithelial electrical resistance (TEER) to determine epithelial permeability. In the entire cohort, there were regional differences in TEER with the lowest TEER (ie, more permeable) in the ileum; duodenum TEER was 43% higher and colon TEER 20% higher than ileum TEER (ANOVA p = 0.0004). When comparing patients with cirrhosis and controls, both TEER (26% lower in cirrhosis, p = 0.006) and alpha diversity differed in the duodenum (27% lower in cirrhosis, p = 0.01) but not ileum or colon. A beta-binomial model found that 26 bacteria were significantly associated with TEER. Bifidobacteriaceae Bifidobacterium in duodenal mucosa was protective of epithelial permeability and future hospitalization for hepatic decompensation. CONCLUSIONS Duodenal epithelial permeability was higher, and mucosal bacteria alpha diversity was lower in cirrhosis compared to controls, while no such differences were seen in the ileum or colon. Specific bacteria were associated with epithelial permeability and future hepatic decompensation.
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Affiliation(s)
- Patricia P. Bloom
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine Bassis
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Borko Nojkov
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna SF Lok
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
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5
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Miles-Jay A, Snitkin ES, Lin MY, Shimasaki T, Schoeny M, Fukuda C, Dangana T, Moore N, Sansom SE, Yelin RD, Bell P, Rao K, Keidan M, Standke A, Bassis C, Hayden MK, Young VB. Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit. Nat Med 2023; 29:2526-2534. [PMID: 37723252 PMCID: PMC10579090 DOI: 10.1038/s41591-023-02549-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
Abstract
Despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States. Current prevention strategies are limited by their failure to account for patients who carry C. difficile asymptomatically, who may act as hidden reservoirs transmitting infections to other patients. To improve the understanding of asymptomatic carriers' contribution to C. difficile spread, we conducted admission and daily longitudinal culture-based screening for C. difficile in a US-based intensive care unit over nine months and performed whole-genome sequencing on all recovered isolates. Despite a high burden of carriage, with 9.3% of admissions having toxigenic C. difficile detected in at least one sample, only 1% of patients culturing negative on admission to the unit acquired C. difficile via cross-transmission. While patients who carried toxigenic C. difficile on admission posed minimal risk to others, they themselves had a 24-times greater risk for developing a healthcare-onset C. difficile infection than noncarriers. Together, these findings suggest that current infection prevention practices can be effective in preventing nosocomial cross-transmission of C. difficile, and that decreasing C. difficile infections in hospitals further will require interventions targeting the transition from asymptomatic carriage to infection.
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Affiliation(s)
- Arianna Miles-Jay
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - Michael Y Lin
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Teppei Shimasaki
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Michael Schoeny
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Christine Fukuda
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Thelma Dangana
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas Moore
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sarah E Sansom
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Rachel D Yelin
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Pamela Bell
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Micah Keidan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christine Bassis
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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6
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Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. Cell Rep 2023; 42:112861. [PMID: 37523264 PMCID: PMC10627504 DOI: 10.1016/j.celrep.2023.112861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/01/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023] Open
Abstract
Clostridioides difficile produces toxins that damage the colonic epithelium, causing colitis. Variation in disease severity is poorly understood and has been attributed to host factors and virulence differences between C. difficile strains. We test 23 epidemic ST1 C. difficile clinical isolates for their virulence in mice. All isolates encode a complete Tcd pathogenicity locus and achieve similar colonization densities. However, disease severity varies from lethal to avirulent infections. Genomic analysis of avirulent isolates reveals a 69-bp deletion in the cdtR gene, which encodes a response regulator for binary toxin expression. Deleting the 69-bp sequence in virulent R20291 strain renders it avirulent in mice with reduced toxin gene transcription. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile isolates without reducing colonization and persistence. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.
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Affiliation(s)
- Qiwen Dong
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Julian R Garneau
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Jonathan K Sia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rita C Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Tracy McMillen
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rosemary L Pope
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Carolyn Metcalfe
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Claire Kohout
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | | | - Evan S Snitkin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G Pamer
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
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7
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Kamineni M, Ötleş E, Oh J, Rao K, Young VB, Li BY, West LR, Hooper DC, Shenoy ES, Guttag JG, Wiens J, Makar M. Prospective evaluation of data-driven models to predict daily risk of Clostridioides difficile infection at 2 large academic health centers. Infect Control Hosp Epidemiol 2023; 44:1163-1166. [PMID: 36120815 PMCID: PMC10024639 DOI: 10.1017/ice.2022.218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Many data-driven patient risk stratification models have not been evaluated prospectively. We performed and compared the prospective and retrospective evaluations of 2 Clostridioides difficile infection (CDI) risk-prediction models at 2 large academic health centers, and we discuss the models' robustness to data-set shifts.
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Affiliation(s)
- Meghana Kamineni
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Erkin Ötleş
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Industrial and Operations Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Jeeheh Oh
- Division of Computer Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - Benjamin Y Li
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
- Division of Computer Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Lauren R West
- Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - David C Hooper
- Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Erica S Shenoy
- Infection Control Unit, Massachusetts General Hospital, Boston, Massachusetts
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - John G Guttag
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jenna Wiens
- Division of Computer Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
| | - Maggie Makar
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Division of Computer Science and Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan
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8
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Bongers KS, Chanderraj R, Woods RJ, McDonald RA, Adame MD, Falkowski NR, Brown CA, Baker JM, Winner KM, Fergle DJ, Hinkle KJ, Standke AK, Vendrov KC, Young VB, Stringer KA, Sjoding MW, Dickson RP. The Gut Microbiome Modulates Body Temperature Both in Sepsis and Health. Am J Respir Crit Care Med 2023; 207:1030-1041. [PMID: 36378114 PMCID: PMC10112447 DOI: 10.1164/rccm.202201-0161oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 11/15/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Among patients with sepsis, variation in temperature trajectories predicts clinical outcomes. In healthy individuals, normal body temperature is variable and has decreased consistently since the 1860s. The biologic underpinnings of this temperature variation in disease and health are unknown. Objectives: To establish and interrogate the role of the gut microbiome in calibrating body temperature. Methods: We performed a series of translational analyses and experiments to determine whether and how variation in gut microbiota explains variation in body temperature in sepsis and in health. We studied patient temperature trajectories using electronic medical record data. We characterized gut microbiota in hospitalized patients using 16S ribosomal RNA gene sequencing. We modeled sepsis using intraperitoneal LPS in mice and modulated the microbiome using antibiotics, germ-free, and gnotobiotic animals. Measurements and Main Results: Consistent with prior work, we identified four temperature trajectories in patients hospitalized with sepsis that predicted clinical outcomes. In a separate cohort of 116 hospitalized patients, we found that the composition of patients' gut microbiota at admission predicted their temperature trajectories. Compared with conventional mice, germ-free mice had reduced temperature loss during experimental sepsis. Among conventional mice, heterogeneity of temperature response in sepsis was strongly explained by variation in gut microbiota. Healthy germ-free and antibiotic-treated mice both had lower basal body temperatures compared with control animals. The Lachnospiraceae family was consistently associated with temperature trajectories in hospitalized patients, experimental sepsis, and antibiotic-treated mice. Conclusions: The gut microbiome is a key modulator of body temperature variation in both health and critical illness and is thus a major, understudied target for modulating physiologic heterogeneity in sepsis.
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Affiliation(s)
| | - Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Medicine Service, Infectious Diseases Section, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Robert J. Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Medicine Service, Infectious Diseases Section, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
- Center for Computational Medicine and Bioinformatics and
| | | | - Mark D. Adame
- Division of Pulmonary and Critical Care Medicine and
| | | | - Christopher A. Brown
- Division of Pulmonary and Critical Care Medicine and
- Institute for Research on Innovation and Science, Institute for Social Research
| | - Jennifer M. Baker
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, Medical School
| | - Katherine M. Winner
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, Medical School
| | | | | | - Alexandra K. Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
| | - Kimberly C. Vendrov
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan
- Department of Microbiology and Immunology, Medical School
| | - Kathleen A. Stringer
- Division of Pulmonary and Critical Care Medicine and
- Department of Clinical Pharmacy, College of Pharmacy, and
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, Michigan
| | - Michael W. Sjoding
- Division of Pulmonary and Critical Care Medicine and
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan; and
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, Michigan
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine and
- Department of Microbiology and Immunology, Medical School
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan; and
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9
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Lotakis DM, Dheer R, Dame MK, Cuttitta AJ, Tigani DJ, Spence JR, Young VB, Ralls MW. A Pilot Study: Transcriptional Profiling, Functional Analysis, and Organoid Modeling of Intestinal Mucosa in Hirschsprung Disease. J Pediatr Surg 2023; 58:1164-1169. [PMID: 36922279 DOI: 10.1016/j.jpedsurg.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital colonic aganglionosis. Many HSCR patients develop enterocolitis despite surgical resection. The pathophysiology of this inflammatory process is poorly understood. We compared transcriptional profiles and function of ganglionic and aganglionic tissue in HSCR patients. METHODS RNA sequencing was performed on mucosal tissues from HSCR patients (n = 6) and controls (n = 3). Function of matched ganglionic and aganglionic regions were investigated utilizing organoids generated from these tissues. RESULTS Transcriptional differences observed in ganglionic and aganglionic regions of HSCR patients included upregulation of genes involving inflammation, cell differentiation and proliferation as well as decreased expression of genes encoding mucins compared to controls. Organoids derived from ganglionic and aganglionic regions of HSCR patients were similar in epithelial cell differentiation, epithelial barrier formation and response to stimulation with bacterial metabolites and pro-inflammatory cytokines. CONCLUSIONS Despite normal ganglionic structure, the section of colon adjacent to the aganglionic region in HSCR patients has perturbed gene expression which resembles the aganglionic segment. Transcriptional and functional changes in colonic epithelium are persevered in the ganglionic colon used for pull-through surgery. This may explain persistence of enterocolitis despite surgical excision of aganglionic colon and subsequent endorectal pull-through performed with ganglionic colon during correction of HSCR. LEVEL OF EVIDENCE N/A.
