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Lam LN, Savage KE, Shakir CN, Lemos JA. Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus. J Bacteriol 2025; 207:e0043824. [PMID: 39902966 PMCID: PMC11925238 DOI: 10.1128/jb.00438-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 01/15/2025] [Indexed: 02/06/2025] Open
Abstract
Enterococci are opportunistic pathogens notorious for causing a variety of infections. While both Enterococcus faecalis and Lactobacillus crispatus are commensal residents of the vaginal tract, the molecular mechanisms that enable E. faecalis to take advantage of a vaginal biome with lower counts of lactobacilli to colonize the vaginal tract and induce aerobic vaginitis remain unknown. Here, we show that L. crispatus eradicates E. faecalis in a contact-independent manner. Using transposon sequencing to identify E. faecalis OG1RF transposon (Tn) mutants that are either under-represented or over-represented when co-cultured with L. crispatus, we found that Tn mutants with disruption in the dltABCD operon, that encodes the proteins responsible for the D-alanylation of teichoic acids, and OG1RF_11697 encoding for an uncharacterized hypothetical protein are more susceptible to killing by L. crispatus. Inversely, Tn mutants with disruption in ldh1, which encodes for L-lactate dehydrogenase, are more resistant to L. crispatus killing. Using the Galleria mellonella infection model, we show that co-injection of L. crispatus with E. faecalis OG1RF enhances larvae survival while this L. crispatus-mediated protection was lost in larvae co-infected with either L. crispatus and E. faecalisΔldh1 or Δldh1Δldh2 strains. Last, using RNA sequencing to identify E. faecalis genes that are differently expressed in the presence of L. crispatus, we found major changes in the expression of genes associated with glycerophospholipid metabolism, central metabolism, and general stress responses. The findings in this study provide insights into how E. faecalis mitigate assaults by L. crispatus.IMPORTANCEEnterococcus faecalis is an opportunistic pathogen notorious for causing a multitude of infections. As vaginal commensals, E. faecalis must interact with Lactobacillus crispatus, but how E. faecalis overcomes or mitigate assaults by L. crispatus killing remains unknown. We show that L. crispatus eradicates E. faecalis temporally in a contact-independent manner. Using high-throughput molecular approaches, we identified genetic determinants that enable E. faecalis to compete with L. crispatus. This study represents an important first step for the identification of adaptive genetic traits required for enterococci to tolerate assaults by lactobacilli.
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Affiliation(s)
- Ling Ning Lam
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Kathryn E. Savage
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Camille N. Shakir
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - José A. Lemos
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
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Takefuji Y. Addressing Bias in Feature Importance: A Hybrid Approach for Risk Prediction in Prognostic Survival Models. JCO Precis Oncol 2025; 9:e2400785. [PMID: 39787463 DOI: 10.1200/po-24-00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 12/10/2024] [Indexed: 01/12/2025] Open
Affiliation(s)
- Yoshiyasu Takefuji
- Yoshiyasu Takefuji, PhD, Faculty of Data Science, Musashino University, Tokyo, Japan
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3
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Lam LN, Sedra A, Kajfasz J, Berges A, Saengpet IS, Adams G, Fairman J, Lemos JA. Trivalent immunization with metal-binding proteins confers protection against enterococci in a mouse infection model. FEMS MICROBES 2024; 5:xtae031. [PMID: 39524556 PMCID: PMC11549557 DOI: 10.1093/femsmc/xtae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 09/13/2024] [Accepted: 10/02/2024] [Indexed: 11/16/2024] Open
Abstract
Enterococcus faecalis is ranked among the top five bacterial pathogens responsible for catheter-associated urinary tract infections, wound infections, secondary root canal infections, and infective endocarditis. Previously, we showed that inactivation of either the manganese- and iron-binding (EfaA) or zinc-binding (AdcA and AdcAII) lipoproteins significantly reduced E. faecalis virulence. Here, we explored whether immunization using a multi-valent approach induces protective immunity against systemic enterococcal infections. We found that multi-antigen antisera raised against EfaA, AdcA, and AdcAII displayed similar capacities to initiate neutrophil-mediated opsonization, like their single-antigen counterparts. Further, these antigen-specific antibodies worked synergistically with calprotectin, a divalent host metal chelator, to inhibit the growth of E. faecalis in laboratory media as well as in human sera. Using the Galleria mellonella invertebrate model and mouse peritonitis model, we showed that passive immunization with multi-antigen antisera conferred robust protection against E. faecalis infection, while the protective effects of single antigen antisera were negligible in G. mellonella, and negligible-to-moderate in the mouse model. Lastly, active immunization with the 3-antigen (trivalent) cocktail significantly protected mice against either lethal or non-lethal E. faecalis infections, with this protection appearing to be far-reaching based on immunization results obtained with contemporary strains of E. faecalis and closely related Enterococcus faecium.
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Affiliation(s)
- Ling Ning Lam
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States
| | - Angie Sedra
- Vaxcyte, Inc., San Carlos, CA 94070, United States
| | - Jessica Kajfasz
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States
| | - Aym Berges
- Vaxcyte, Inc., San Carlos, CA 94070, United States
| | - Irene S Saengpet
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States
| | - Grace Adams
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States
| | | | - José A Lemos
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States
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4
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Hourigan D, Stefanovic E, Hill C, Ross RP. Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC Microbiol 2024; 24:103. [PMID: 38539119 PMCID: PMC10976773 DOI: 10.1186/s12866-024-03243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024] Open
Abstract
Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
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Affiliation(s)
- David Hourigan
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - Ewelina Stefanovic
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland.
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland.
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland.
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5
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Rubin IMC, Knudsen MJS, Halkjær SI, Ilsby CS, Pinholt M, Petersen AM. Lacticaseibacillus rhamnosus GG