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Affiliation(s)
- Dimitra M Lotakis
- University of Michigan, Department of Surgery, Division of Pediatric Surgery, 1540 East Hospital Drive, Ann Arbor, MI, 48109-4211, USA.
| | - Rishu Dheer
- University of Michigan, Department of Internal Medicine, Division of Infectious Disease, Ann Arbor, MI, 48109, USA
| | - Michael K Dame
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA
| | - Ashley J Cuttitta
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA
| | - Dominic J Tigani
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA
| | - Jason R Spence
- University of Michigan, Department of Internal Medicine, Division of Gastroenterology, Ann Arbor, MI, 48109, USA; University of Michigan Medical School, Department of Cell and Developmental Biology, Ann Arbor, MI, 48109, USA; University of Michigan Medical School, Department of Biomedical Engineering Medicine, Ann Arbor, MI, 48109, USA
| | - Vincent B Young
- University of Michigan, Department of Internal Medicine, Division of Infectious Disease, Ann Arbor, MI, 48109, USA; University of Michigan, Department of Microbiology & Immunology, Ann Arbor, MI, 48109, USA
| | - Matthew W Ralls
- University of Michigan, Department of Surgery, Division of Pediatric Surgery, 1540 East Hospital Drive, Ann Arbor, MI, 48109-4211, USA
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10
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Berinstein JA, Steiner CA, Rifkin S, Alexander Perry D, Micic D, Shirley D, Higgins PDR, Young VB, Lee A, Rao K. A Predictive Model to Identify Complicated Clostridiodes difficile Infection. Open Forum Infect Dis 2023; 10:ofad049. [PMID: 36820317 PMCID: PMC9938520 DOI: 10.1093/ofid/ofad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Background Clostridioides difficile infection (CDI) is a leading cause of health care-associated infection and may result in organ dysfunction, colectomy, and death. Published risk scores to predict severe complications from CDI demonstrate poor performance upon external validation. We hypothesized that building and validating a model using geographically and temporally distinct cohorts would more accurately predict risk for complications from CDI. Methods We conducted a multicenter retrospective cohort study of adults diagnosed with CDI. After randomly partitioning the data into training and validation sets, we developed and compared 3 machine learning algorithms (lasso regression, random forest, stacked ensemble) with 10-fold cross-validation to predict disease-related complications (intensive care unit admission, colectomy, or death attributable to CDI) within 30 days of diagnosis. Model performance was assessed using the area under the receiver operating curve (AUC). Results A total of 3646 patients with CDI were included, of whom 217 (6%) had complications. All 3 models performed well (AUC, 0.88-0.89). Variables of importance were similar across models, including albumin, bicarbonate, change in creatinine, non-CDI-related intensive care unit admission, and concomitant non-CDI antibiotics. Sensitivity analyses indicated that model performance was robust even when varying derivation cohort inclusion and CDI testing approach. However, race was an important modifier, with models showing worse performance in non-White patients. Conclusions Using a large heterogeneous population of patients, we developed and validated a prediction model that estimates risk for complications from CDI with good accuracy. Future studies should aim to reduce the disparity in model accuracy between White and non-White patients and to improve performance overall.
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Affiliation(s)
| | | | | | - D Alexander Perry
- Division of Infectious Diseases, University of Arizona, Tucson, Arizona, USA
| | - Dejan Micic
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois, USA
| | - Daniel Shirley
- Division of Infectious Diseases, University of Wisconsin, Madison, Wisconsin, USA
| | - Peter D R Higgins
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Allen Lee
- Correspondence: Allen Lee, MD, MS, 3912 Taubman Center, 1500 E. Medical Center Drive, SPC 5362, Ann Arbor, MI 48109 (); or Krishna Rao, MD, MS, 1150 West Medical Center Drive, MSRB I, Room 1510B, Ann Arbor, MI, 48109 ()
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11
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Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. bioRxiv 2023:2023.01.12.523823. [PMID: 36711955 PMCID: PMC9882218 DOI: 10.1101/2023.01.12.523823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Clostridioides difficile (C. difficile) , a leading cause of nosocomial infection, produces toxins that damage the colonic epithelium and results in colitis that varies from mild to fulminant. Variation in disease severity is poorly understood and has been attributed to host factors (age, immune competence and intestinal microbiome composition) and/or virulence differences between C. difficile strains, with some, such as the epidemic BI/NAP1/027 (MLST1) strain, being associated with greater virulence. We tested 23 MLST1(ST1) C. difficile clinical isolates for virulence in antibiotic-treated C57BL/6 mice. All isolates encoded a complete Tcd pathogenicity locus and achieved similar colonization densities in mice. Disease severity varied, however, with 5 isolates causing lethal infections, 16 isolates causing a range of moderate infections and 2 isolates resulting in no detectable disease. The avirulent ST1 isolates did not cause disease in highly susceptible Myd88 -/- or germ-free mice. Genomic analysis of the avirulent isolates revealed a 69 base-pair deletion in the N-terminus of the cdtR gene, which encodes a response regulator for binary toxin (CDT) expression. Genetic deletion of the 69 base-pair cdtR sequence in the highly virulent ST1 R20291 C. difficile strain rendered it avirulent and reduced toxin gene transcription in cecal contents. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile strain without reducing colonization and persistence in the gut. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.
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Affiliation(s)
- Qiwen Dong
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Julian R. Garneau
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jonathan K. Sia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Rita C. Smith
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Tracy McMillen
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rosemary L. Pope
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - Carolyn Metcalfe
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Claire Kohout
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | | | - Evan S Snitkin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Eric G. Pamer
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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12
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Abstract
INTRODUCTION The gut microbiome is implicated in Clostridioides difficile infection (CDI) and recurrent CDI (rCDI). AREAS COVERED This review covers the mechanisms by which microbiome therapeutics treat rCDI, their efficacy and safety, and clinical trial design considerations for future research. EXPERT OPINION Altering the chemical environment of the gut and reconstituting colonization resistance is a promising strategy for preventing and treating rCDI. Fecal microbiota transplant (FMT) is safe and effective for the treatment of rCDI. However, limitations of FMT have prompted investigation into alternative microbiome therapeutics. These alternative microbiome therapies require further evaluation, and adaptive trial designs should be strongly considered to more rapidly discern variables including the need for bowel preparation, timing and selection of pre-treatment antibiotics, and dose and duration of microbiome therapeutics. A broad range of adverse events must be prospectively evaluated in these controlled trials, as microbiome therapeutics have the potential for numerous effects. Future studies will lead to a greater understanding of the mechanisms by which microbiome therapies can break the cycle of rCDI, which should ultimately yield a personalized approach to rCDI treatment that restores an individual's specific deficit(s) in colonization resistance to C. difficile.
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Affiliation(s)
- Patricia P Bloom
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, USA.,Department of Microbiology and Immunology, University of Michigan, USA
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13
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Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. Microbiome 2022; 10:206. [PMID: 36457108 PMCID: PMC9716758 DOI: 10.1186/s40168-022-01412-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA.
| | - Alexander G McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Ryan A Blaustein
- Department of Nutrition and Food Science, University of Maryland, College Park, USA
| | - Laura J Rose
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
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14
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Azcutia V, Kelm M, Kim S, Luissint AC, Flemming S, Abernathy-Close L, Young VB, Nusrat A, Miller MJ, Parkos CA. Distinct stimulus-dependent neutrophil dynamics revealed by real-time imaging of intestinal mucosa after acute injury. PNAS Nexus 2022; 1:pgac249. [PMID: 36712325 PMCID: PMC9802210 DOI: 10.1093/pnasnexus/pgac249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Clinical symptoms in many inflammatory diseases of the intestine are directly related to neutrophil (PMN) migration across colonic mucosa and into the intestinal lumen, yet in-vivo studies detailing this process are lacking. Using real-time intravital microscopy and a new distal colon loop model, we report distinct PMN migratory dynamics in response to several models of acute colonic injury. PMNs exhibited rapid swarming responses after mechanically induced intestinal wounds. Similar numbers of PMNs infiltrated colonic mucosa after wounding in germ-free mice, suggesting microbiota-independent mechanisms. By contrast, acute mucosal injury secondary to either a treatment of mice with dextran sodium sulfate or an IL-10 receptor blockade model of colitis resulted in lamina propria infiltration with PMNs that were largely immotile. Biopsy wounding of colonic mucosa in DSS-treated mice did not result in enhanced PMN swarming however, intraluminal application of the neutrophil chemoattractant LTB4 under such conditions resulted in enhanced transepithelial migration of PMNs. Analyses of PMNs that had migrated into the colonic lumen revealed that the majority of PMNs were directly recruited from the circulation and not from the immotile pool in the mucosa. Decreased PMN motility parallels upregulation of the receptor CXCR4 and apoptosis. Similarly, increased expression of CXCR4 on human PMNs was observed in colonic biopsies from people with active ulcerative colitis. This new approach adds an important tool to investigate mechanisms regulating PMN migration across mucosa within the distal intestine and will provide new insights for developing future anti-inflammatory and pro-repair therapies.
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Affiliation(s)
- Veronica Azcutia
- Department of Pathology, University of Michigan; Ann Arbor, MI 48109, USA
| | - Matthias Kelm
- Department of Pathology, University of Michigan; Ann Arbor, MI 48109, USA
| | - Seonyoung Kim
- Department of Internal Medicine, Washington University School of Medicine; Saint Louis, MO 63110, USA
| | | | - Sven Flemming
- Department of Pathology, University of Michigan; Ann Arbor, MI 48109, USA
| | - Lisa Abernathy-Close
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan; Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan; Ann Arbor, MI 48109, USA.,Department of Microbiology and Immunology, University of Michigan; Ann Arbor, MI 48109, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan; Ann Arbor, MI 48109, USA
| | - Mark J Miller
- Department of Internal Medicine, Washington University School of Medicine; Saint Louis, MO 63110, USA
| | - Charles A Parkos
- Department of Pathology, University of Michigan; Ann Arbor, MI 48109, USA
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15
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Lawrence ALE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Sule GJ, Knight JS, Wobus CE, Spence JR, Young VB, O’Riordan MX, Abuaita BH. Human neutrophil IL1β directs intestinal epithelial cell extrusion during Salmonella infection. PLoS Pathog 2022; 18:e1010855. [PMID: 36191054 PMCID: PMC9578578 DOI: 10.1371/journal.ppat.1010855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/18/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Infection of the human gut by Salmonella enterica Typhimurium (STM) results in a localized inflammatory disease that is not mimicked in murine infections. To determine mechanisms by which neutrophils, as early responders to bacterial challenge, direct inflammatory programming of human intestinal epithelium, we established a multi-component human intestinal organoid (HIO) model of STM infection. HIOs were micro-injected with STM and seeded with primary human polymorphonuclear leukocytes (PMN-HIOs). PMNs did not significantly alter luminal colonization of Salmonella, but their presence reduced intraepithelial bacterial burden. Adding PMNs to infected HIOs resulted in substantial accumulation of shed TUNEL+ epithelial cells that was driven by PMN Caspase-1 activity. Inhibition of Caspases-1, -3 or -4 abrogated epithelial cell death and extrusion in the infected PMN-HIOs but only Caspase-1 inhibition significantly increased bacterial burden in the PMN-HIO epithelium. Thus, PMNs promote cell death in human intestinal epithelial cells through multiple caspases as a protective response to infection. IL-1β was necessary and sufficient to induce cell shedding in the infected HIOs. These data support a critical innate immune function for human neutrophils in amplifying cell death and extrusion of human epithelial cells from the Salmonella-infected intestinal monolayer. Neutrophils are early responders to Salmonella intestinal infection, but how they influence infection progression and outcome is unknown. Here we use a co-culture model of human intestinal organoids and human primary neutrophils to study the contribution of human neutrophils to Salmonella infection of the intestinal epithelium. We found that neutrophils markedly enhanced epithelial defenses, including enhancing cell extrusion to reduce intraepithelial burden of Salmonella and close association with the epithelium. These findings reveal an early role for neutrophils in the gut in shaping the gut environment to control epithelial infection.
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Affiliation(s)
- Anna-Lisa E. Lawrence
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan P. Berger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Veda K. Yadagiri
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brooke Bons
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Courtney Fields
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Gautam J. Sule
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason S. Knight
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Vincent B. Young
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (MXO); (BHA)
| | - Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (MXO); (BHA)
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16
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Abstract
Clostridioides difficile (formerly Clostridium difficile) infection is a substantial health and economic burden worldwide. Great strides have been made over the past several years in characterizing the physiology of C. difficile infection, particularly regarding how gut microorganisms and their host work together to provide colonization resistance. As mammalian hosts and their indigenous gut microbiota have co-evolved, they have formed a complex yet stable relationship that prevents invading microorganisms from establishing themselves. In this Review, we discuss the latest advances in our understanding of C. difficile physiology that have contributed to its success as a pathogen, including its versatile survival factors and ability to adapt to unique niches. Using discoveries regarding microorganism-host and microorganism-microorganism interactions that constitute colonization resistance, we place C. difficile within the fiercely competitive gut environment. A comprehensive understanding of these relationships is required to continue the development of precision medicine-based treatments for C. difficile infection.
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Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
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17
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Abstract
The gastrointestinal ecosystem is formed from interactions between the host, indigenous gut microbiota, and external world. When colonizing the gut, bacteria must overcome barriers imposed by the intestinal environment, such as host immune responses and microbiota-mediated nutrient limitation. Thus, understanding bacterial colonization requires determining how the gut landscape interacts with microbes attempting to establish within the ecosystem. However, the complicated network of interactions between elements of the intestinal environment makes it challenging to uncover emergent properties of the system using only reductionist methods. A systems biology approach, which aims to investigate complex systems by examining the behavior and relationships of all elements of the system, may afford a more holistic perspective of the colonization process. Here, we examine the confluence between the gut landscape and bacterial colonization through the lens of systems biology. We offer an overview of the conceptual and methodological underpinnings of systems biology, followed by a discussion of key elements of the gut ecosystem as they pertain to bacterial establishment and growth. We conclude by reintegrating these elements to guide future comprehensive investigations of the ecosystem in the context of bacterial intestinal colonization.
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Affiliation(s)
- Madeline R. Barron
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
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18
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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19
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Ginga NJ, Slyman R, Kim GA, Parigoris E, Huang S, Yadagiri VK, Young VB, Spence JR, Takayama S. Perfusion System for Modification of Luminal Contents of Human Intestinal Organoids and Realtime Imaging Analysis of Microbial Populations. Micromachines (Basel) 2022; 13:131. [PMID: 35056297 PMCID: PMC8779378 DOI: 10.3390/mi13010131] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023]
Abstract
Intestinal organoids are 3D cell structures that replicate some aspects of organ function and are organized with a polarized epithelium facing a central lumen. To enable more applications, new technologies are needed to access the luminal cavity and apical cell surface of organoids. We developed a perfusion system utilizing a double-barrel glass capillary with a pressure-based pump to access and modify the luminal contents of a human intestinal organoid for extended periods of time while applying cyclic cellular strain. Cyclic injection and withdrawal of fluorescent FITC-Dextran coupled with real-time measurement of fluorescence intensity showed discrete changes of intensity correlating with perfusion cycles. The perfusion system was also used to modify the lumen of organoids injected with GFP-expressing E. coli. Due to the low concentration and fluorescence of the E. coli, a novel imaging analysis method utilizing bacteria enumeration and image flattening was developed to monitor E. coli within the organoid. Collectively, this work shows that a double-barrel perfusion system provides constant luminal access and allows regulation of luminal contents and luminal mixing.
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Affiliation(s)
- Nicholas J. Ginga
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Raleigh Slyman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ge-Ah Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Eric Parigoris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sha Huang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (J.R.S.)
| | - Veda K. Yadagiri
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (V.K.Y.); (V.B.Y.)
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (V.K.Y.); (V.B.Y.)
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.H.); (J.R.S.)
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA 30332, USA; (N.J.G.); (R.S.); (G.-A.K.); (E.P.)
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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20
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Ötleş E, Oh J, Patel A, Keidan M, Young VB, Rao K, Wiens J. 17. Comparative Assessment of a Machine Learning Model and Rectal Swab Surveillance to Predict Hospital Onset Clostridioides difficile. Open Forum Infect Dis 2021. [PMCID: PMC8644772 DOI: 10.1093/ofid/ofab466.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Hospital onset Clostridioides difficile infection (HO-CDI) is associated with significant morbidity and mortality. Screening individuals at risk could help limit transmission, however swab-based surveillance for HO-CDI is resource intensive. Applied to electronic health records (EHR) data, machine learning (ML) models present an efficient approach to assess patient risk. We compare the effectiveness of swab surveillance against daily risk estimates produced by a ML model in detecting patients who will develop HO-CDI.
Methods
Patients presenting to Michigan Medicine’s ICUs and oncology wards between June 6th and October 8th 2020 had rectal swabs collected on admission, weekly, and at discharge from the unit, as part of VRE surveillance. We performed anaerobic culture on the residual media followed by a custom, multiplex PCR on isolates to identify toxigenic C. difficile. Risk of HO-CDI was calculated daily for each patient using a previously validated EHR-based ML model. Swab results and model risk scores were aggregated for each admission and assessed as predictors of HO-CDI. Holding sensitivity equal, we evaluated both approaches in terms of accuracy, specificity, and positive predictive value (PPV).
Results
Of 2,044 admissions representing 1,859 patients, 39 (1.9%) developed HO-CDI. 23.1% (95% CI: 11.1–37.8%) of HO-CDI cases had at least one positive swab. At this sensitivity, model performance was significantly better than random but worse compared to swab surveillance—accuracy: 87.5% (86.0–88.9%) vs. 94.3% (93.3–95.3%), specificity: 88.7% (87.3–90.0%) vs. 95.7% (94.8–96.6%), PPV: 3.8% (1.6–6.4%) vs. 9.4% (4.3–16.1%). Combining swab AND model yielded lower sensitivity 2.6% (0.0–8.9%) compared to combining swab OR model at 43.6% (27.3–60.0%), and yielded PPV 7.1% (0.0–25.0%) vs. 43.6% (27.3–60.0%) respectively (Figure 1).
Figure 1. Surveillance & risk score performance.
Binary classification performance metrics of ML model (Model), toxigenic C. difficile rectal swab surveillance (Swab), and combination approaches (Model AND Swab and Model OR Swab), reported in terms of percentage points. Bold numbers highlight the best performing approach for a given performance metric. The combined approach of monitoring the Model AND Swab yielded the highest accuracy 97.5% (95% confidence interval: 96.8%, 98.1%), it also had the highest specificity 99.4% (99.0%, 99.7%). The combined approach of monitoring the Model OR Swab yielded the highest sensitivity 43.6% (27.3%, 60.0%) and negative predictive value (NPV) 98.7% (98.2, 99.2%). Using the Swab alone yielded the highest PPV 9.4% (4.3%, 16.1%) and F1 score 13.3% (6.2%, 21.8%). These results highlight the complementarity of the model and swab-based approaches.
Conclusion
Compared to swab surveillance using a ML model for predicting HO-CDI results in more false positives. The ML model provides daily risk scores and can be deployed using different thresholds. Thus, it can inform varied prevention strategies for different risk categories, without the need for resource intensive swabbing. Additionally, the approaches may be complimentary as the patients with HO-CDI identified by each approach differ.
Disclosures
Vincent B. Young, MD, PhD, American Society for Microbiology (Other Financial or Material Support, Senior Editor for mSphere)Vedanta Biosciences (Consultant) Krishna Rao, MD, MS, Bio-K+ International, Inc. (Consultant)Merck & Co., Inc. (Grant/Research Support)Roche Molecular Systems, Inc. (Consultant)Seres Therapeutics (Consultant)
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Affiliation(s)
| | - Jeeheh Oh
- University of Michigan, Ann Arbor, Michigan
| | | | | | | | - Krishna Rao
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan, Ann Arbor, MI
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21
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Abstract
Hepatic encephalopathy (HE) is a complication of cirrhosis characterised by neuropsychiatric and motor dysfunction. Microbiota-host interactions play an important role in HE pathogenesis. Therapies targeting microbial community composition and function have been explored for the treatment of HE. Prebiotics, probiotics and faecal microbiota transplant (FMT) have been used with the aim of increasing the abundance of potentially beneficial taxa, while antibiotics have been used to decrease the abundance of potentially harmful taxa. Other microbiome therapeutics, including postbiotics and absorbents, have been used to target microbial products. Microbiome-targeted therapies for HE have had some success, notably lactulose and rifaximin, with probiotics and FMT also showing promise. However, there remain several challenges to the effective application of microbiome therapeutics in HE, including the resilience of the microbiome to sustainable change and unpredictable clinical outcomes from microbiota alterations. Future work in this space should focus on rigorous trial design, microbiome therapy selection, and a personalised approach to HE.
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Affiliation(s)
- Patricia P Bloom
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, USA.
| | - Elliot B Tapper
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, USA; Department of Microbiology and Immunology, University of Michigan, USA
| | - Anna S Lok
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, USA
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22
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Abuaita BH, Lawrence ALE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Wobus CE, Spence JR, Young VB, O’Riordan MX. Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids. PLoS Pathog 2021; 17:e1009987. [PMID: 34669717 PMCID: PMC8570492 DOI: 10.1371/journal.ppat.1009987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/05/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
Salmonella enterica represents over 2500 serovars associated with a wide-ranging spectrum of disease; from self-limiting gastroenteritis to invasive infections caused by non-typhoidal serovars (NTS) and typhoidal serovars, respectively. Host factors strongly influence infection outcome as malnourished or immunocompromised individuals can develop invasive infections from NTS, however, comparative analyses of serovar-specific host responses have been constrained by reliance on limited model systems. Here we used human intestinal organoids (HIOs), a three-dimensional “gut-like” in vitro system derived from human embryonic stem cells, to elucidate similarities and differences in host responses to NTS and typhoidal serovars. HIOs discriminated between the two most prevalent NTS, Salmonella enterica serovar Typhimurium (STM) and Salmonella enterica serovar Enteritidis (SE), and typhoidal serovar Salmonella enterica serovar Typhi (ST) in epithelial cell invasion, replication and transcriptional responses. Pro-inflammatory signaling and cytokine output was reduced in ST-infected HIOs compared to NTS infections, consistent with early stages of NTS and typhoidal diseases. While we predicted that ST would induce a distinct transcriptional profile from the NTS strains, more nuanced expression profiles emerged. Notably, pathways involved in cell cycle, metabolism and mitochondrial functions were downregulated in STM-infected HIOs and upregulated in SE-infected HIOs. These results correlated with suppression of cellular proliferation and induction of host cell death in STM-infected HIOs and in contrast, elevated levels of reactive oxygen species production in SE-infected HIOs. Collectively, these results suggest that the HIO model is well suited to reveal host transcriptional programming specific to infection by individual Salmonella serovars, and that individual NTS may provoke unique host epithelial responses during intestinal stages of infection. Salmonella enterica is the major causative agent of bacterial infections associated with contaminated food and water. Salmonella enterica consists of over 2500 serovars of which Typhimurium (STM), Enteritidis (SE) and Typhi (ST) are the three major serovars with medical relevance to humans. These serovars elicit distinctive immune responses and cause different diseases in humans, including self-limiting diarrhea, gastroenteritis and typhoid fever. Differences in the human host response to these serovars are likely to be a major contributing factor to distinct disease outcomes but are not well characterized, possibly due to the limitations of human-derived physiological infection models. Distinct from immortalized epithelial cell culture models, human intestinal organoids (HIOs) are three-dimensional structures derived from embryonic stem cells that differentiate into intestinal mesenchymal and epithelial cells, mirroring key organizational aspects of the intestine. In this study, we used HIOs to monitor transcriptional changes during early stages of STM, SE and ST infection. Our comparative analysis showed that HIO inflammatory responses are the dominant response in all infections, but ST infection induces the weakest upregulation of inflammatory mediators relative to the other serovars. In addition, we identified several cellular processes, including cell cycle and mitochondrial functions, that were inversely regulated between STM and SE infection despite these serovars causing similar localized intestinal infection in humans. Our findings reinforce HIOs as an emerging model system to study Salmonella serovar infection and define global host transcriptional response profiles as a foundation for understanding human infection outcomes.
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Affiliation(s)
- Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Anna-Lisa E. Lawrence
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan P. Berger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Veda K. Yadagiri
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brooke Bons
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Courtney Fields
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Vincent B. Young
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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23
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Perry DA, Shirley D, Micic D, Patel CP, Putler R, Menon A, Young VB, Rao K. External Validation and Comparison of Clostridioides difficile Severity Scoring Systems. Clin Infect Dis 2021; 74:2028-2035. [PMID: 34459885 DOI: 10.1093/cid/ciab737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Many models have been developed to predict severe outcomes from Clostridioides difficile infection. These models are usually developed at a single institution and largely are not externally validated. This aim of this study was to validate previously published risk scores in a multicenter cohort of patients with CDI. METHODS Retrospective study on four separate inpatient cohorts with CDI from three distinct sites: The Universities of Michigan (2010-2012 and 2016), Chicago (2012), and Wisconsin (2012). The primary composite outcome was admission to an intensive care unit, colectomy, and/or death attributed to CDI within 30 days of positive testing. Both within each cohort and combined across all cohorts, published CDI severity scores were assessed and compared to each other and the IDSA guideline definitions of severe and fulminant CDI. RESULTS A total of 3,646 patients were included for analysis. Including the two IDSA guideline definitions, fourteen scores were assessed. Performance of scores varied within each cohort and in the combined set (mean area under the receiver operator characteristic curve(AUC 0.61, range 0.53-0.66). Only half of the scores had performance at or better than IDSA severe and fulminant definitions (AUCs 0.64 and 0.63, respectively). Most of the scoring systems had more false than true positives in the combined set (mean: 81.5%, range:0-91.5%). CONCLUSIONS No published CDI severity score showed stable, good predictive ability for adverse outcomes across multiple cohorts/institutions or in a combined multicenter cohort.
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Affiliation(s)
- D Alexander Perry
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, Ann Arbor, MI, USA
| | - Daniel Shirley
- Division of Infectious Disease, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Dejan Micic
- Department of Internal Medicine, Section of Gastroenterology, Hepatology and Nutrition, University of Chicago Medicine, Chicago, IL, USA
| | - C Pratish Patel
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rosemary Putler
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, Ann Arbor, MI, USA
| | - Anitha Menon
- University of Michigan Medical School, Ann Arbor, MI, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,Department of Microbiology and Immunology, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, Ann Arbor, MI, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, Ann Arbor, MI, USA
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24
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Miles-Jay A, Young VB, Pamer EG, Savidge TC, Kamboj M, Garey KW, Snitkin ES. A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains. Microb Genom 2021; 7. [PMID: 34180789 PMCID: PMC8461479 DOI: 10.1099/mgen.0.000590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Clostridioides difficile is the leading cause of healthcare-associated infectious diarrhoea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare environments, and that the primary sites of C. difficile transmission may be strain-dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs community spread for two of the most common C. difficile strains in the USA: sequence type (ST) 1 (associated with ribotype 027) and ST2 (associated with ribotype 014/020). We performed whole-genome sequencing and phylogenetic analyses on 382 ST1 and ST2 C. difficile isolates recovered from stool specimens collected during standard clinical care at 3 geographically distinct US medical centres between 2010 and 2017. ST1 and ST2 isolates both displayed some evidence of phylogenetic clustering by study site, but clustering was stronger and more apparent in ST1, consistent with our healthcare-based study more comprehensively sampling local transmission of ST1 compared to ST2 strains. Analyses of pairwise single-nucleotide variant (SNV) distance distributions were also consistent with more evidence of healthcare transmission of ST1 compared to ST2, with 44 % of ST1 isolates being within two SNVs of another isolate from the same geographical collection site compared to 5.5 % of ST2 isolates (P-value=<0.001). Conversely, ST2 isolates were more likely to have close genetic neighbours across disparate geographical sites compared to ST1 isolates, further supporting non-healthcare routes of spread for ST2 and highlighting the potential for misattributing genomic similarity among ST2 isolates to recent healthcare transmission. Finally, we estimated a lower evolutionary rate for the ST2 lineage compared to the ST1 lineage using Bayesian timed phylogenomic analyses, and hypothesize that this may contribute to observed differences in geographical concordance among closely related isolates. Together, these findings suggest that ST1 and ST2, while both common causes of C. difficile infection in hospitals, show differential reliance on community and hospital spread. This conclusion supports the need for strain-specific criteria for interpreting genomic linkages and emphasizes the importance of considering differences in the epidemiology of circulating strains when devising interventions to reduce the burden of C. difficile infections.
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Affiliation(s)
| | | | - Eric G Pamer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,The University of Chicago, Chicago, IL, USA
| | | | - Mini Kamboj
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, TX, USA
| | - Evan S Snitkin
- University of Michigan Medical School, Ann Arbor, MI, USA
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25
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Ranallo RT, McDonald LC, Halpin AL, Hiltke T, Young VB. The State of Microbiome Science at the Intersection of Infectious Diseases and Antimicrobial Resistance. J Infect Dis 2021; 223:S187-S193. [PMID: 33667294 PMCID: PMC8206797 DOI: 10.1093/infdis/jiab020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Along with the rise in modern chronic diseases, ranging from diabetes to asthma, there are challenges posed by increasing antibiotic resistance, which results in difficult-to-treat infections, as well as sepsis. An emerging and unifying theme in the pathogenesis of these diverse public health threats is changes in the microbial communities that inhabit multiple body sites. Although there is great promise in exploring the role of these microbial communities in chronic disease pathogenesis, the shorter timeframe of most infectious disease pathogenesis may allow early translation of our basic scientific understanding of microbial ecology and host-microbiota-pathogen interactions. Likely translation avenues include development of preventive strategies, diagnostics, and therapeutics. For example, as basic research related to microbial pathogenesis continues to progress, Clostridioides difficile infection is already being addressed clinically through at least 2 of these 3 avenues: targeted antibiotic stewardship and treatment of recurrent disease through fecal microbiota transplantation.
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Affiliation(s)
- Ryan T Ranallo
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - L Clifford McDonald
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas Hiltke
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, Michigan, USA
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26
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Vornhagen J, Bassis CM, Ramakrishnan S, Hein R, Mason S, Bergman Y, Sunshine N, Fan Y, Holmes CL, Timp W, Schatz MC, Young VB, Simner PJ, Bachman MA. A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor. PLoS Pathog 2021; 17:e1009537. [PMID: 33930099 PMCID: PMC8115787 DOI: 10.1371/journal.ppat.1009537] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/12/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Klebsiella pneumoniae (Kp) is an important cause of healthcare-associated infections, which increases patient morbidity, mortality, and hospitalization costs. Gut colonization by Kp is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. Our previous comparative genomics study, between disease-causing and asymptomatically colonizing Kp isolates, identified a plasmid-encoded tellurite (TeO3-2)-resistance (ter) operon as strongly associated with infection. However, TeO3-2 is extremely rare and toxic to humans. Thus, we used a multidisciplinary approach to determine the biological link between ter and Kp infection. First, we used a genomic and bioinformatic approach to extensively characterize Kp plasmids encoding the ter locus. These plasmids displayed substantial variation in plasmid incompatibility type and gene content. Moreover, the ter operon was genetically independent of other plasmid-encoded virulence and antibiotic resistance loci, both in our original patient cohort and in a large set (n = 88) of publicly available ter operon-encoding Kp plasmids, indicating that the ter operon is likely playing a direct, but yet undescribed role in Kp disease. Next, we employed multiple mouse models of infection and colonization to show that 1) the ter operon is dispensable during bacteremia, 2) the ter operon enhances fitness in the gut, 3) this phenotype is dependent on the colony of origin of mice, and 4) antibiotic disruption of the gut microbiota eliminates the requirement for ter. Furthermore, using 16S rRNA gene sequencing, we show that the ter operon enhances Kp fitness in the gut in the presence of specific indigenous microbiota, including those predicted to produce short chain fatty acids. Finally, administration of exogenous short-chain fatty acids in our mouse model of colonization was sufficient to reduce fitness of a ter mutant. These findings indicate that the ter operon, strongly associated with human infection, encodes factors that resist stress induced by the indigenous gut microbiota during colonization. This work represents a substantial advancement in our molecular understanding of Kp pathogenesis and gut colonization, directly relevant to Kp disease in healthcare settings.
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Affiliation(s)
- Jay Vornhagen
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
| | - Christine M. Bassis
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan, Ann Arbor, MI, United States of America
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert Hein
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan, Ann Arbor, MI, United States of America
| | - Sophia Mason
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Yehudit Bergman
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Nicole Sunshine
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Yunfan Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Caitlyn L. Holmes
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States of America
- Simons Center for Quantitative Biology, Cold Spring Harbor, NY, United States of America
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan, Ann Arbor, MI, United States of America
| | - Patricia J. Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Michael A. Bachman
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, United States of America
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27
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Shen J, McFarland AG, Young VB, Hayden MK, Hartmann EM. Toward Accurate and Robust Environmental Surveillance Using Metagenomics. Front Genet 2021; 12:600111. [PMID: 33747038 PMCID: PMC7973286 DOI: 10.3389/fgene.2021.600111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/21/2021] [Indexed: 01/23/2023] Open
Abstract
Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mary K. Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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28
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Gilbert J, Leslie J, Putler R, Weiner S, Standke A, Penkevich A, Keidan M, Young VB, Rao K. Anti-toxin antibody is not associated with recurrent Clostridium difficile infection. Anaerobe 2021; 67:102299. [PMID: 33227427 PMCID: PMC8094835 DOI: 10.1016/j.anaerobe.2020.102299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/23/2020] [Accepted: 11/16/2020] [Indexed: 02/08/2023]
Abstract
Clostridium difficile infection (CDI) recurs in ∼20% of patients. Prior studies indicated that antibody responses directed against the C. difficile toxins A and B were potentially associated with lower risk of recurrent CDI. Here we tested the hypothesis that circulating anti-toxin IgG antibody levels associate with reduced risk of recurrent CDI. A cohort study with prospective enrollment and retrospective data abstraction examined antibody levels in 275 adult patients at the University of Michigan with CDI. We developed an enzyme linked immunosorbent assay to detect IgG antibodies against toxin A and toxin B in sera obtained at the time of diagnosis. Logistic regression examined the relationship between antibody levels and recurrence, and sensitivity tests evaluated for follow-up and survivor biases, history of CDI, and PCR ribotype. Follow-up data were available for 174 subjects, of whom 36 (20.7%) had recurrence. Comparing antibody levels vs. recurrence and CDI history, anti-toxin A levels were similar, while anti-toxin B levels had a greater range of values. In unadjusted analysis, detection of anti-toxin A antibodies, but not anti-toxin B antibodies, associated with an increased risk of recurrence (OR 2.71 [1.06, 8.37], P = .053). Adjusting for confounders weakened this association. The results were the same in sensitivity analyses. We observed a borderline increased risk of recurrence in patients positive for anti-toxin A antibodies, and sensitivity analyses showed this was not simply a reflection of prior exposure status. Future studies are needed to assess how neutralizing antibody or levels after treatment associate with recurrence.
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Affiliation(s)
| | | | - Rose Putler
- Department of Microbiology and Immunology, USA
| | - Shayna Weiner
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Standke
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Aline Penkevich
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Micah Keidan
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, USA; Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.
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Blaser MJ, Devkota S, McCoy KD, Relman DA, Yassour M, Young VB. Lessons learned from the prenatal microbiome controversy. Microbiome 2021; 9:8. [PMID: 33436098 PMCID: PMC7805060 DOI: 10.1186/s40168-020-00946-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 05/24/2023]
Abstract
For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid, meconium, and even fetal tissues have challenged the dogma of a sterile womb, and additional reports have emerged that used culture, microscopy, and quantitative PCR to support the presence of a low-biomass microbial community at prenatal sites. Given the substantial implications of prenatal exposure to microbes for the development and health of the host, the findings have gathered substantial interest from academics, high impact journals, the public press, and funding agencies. However, an increasing number of studies have challenged the prenatal microbiome identifying contamination as a major issue, and scientists that remained skeptical have pointed to inconsistencies with in utero colonization, the impact of c-sections on early microbiome assembly, and the ability to generate germ-free mammals. A lively academic controversy has emerged on the existence of the wider importance of prenatal microbial communities. Microbiome has asked experts to discuss these issues and provide their thoughts on the implications. To allow for a broader perspective of this discussion, we have specifically selected scientists, who have a long-standing expertise in microbiome sciences but who have not directly been involved in the debate so far.
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Affiliation(s)
- Martin J Blaser
- Departments of Medicine and Pathology and Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, USA.
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.
- Department of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, USA.
| | - Kathy D McCoy
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
| | - David A Relman
- Departments of Medicine, and of Microbiology & Immunology, Stanford University, Stanford, USA.
- Section of Infectious Diseases, Veterans Affairs Palo Alto Health Care System, Palo Alto, USA.
- Chan Zuckerberg Biohub Microbiome Initiative, San Francisco, California, USA.
| | - Moran Yassour
- Microbiology and Molecular Genetics Department, Faculty of Medicine, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, Department of Microbiology & Immunology, The University of Michigan, Ann Arbor, USA.
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Abstract
PURPOSE OF REVIEW In this review, we will summarize the recent progress made in generating stem-cell-based organoid and enteroid models of the gastrointestinal tract and their importance in understanding the role of microbes in intestinal epithelial homeostasis and disease. RECENT FINDING Intestinal stem-cell-derived culture systems are self-organizing three-dimensional organotypic cultures that recapitulate many cellular, architectural and functional aspects of the human intestine. Progress has been made in the development of methods to incorporate additional cell lineages and physiological cues to better mimic the complexity of the intestine. Current model systems have facilitated both the study of gastrointestinal infections and interactions with normally nonpathogenic microbial residents of the gastrointestinal tract. These studies have illustrated how live microbes, or their metabolites, ligands and virulence factors influence epithelial cell differentiation, maintenance, repair, function and intestine development. SUMMARY Organotypic models are invaluable tools for studying host-microbe interactions that complement in-vivo experimental model systems. These models have evolved in terms of complexity and fidelity. The stem-cell-based models are already at forefront for studying host-microbe interactions and with continued development, the future looks even more promising.
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Affiliation(s)
- Rishu Dheer
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA 48109
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA 48109
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Sansom S, Lin MY, Schoeny M, Fukuda C, Bassis C, Shimasaki T, Dangana TE, Moore NM, Yelin R, Liu S, Young VB, Rhee Y, Tabith L, Sheng J, Cisneros EC, Murray J, Chang K, Lolans K, Ariston M, Rotunno W, Ramos H, Li H, Aboushaala K, Iwai N, Hayden MK. 919. Understanding Intermittent Detection of Multidrug-Resistant Organisms (MDROs) in Rectally Colonized Patients. Open Forum Infect Dis 2020. [PMCID: PMC7777592 DOI: 10.1093/ofid/ofaa439.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background MDRO detection in colonized patients may be intermittent for reasons that are incompletely understood. We examined temporal patterns of gut MDRO colonization after initial MDRO detection by rectal swab screening, and determined the relationship of culture positivity to the relative abundance of corresponding MDRO operational taxonomic units (OTUs) identified by 16S rRNA gene sequence analysis. Methods Rectal or fecal swabs were collected daily from MICU patients 1/11/2017-1/11/2018. First MICU admissions with ≥2 swabs and MICU stays ≥3 days were studied. Samples were cultured for vancomycin-resistant enterococci (VRE), carbapenem-resistant Enterobacteriaceae (CRE) and P. aeruginosa (CRPA), and extended-spectrum β-lactamase-producing (ESBL) Enterobacteriaceae by selective media. Resistance mechanisms were confirmed by phenotypic methods and/or PCR. Limit of detection was similar for different MDROs (24-52 CFU/sample). OTU categories corresponding to MDRO species were identified by taxonomy and BLAST. Multilevel regression models estimated the association between MDRO detection and relative abundance of the corresponding OTU. Results 796 unique patients with 3519 swabs were studied. Median (IQR) age was 64 (51-74) years, MICU length of stay was 5 (3-8) days, and number of samples-per-patient was 3 (2-5). Following initial MDRO detection, the probability of subsequent detection varied by MDRO type, and was highest for VRE and lowest for CRPA [Figure 1]. Within each sample, we found a significant association between MDRO detection and relative abundance of the corresponding OTU [Table 1]. In contrast, relative OTU abundance in the first sample with MDRO detection was not predictive of odds of future MDRO detection (p >0.05 for all comparisons). Carriage of >1 MDRO did not affect the odds of MDRO detection in later samples. Figure 1. Probability of Subsequent MDRO Detection after First Positive Varies by MDRO Type ![]()
Table 1. Higher Mean Corresponding OTU Relative Abundance Within Each Sample is Associated with MDRO Detection ![]()
Conclusion MDRO culture positivity in rectally colonized patients was correlated with relative abundance of the corresponding OTU in the same sample. Serial detection of different MDRO types was variable, possibly due to distinct microbial community dynamics of different MDRO types. Intermittent failure to detect MDROs could result in misattribution of MDRO acquisition, resulting in inappropriate investigation or intervention. Disclosures All Authors: No reported disclosures
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sophia Liu
- University of Michigan-Ann Arbor, Ann Arbor, Michigan
| | | | - Yoona Rhee
- Rush University Medical Center, Berwyn, IL
| | | | | | | | | | - Kyle Chang
- Rush University Medical Center, Berwyn, IL
| | | | | | | | | | - Haiying Li
- Rush University Medical Center, Berwyn, IL
| | | | - Naomi Iwai
- Rush University Medical Center, Berwyn, IL
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Tan JY, Wang S, Dick GJ, Young VB, Sherman DH, Burns MA, Lin XN. Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. Integr Biol (Camb) 2020; 12:263-274. [PMID: 33089329 PMCID: PMC7671993 DOI: 10.1093/intbio/zyaa021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/05/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
While the 'unculturable' majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial 'dark matter' with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.
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Affiliation(s)
- James Y Tan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sida Wang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Deparment of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Infectious Diseases Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - David H Sherman
- Deparment of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Mark A Burns
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoxia N Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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Ransom EM, Burnham CAD, Jones L, Kraft CS, McDonald LC, Reinink AR, Young VB. Fecal Microbiota Transplantations: Where Are We, Where Are We Going, and What Is the Role of the Clinical Laboratory? Clin Chem 2020; 66:512-517. [PMID: 32232453 DOI: 10.1093/clinchem/hvaa021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 01/13/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Eric M Ransom
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Lee Jones
- President and CEO, Rebiotix, A Ferring Company, Roseville, MN
| | - Colleen S Kraft
- Associate Professor, Department of Pathology and Laboratory Medicine, Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA
| | - L Clifford McDonald
- Associate Director for Science, Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA
| | - Andrew R Reinink
- Assistant Professor, Minneapolis VA Medical Center and University of Minnesota School of Medicine, Division of Gastroenterology, Hepatology, & Nutrition, Minneapolis, MN
| | - Vincent B Young
- Professor, Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI
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Menon A, Perry DA, Motyka J, Weiner S, Standke A, Penkevich A, Keidan M, Young VB, Rao K. Changes in the Association between Diagnostic Testing Method, PCR Ribotype, and Clinical Outcomes from Clostridioides difficile Infection: One Institution's Experience. Clin Infect Dis 2020; 73:e2883-e2889. [PMID: 32930705 DOI: 10.1093/cid/ciaa1395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In patients with Clostridioides difficile infection (CDI), the relationship between clinical, microbial, and temporal/epidemiological trends relate and disease severity and adverse outcomes is incompletely understood. Here, in a follow-up to our study conducted in 2010-2013, we evaluate stool toxin levels and C. difficile PCR ribotypes. We hypothesized that elevated stool toxins and infection with ribotype 027 associate with severe disease and adverse outcomes. METHODS In a cohort of 565 subjects at the University of Michigan with CDI diagnosed by positive testing for toxins A/B by EIA or PCR for the tcdB gene, we quantified stool toxin levels via a modified cell cytotoxicity assay, isolated C. difficile by anaerobic culture, and performed PCR ribotyping. Severe CDI was defined by IDSA criteria, and primary outcomes were all-cause 30-day mortality and a composite of colectomy, ICU admission, and/or death attributable to CDI within 30 days. Analyses included bivariable tests and adjusted logistic regression. RESULTS 199 samples were diagnosed by EIA and 447 were diagnosed by PCR. Toxin positivity associated with IDSA severity, but not primary outcomes. In 2016, compared to 2010-2013, ribotype 106 newly emerged, accounting for 10.6% of strains, ribotype 027 fell from 16.5% to 9.3%, and ribotype 014-027 remained stable at 18.9%. Ribotype 014-020 associated with IDSA severity and 30-day mortality (P=.001). CONCLUSION Toxin positivity by EIA and CCA associated with IDSA severity, but not with subsequent adverse outcomes. The molecular epidemiology of C. difficile has shifted, and this may have implications for the optimal diagnostic strategy for and clinical severity of CDI.
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Affiliation(s)
- Anitha Menon
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - D Alex Perry
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jonathan Motyka
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shayna Weiner
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alexandra Standke
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aline Penkevich
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Micah Keidan
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
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McKee KS, Carter KA, Bassis C, Young VB, Reed B, Harper DM, Ruffin MT, Bell JD. The vaginal microbiota, high-risk human papillomavirus infection, and cervical cytology: results from a population-based study. Gynecol Pelvic Med 2020; 3. [PMID: 35252846 PMCID: PMC8896808 DOI: 10.21037/gpm-20-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background: The relationship between the vaginal microbiota, high-risk human papillomavirus infection, and abnormal cervical cytology has not been well characterized. Our objective was to characterize the vaginal microbiota in a stratified random sample of women from a population-based study in Appalachia. Methods: We analyzed a random sample of 308 women in the Community Access, Resources and Education: Project 3 study across 16 clinics in Ohio and West Virginia. Using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we characterized the vaginal microbiota among (I) 109 women randomly chosen with abnormal cervical cytology (i.e., the majority were atypical squamous cells of undetermined significance (n=55) and low-grade squamous intraepithelial lesions (n=45) while n=6 were high-grade squamous intraepithelial lesions and n=3 were atypical glandular cells); (II) 110 high-risk human papillomavirus infection only without cytologic abnormality; and (III) 89 women from a stratified random sample without cytologic abnormalities (negative for intraepithelial lesion or malignancy or any human papillomavirus infection). Among the women with abnormal cervical cytology (n=109), 80 had human papillomavirus infection, the majority of which were positive for a high-risk type (n=61). Results: Nearly all of the women were non-Hispanic White (94.5%), and the mean age was 26 (IQR=21–39) years. Women with abnormal cervical cytology or who were HPV+ were more likely to have a diverse vaginal microbiota characterized by higher Gardnerella vaginalis relative abundance, compared to women without cytologic abnormalities whose communities were more likely to be Lactobacillus spp. dominant (P<0.04). Women without cytologic abnormalities had a higher prevalence of L. iners dominated communities than women with abnormal cervical cytology and HR HPV+ respectively (P<0.04), and L. gasseri relative abundance was differentially greater among these women compared to women with abnormal cervical cytology or who were high-risk HPV+ (Linear discriminant analysis effect size =4.17; P=0.0009). After adjustment for age, white race, current smoking, and ≥2 male partners in the last year, however, we did not detect differences in the vaginal microbiota community states across the three outcome groups. Conclusions: Compared to women without cytologic abnormalities, the vaginal microbiota of women with abnormal cervical cytology or who were high-risk HPV+ were characterized by a diverse community with increased relative abundance of G. vaginalis and reduced relative abundance of L. gasseri. However, these differences were attenuated after adjustment for other factors. Further study and validation of these differences for prognostic use is warranted.
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Affiliation(s)
- Kimberly S. McKee
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kayla A. Carter
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Christine Bassis
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B. Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Barbara Reed
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Diane M. Harper
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mack T. Ruffin
- Department of Family and Community Medicine, Penn State Health, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Jason D. Bell
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
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Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG, Kuffa P, Goto Y, Jenq RR, Ishii C, Hirayama A, Seekatz AM, Martens EC, Eaton KA, Kao JY, Fukuda S, Higgins PDR, Karlsson NG, Young VB, Kamada N. Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nat Med 2020; 26:608-617. [PMID: 32066975 PMCID: PMC7160049 DOI: 10.1038/s41591-020-0764-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
Abstract
The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.
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Affiliation(s)
- Hiroko Nagao-Kitamoto
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jhansi L Leslie
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- The University of Virginia, Washington, VA, USA
| | - Sho Kitamoto
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chunsheng Jin
- Institute of Biomedicine, Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Kristina A Thomsson
- Institute of Biomedicine, Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Merritt G Gillilland
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Kuffa
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yoshiyuki Goto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
- Division of Mucosal Symbiosis, International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Robert R Jenq
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston TX, USA
| | - Chiharu Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Anna M Seekatz
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Clemson University, Columbia, SC, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Ebina, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Peter D R Higgins
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Niclas G Karlsson
- Institute of Biomedicine, Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Vincent B Young
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BJM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer 2020; 6:192-204. [PMID: 32101723 PMCID: PMC7098063 DOI: 10.1016/j.trecan.2020.01.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/29/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023]
Abstract
The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.
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Affiliation(s)
- Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph Skufca
- Department of Mathematics, Clarkson University, Potsdam, NY, USA
| | | | - Traci Testerman
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Alexander T Pearson
- Section of Hematology/Oncology, Department of Medicine, Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, IL, USA
| | - Paul Macklin
- Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Amir Mitchell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Lei Xie
- Hunter College, Department of Computer Science, New York, NY, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Nicole L Simone
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Heather H Gustafson
- Seattle Children's Research Institute, Ben Towne Center for Childhood Cancer Research, Seattle, WA, USA
| | - Daniel J Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - Marina R S Walther-Antonio
- Department of Surgery, Department of Obstetrics and Gynecology, and Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tal Korem
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Christian Jobin
- Departments of Medicine, Anatomy, and Cell Biology, and of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Y Koh
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | | | - Jennifer A Wargo
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Lee AA, Rao K, Limsrivilai J, Gillilland M, Malamet B, Briggs E, Young VB, Higgins PDR. Temporal Gut Microbial Changes Predict Recurrent Clostridiodes Difficile Infection in Patients With and Without Ulcerative Colitis. Inflamm Bowel Dis 2020; 26:1748-1758. [PMID: 31971239 PMCID: PMC7755141 DOI: 10.1093/ibd/izz335] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Ulcerative colitis (UC) carries an increased risk of primary and recurrent Clostridiodes difficile infection (rCDI), and CDI is associated with UC flares. We hypothesized that specific fecal microbial changes associate with UC flare and rCDI. METHODS We conducted a prospective observational cohort study of 57 patients with UC and CDI, CDI only, and UC only. Stool samples were collected at baseline, at the end of antibiotic therapy, and after reconstitution for 16S rRNA sequencing. The primary outcomes were recurrent UC flare and rCDI. Logistic regression and Lasso models were constructed for analysis. RESULTS There were 21 (45.7%) patients with rCDI, whereas 11 (34.4%) developed UC flare. Patients with rCDI demonstrated significant interindividual (P = 0.008) and intraindividual differences (P = 0.004) in community structure by Jensen-Shannon distance (JSD) compared with non-rCDI. Two cross-validated Lasso regression models predicted risk of rCDI: a baseline model with female gender, hospitalization for UC in the past year, increased Ruminococcaceae and Verrucomicrobia, and decreased Eubacteriaceae, Enterobacteriaceae, Lachnospiraceae, and Veillonellaceae (AuROC, 0.94); and a model 14 days after completion of antibiotics with female gender, increased Shannon diversity, Ruminococcaceae and Enterobacteriaceae, and decreased community richness and Faecalibacterium (AuROC, 0.9). Adding JSD between baseline and post-treatment samples to the latter model improved fit (AuROC, 0.94). A baseline model including UC hospitalization in the past year and increased Bacteroidetes was associated with increased risk for UC flare (AuROC, 0.88). CONCLUSION Fecal microbial features at baseline and after therapy predict rCDI risk in patients with and without UC. These results may help risk stratify patients to guide management.
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Affiliation(s)
- Allen A Lee
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI,Address correspondence to: Allen Lee, MD, 3912 Taubman Center, 1500 E. Medical Center Dr., SPC 5352, Ann Arbor, MI 48109, USA. E-mail:
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Julajak Limsrivilai
- Division of Gastroenterology, Department of Internal Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Merritt Gillilland
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Benjamin Malamet
- Oakland University William Beaumont School of Medicine, Rochester, MI
| | - Emily Briggs
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI,Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI
| | - Peter D R Higgins
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
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Schnizlein MK, Vendrov KC, Edwards SJ, Martens EC, Young VB. Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization. mSphere 2020; 5:e00708-19. [PMID: 31915217 PMCID: PMC6952194 DOI: 10.1128/msphere.00708-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 01/16/2023] Open
Abstract
Dietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects against Clostridioides difficile colonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota and C. difficile colonization. We added 5% xanthan gum to the diet of C57BL/6 mice and examined its effect on the microbiota through 16S rRNA gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice with C. difficile and measured colonization by monitoring the CFU. Xanthan gum administration is associated with increases in fiber-degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber-degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to no C. difficile colonization. Xanthan gum administration alters mouse susceptibility to C. difficile colonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.IMPORTANCE A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C. difficile colonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective against C. difficile colonization.
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Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kimberly C Vendrov
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Summer J Edwards
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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Das NK, Schwartz AJ, Barthel G, Inohara N, Liu Q, Sankar A, Hill DR, Ma X, Lamberg O, Schnizlein MK, Arqués JL, Spence JR, Nunez G, Patterson AD, Sun D, Young VB, Shah YM. Microbial Metabolite Signaling Is Required for Systemic Iron Homeostasis. Cell Metab 2020; 31:115-130.e6. [PMID: 31708445 PMCID: PMC6949377 DOI: 10.1016/j.cmet.2019.10.005] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/23/2019] [Accepted: 10/14/2019] [Indexed: 12/16/2022]
Abstract
Iron is a central micronutrient needed by all living organisms. Competition for iron in the intestinal tract is essential for the maintenance of indigenous microbial populations and for host health. How symbiotic relationships between hosts and native microbes persist during times of iron limitation is unclear. Here, we demonstrate that indigenous bacteria possess an iron-dependent mechanism that inhibits host iron transport and storage. Using a high-throughput screen of microbial metabolites, we found that gut microbiota produce metabolites that suppress hypoxia-inducible factor 2α (HIF-2α) a master transcription factor of intestinal iron absorption and increase the iron-storage protein ferritin, resulting in decreased intestinal iron absorption by the host. We identified 1,3-diaminopropane (DAP) and reuterin as inhibitors of HIF-2α via inhibition of heterodimerization. DAP and reuterin effectively ameliorated systemic iron overload. This work provides evidence of intestine-microbiota metabolic crosstalk that is essential for systemic iron homeostasis.
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Affiliation(s)
- Nupur K Das
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew J Schwartz
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabrielle Barthel
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Naohiro Inohara
- Department of Pathology and Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qing Liu
- Department of Veterinary and Biomedical Sciences, the Pennsylvania State University, University Park, PA 16802, USA
| | - Amanda Sankar
- Department of Pediatrics, Division of Hematology-Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoya Ma
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olivia Lamberg
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Juan L Arqués
- Departamento Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, Madrid 28040, Spain
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel Nunez
- Department of Pathology and Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, the Pennsylvania State University, University Park, PA 16802, USA
| | - Duxin Sun
- College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA.
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Saund K, Rao K, Young VB, Snitkin ES. Genetic Determinants of Trehalose Utilization Are Not Associated With Severe Clostridium difficile Infection Outcome. Open Forum Infect Dis 2020; 7:ofz548. [PMID: 31976356 PMCID: PMC6966243 DOI: 10.1093/ofid/ofz548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/31/2019] [Indexed: 11/20/2022] Open
Abstract
In a case–control study of patients with Clostridium difficile infection, we found no statistically significant association between the presence of trehalose utilization variants in infecting C. difficile strains and development of severe infection outcome. These results do not support trehalose utilization conferring enhanced virulence in the context of human C. difficile infections.
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Affiliation(s)
- Katie Saund
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Krishna Rao
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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Perry DA, Shirley D, Micic D, Putler RKB, Patel P, Menon A, Higgins P, Young VB, Rao K. 2409. External Validation and Comparison of Clostridioides difficile Severity Scoring Systems. Open Forum Infect Dis 2019. [PMCID: PMC6810436 DOI: 10.1093/ofid/ofz360.2087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Annually in the US alone, Clostridioides difficile infection (CDI) afflicts nearly 500,000 patients causing 29,000 deaths. Since early and aggressive interventions could save lives but are not optimally deployed in all patients, numerous studies have published predictive models for adverse outcomes. These models are usually developed at a single institution, and largely are not externally validated. This aim of this study was to validate the predictability for severe CDI with previously published risk scores in a multicenter cohort of patients with CDI.
Methods
We conducted a retrospective study on four separate inpatient cohorts with CDI from three distinct sites: the Universities of Michigan (2010–2012 and 2016), Chicago (2012), and Wisconsin (2012). The primary composite outcome was admission to an intensive care unit, colectomy, and/or death attributed to CDI within 30 days of positive test. Structured query and manual chart review abstracted data from the medical record at each site. Published CDI severity scores were assessed and compared with each other and the IDSA guideline definition of severe CDI. Sensitivity, specificity, area under the receiver operator characteristic curve (AuROC), precision-recall curves, and net reclassification index (NRI) were calculated to compare models.
Results
We included 3,775 patients from the four cohorts (Table 1) and evaluated eight severity scores (Table 2). The IDSA (baseline comparator) model showed poor performance across cohorts(Table 3). Of the binary classification models, including those that were most predictive of the primary composite outcome, Jardin, performed poorly with minimal to no NRI improvement compared with IDSA. The continuous score models, Toro and ATLAS, performed better, but the AuROC varied by site by up to 17% (Table 3). The Gujja model varied the most: from most predictive in the University of Michigan 2010–2012 cohort to having no predictive value in the 2016 cohort (Table 3).
Conclusion
No published CDI severity score showed stable, acceptable predictive ability across multiple cohorts/institutions. To maximize performance and clinical utility, future efforts should focus on a multicenter-derived and validated scoring system, and/or incorporate novel biomarkers.
Disclosures
All authors: No reported disclosures.
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Affiliation(s)
| | - Daniel Shirley
- University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin
| | | | | | | | | | | | | | - Krishna Rao
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan, Ann Arbor, Michigan
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Menon A, Perry DA, Motyka J, Weiner S, Standke A, Penkevich A, Keidan M, Young VB, Rao K. 2355. The Association Between Diagnostic Testing Method and Clostridium difficile Infection Severity. Open Forum Infect Dis 2019. [PMCID: PMC6810784 DOI: 10.1093/ofid/ofz360.2033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The optimal diagnostic strategy for Clostridium difficile infection (CDI) is not known, and no test is shown to clearly differentiate colonization from symptomatic infection. We hypothesized that detection and/or quantification of stool toxins would associate with severe disease and adverse outcomes. Methods We conducted a retrospective cohort study among subjects with CDI diagnosed in 2016 at the University of Michigan. The clinical microbiology laboratory tested for glutamate dehydrogenase antigen and toxins A/B by enzyme immunoassay (EIA). Discordant results reflexed to PCR for the tcdB gene. Stool toxin levels were quantified via a modified cell cytotoxicity assay (CCA). C. difficile was isolated by anaerobic culture and ribotyped. Severe CDI was defined by the IDSA criteria: white blood cell count >15,000 cells/µL or a 1.5-fold increase in serum creatinine above baseline. The primary outcomes were all-cause 30-day mortality and a composite of colectomy, ICU admission, and/or death attributable to CDI within 30 days. Analysis included standard bivariable tests and adjusted models via logistic regression. Results From 565 adult patients, we obtained 646 samples; 199 (30.8%) contained toxins by EIA. Toxin positivity associated with IDSA severity (Table 1), but not our primary outcomes on unadjusted analysis. After adjustment for putative confounders, we still did not observe an association between toxin positivity and our primary outcomes. Stool toxin levels by CCA >6.4 ng/mL associated with IDSA severity (Table 1), but not the primary outcomes. Compared with the period from 2010 to 2013, the circulating ribotypes of C. difficile at our institution changed in 2016. Notably ribotype 106 newly emerged, accounting for 10.6% of strains, and ribotype 027 fell to 9.3% (Table 2). The incidence of ribotype 014-027 has remained stable at 18.9%, but this strain was associated with both IDSA severity and 30-day mortality (OR = 3.32; P = 0.001). Conclusion Toxin detection by EIA/CCA associated with IDSA severity, but this study was unable to confirm an association with subsequent adverse outcomes. The molecular epidemiology of C. difficile has shifted, and this may have implications for the optimal diagnostic strategy for CDI. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | | | - Jonathan Motyka
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Shayna Weiner
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Alexandra Standke
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Aline Penkevich
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Micah Keidan
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | | | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
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Dieterle MG, Putler RKB, Perry DA, Menon A, Abernathy-Close L, Perlman N, Penkevich A, Standke A, Keidan M, Vendrov K, Bergin IL, Young VB, Rao K. 76. Validation of Systemic Inflammatory Mediators as Biomarkers for Severity and Adverse Outcomes in Clostridium difficile Infection. Open Forum Infect Dis 2019. [PMCID: PMC6809347 DOI: 10.1093/ofid/ofz359.000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Clostridium difficile infection (CDI) can result in severe disease and death. We are currently unable to identify patients at risk for developing adverse outcomes. We previously showed multiple inflammatory mediators were associated with severity and adverse outcomes. Here, we set out to validate these findings in patients and a murine model of CDI.
Methods
CDI was diagnosed by the clinical microbiology laboratory. Sera were collected ≤48 hours after diagnosis from pilot (October 2010–November 2012) and validation (January–September 2016) cohorts. Inflammatory mediators were measured with a custom multiplex assay. IDSA severity was defined as serum creatinine >1.5-fold above baseline or white blood cell count >15,000 cells/mL. The 30-day outcomes were all-cause mortality and disease-related complications (DRCs): ICU admission, colectomy, or death attributed to CDI. We sought to validate our patient findings in a murine model of CDI: 67 antibiotic-treated mice were infected with 630 g (37 mice), a low virulence strain, or VPI 10463 (30 mice), a highly virulent strain. Host responses were assessed with a murine version of the multiplex panel. Unadjusted and adjusted models were built using logistic and L1 regression, respectively.
Results
The pilot cohort had 156 CDI cases; 63 (40%) with IDSA severity. The inflammatory response in IDSA severe cases was distinct based on redundancy analysis of all measured analytes (P = 0.01). In unadjusted analysis, IL-2R, IL-6, and procalcitonin associated with severity (P < 0.001, P = 0.003, and P = 0.003, respectively). The same findings were seen in the validation cohort of 272 cases (Figure 1). Unadjusted analyses revealed several predictors of severity and outcomes (Table 1). Adjusted models performed well (Figure 2) with AUCs of 0.74 [0.67–0.81] (IDSA severity), 0.89 [0.83–0.95] (death), and 0.84 [0.74–0.95] (DRCs). Application of each model to the mouse cohort for high vs. low virulence infections revealed AUCs of 0.59 [0.44–0.74], 0.96 [0.90–1.0], and 0.89 [0.81–0.97] (Figure 3).
Conclusion
In both humans and a murine CDI model, a panel of biomarkers from sera associated with severe CDI and predicted adverse outcomes. Our results support the possibility of a serum-based biomarker panel to inform medical decision-making for patients with CDI.
Disclosures
All Authors: No reported Disclosures.
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Affiliation(s)
- Michael G Dieterle
- Medical Scientist Training Program (MSTP), Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | | | | | | | | | | | - Aline Penkevich
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Alexandra Standke
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan
| | - Micah Keidan
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Kimberly Vendrov
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan
| | | | | | - Krishna Rao
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan
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Bassis C, Seekatz A, Dangana TE, Shimasaki T, Yelin RD, Schoeny M, Rhee Y, Ariston M, Lolans K, Cornejo Cisneros E, Aboushaala K, Thabit L, Murray J, Sheng J, Ollison S, Bell PB, Fogg L, Weinstein RA, Lin MY, Young VB, Hayden MK. 2849. Gut Microbiota Differences at the Time of Medical Intensive Care Unit (MICU) Admission Are Associated with Acquisition of Multi-drug-Resistant Organisms (MDROs) Among Patients Not Already Colonized with an MDRO. Open Forum Infect Dis 2019. [PMCID: PMC6808848 DOI: 10.1093/ofid/ofz359.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Among hospitalized patients, underlying variation in gut microbiota may confer differential risk for gut MDRO acquisition. Methods Rectal swab samples were collected from patients ≤2 days of MICU admission and then daily in the 27-bed MICU of an acute care hospital in Chicago, IL over 1 year. Patients were screened for MDRO colonization by selective culture (see Figure 1 for MDRO types); those with ≥2 swabs and MICU stays ≥3 days were studied. Bacterial 16S rRNA gene amplicon sequences were used for microbiota analysis. Medical records were reviewed. Results In preliminary analysis, 2,480 samples were collected from 627 patients who acquired 170 MDROs (Figure 1). Debilitation, co-morbidities, and certain medical devices were associated with MDRO acquisition, though admission MDRO status was not (table). While no interactions were detected between admission MDRO status and clinical predictors of MDRO acquisition, there were significant differences in gut microbiota composition at the time of MICU admission between patients colonized with an MDRO on admission and those not colonized (P < 0.001, using analysis of molecular variance (AMOVA) on distances). Therefore, we stratified our analysis by admission MDRO colonization status. For patients MDRO-colonized at admission, there were no significant differences in microbiota of patients who later did or did not acquire a new MDRO (AMOVA P-value = 0.32). For patients not MDRO-colonized on admission, there was a significant difference in microbiota of patients who later acquired an MDRO and those who did not (AMOVA P-value: 0.026). Differentially abundant operational taxonomic units (OTUs, based on 3% sequence difference) included OTUs classified as Anaerococcus and as other Clostridiales (higher in patients who remained uncolonized) and as Enterococcus (higher in patients who acquired an MDRO) (Figure 2). Diversity was also higher in patients who remained uncolonized (Wilcoxon test P-value: 0.035) (Figure 3). Conclusion Among patients not already colonized with an MDRO on admission, we identified gut microbiota differences associated with MDRO acquisition that could help explain patient-level variation in MDRO colonization resistance. ![]()
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Disclosures All Authors: No reported Disclosures.
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Affiliation(s)
| | | | | | | | | | | | - Yoona Rhee
- Rush University Medical Center, Chicago, Illinois
| | | | - Karen Lolans
- Rush University Medical Center, Chicago, Illinois
| | | | | | | | - John Murray
- Rush University Medical Center, Chicago, Illinois
| | | | | | | | - Louis Fogg
- Rush University Medical Center, Chicago, Illinois
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Young VB, Keidan M, Yelin RD, Dangana TE, Bell PB, Rao K, Hayden MK. 2424. Shedding of Viable Clostridiodes difficile in Patients Admitted to a Medical Intensive Care Unit. Open Forum Infect Dis 2019. [PMCID: PMC6810365 DOI: 10.1093/ofid/ofz360.2102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Hospitalized patients are at risk of colonization with a range of healthcare-associated bacterial pathogens, including C. difficile. In patients admitted to intensive care units (ICUs), in whom C. difficile infection (CDI) is associated with increased morbidity and mortality. To understand the risk for acquisition of C. difficile and development of CDI, we monitored ICU patients daily for shedding of C. difficile by culture. Methods We conducted a secondary analysis of daily rectal/fecal swab samples collected from medical ICU patients of a 720-bed academic medical center in Chicago, IL. Selective culture for C. difficile was performed on swab samples from patients who had 2 or more samples obtained using selective media. Confirmation of putative C. difficile isolates was done by specific PCR assays for the 16S rRNA-encoding gene and the toxin genes tcdA, tcdB, cdtA and cdtB. Clinical testing for CDI was performed using the Xpert® C. difficile PCR assay (Cepheid). Clinical and demographic metadata were collected at bedside and by electronic medical record review. Results Culture was attempted on 2106 swab samples from 451 patients (486 ICU admissions) (Figure 1). A mean of 4.33 samples was obtained from each patient. C. difficile was isolated from 211 (10%) samples from 79 patients (Table 1). The first sample was positive by culture for 48 (9.9%) of patient admissions to the ICU. 31 (6.4%) patients who were initially negative by culture had a subsequent sample from which C. difficile was isolated. Persistence of culture-positivity varied from patient to patient (Figure 2). Of 80 patients who were tested for CDI based on physician suspicion, 12 patients had a positive Cepheid PCR test; 9 had diarrhea and were treated for CDI. Conclusion Surveillance for shedding of C. difficile by daily culture reveals that patients admitted to the ICU can shed the pathogen intermittently without attributable disease. This can be in the form patients who are admitted carrying the organism as well as those who appear to acquire the organism during their stay. It is unclear whether patient or microbiome factors underlie the differences seen in patterns of shedding. Furthermore, intermittent shedding may reflect multiple episodes of exposure to C. difficile spores and asymptomatic shedding without stable colonization. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | - Micah Keidan
- University of Michigan, Department of Internal Medicine, Division of Infectious Diseases, Ann Arbor, Michigan
| | | | | | | | - Krishna Rao
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan, Ann Arbor, Michigan
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Motyka J, Cheng HT, Lin CY, Keidan M, Young VB, Kao J, Rao K. 2403. Clostridium difficile ribotypes and human microbiota differ in Taiwan and the United States with respect to diarrheal patients. Open Forum Infect Dis 2019. [PMCID: PMC6810612 DOI: 10.1093/ofid/ofz360.2081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Clostridium difficile infection (CDI) has high incidence in the United States, but less so in East Asian countries such as Taiwan. The reason for this is not understood, but microbial studies could reveal important epidemiologic insights. We hypothesized that the circulating strains of C. difficile and the gut microbiota differ between the United States and Taiwan. Methods Patients with diarrhea ± CDI from the University of Michigan and Chang Gung Memorial Hospital were included. CDI was defined by + enzyme immunoassay for the glutamate dehydrogenase gene and toxins A/B, with reflex to tcdB gene PCR for discordants. C. difficile was isolated by anaerobic culture and characterized by PCR ribotype. The fecal microbiota was assessed by sequence analysis of 16S rRNA-encoding gene amplicons targeting the V4 region. Amplicon sequences were processed using the mothur bioinformatics pipeline, with an operational taxonomic unit (OTU) defined by < = 3% sequence homology. Analysis was performed via logistic regression, principal coordinates (PCoA), and ANOVA. Results Community diversity by Shannon index of CDI- patients was lower (Figure 1); this difference was greater in Taiwan (P < .001, OR = 3.9 per unit Shannon). Taiwanese CDI- patients had lower Bacteroidetes relative abundance (RA) (Figure 2). The Taiwanese CDI- group also differed on PCoA and ANOVA (Figure 3, P < .001). OTU1 (genus Firmicutes) was depleted in CDI+ patients (P < .001, OR = 0.69 per 10% RA increase). Circulating ribotypes (Table 1) differ between countries, with no epidemic strains (R027/R078) present in Taiwan (P = .027). R027 and 014/020 comprised > 50% of US isolates while > 50% of Taiwanese isolates were R002. Conclusion Taiwan and US CDI+ patients differ in dominant ribotypes. It is overall difficult to differentiate diarrheal CDI+ and CDI- patients by the microbiome. Taiwanese CDI- patients are outliers, and possible reasons (e.g., differential burden of parasitic infection; diet) require further study. The increased diversity and lower Bacteroidetes in CDI+ vs. CDI- diarrheal patients contrast with prior studies that instead compared with CDI- non-diarrheal patients. Circulating strains in Taiwan include no epidemic variants; whether this explains the differential incidence needs further study. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Jonathan Motyka
- University of Michigan, Department of Internal Medicine, Division of Infectious Diseases, Ann Arbor, Michigan
| | - Hao-Tsai Cheng
- Chang Gung Memorial Hospital, Department of Gastroenterology and Hepatology, Linkou, Taoyuan, Taiwan (Republic of China)
| | - Cheng-Yu Lin
- Chang Gung Memorial Hospital, Department of Gastroenterology and Hepatology, Linkou, Taoyuan, Taiwan (Republic of China)
| | - Micah Keidan
- University of Michigan, Department of Internal Medicine, Division of Infectious Diseases, Ann Arbor, Michigan
| | | | - John Kao
- University of Michigan, Department of Internal Medicine, Gastroenterology, Ann Arbor, Michigan
| | - Krishna Rao
- Department of Internal Medicine, Infectious Diseases Division University of Michigan, Ann Arbor, Michigan, Ann Arbor, Michigan
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Motyka J, Penkevich A, Perry DA, Weiner S, Standke A, Keidan M, Young VB, Rao K. 2236. Stool-Derived Inflammatory Mediators Serve as Biomarkers of Severity in Clostridium difficile Infection. Open Forum Infect Dis 2019. [PMCID: PMC6809826 DOI: 10.1093/ofid/ofz360.1914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Clostridium difficile infection (CDI) is a major public health concern and frequently results in severe disease, including death. Predicting subsequent complications early in the course can help optimize treatments and improve outcomes. However, models based on clinical criteria alone are not accurate and/or do not validate. We hypothesized that inflammatory mediators from the stool would be biomarkers for severity and complications. Methods Subjects were included after testing positive for toxigenic C. difficile by the clinical microbiology laboratory via enzyme immunoassay (EIA) for glutamate dehydrogenase and toxins A/B, with reflex to tcdB gene PCR for discordants. Stool was thawed on ice, diluted 1:1 with PBS and protease inhibitor, centrifuged, and the supernatant was analyzed by a custom antibody-linked bead array with 17 inflammatory mediators. Measurements were normalized and log-transformed. IDSA severity was defined by serum white blood cell count > 15000 cells/µL or creatinine 1.5-fold above baseline. Primary 30-day outcomes were all-cause mortality and attributable disease-related complications (DRC): ICU admission, colectomy, and/or death. Analyses included principal components, permutational multivariate ANOVA (PERMANOVA), and logistic regression ± L1 regularization and 5-fold cross validation. The area under the receiver operator characteristic curve (AuROC) was computed. Results We included 225 subjects, with 124 females (55.1%), average age 58.5 (±17), and more PCR+ than toxin EIA+ (170 vs. 55, respectively). IDSA severity, death, and DRCs occurred in 79 (35.1%), 14 (6.2%), and 12 (5.3%) subjects, respectively. PCA and PERMANOVA showed IDSA severity (P = 0.009) but not death or DRCs associated with the panel (figure). Several inflammatory mediators associated with IDSA severity and death (table). Machine learning models had AuROCs of 0.77 (IDSA severity), 0.84 (death), and 0.7 (DRCs). Conclusion We found that specific inflammatory mediators from the stool of patients with CDI associate with severity and complications. These results are promising, but need replication in a larger dataset and should be incorporated into models that include clinical covariates prior to deployment. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Jonathan Motyka
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Aline Penkevich
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - D Alex Perry
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Shayna Weiner
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Alexandra Standke
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | - Micah Keidan
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
| | | | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan
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Woodworth MH, Hayden MK, Young VB, Kwon JH. Corrigendum: The Role of Fecal Microbiota Transplantation in Reducing Intestinal Colonization With Antibiotic-Resistant Organisms: The Current Landscape and Future Directions. Open Forum Infect Dis 2019; 6:ofz391. [PMID: 31660354 PMCID: PMC6800889 DOI: 10.1093/ofid/ofz391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
[This corrects the article DOI: 10.1093/ofid/ofz288.][This corrects the article DOI: 10.1093/ofid/ofz288.].
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Abernathy-Close L, Young VB. Intestinal Damage Fades, but Insults Linger: Setting the Immunological Tone for Infection. Cell Host Microbe 2019; 25:636-637. [PMID: 31071292 DOI: 10.1016/j.chom.2019.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Clostridium difficile has emerged as a noteworthy pathogen in patients with inflammatory bowel disease. In this issue of Cell Host & Microbe, Saleh et al. (2019) demonstrate that Th17 responses induced by acute colitis contribute to increased disease severity during subsequent C. difficile infection.
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Affiliation(s)
- Lisa Abernathy-Close
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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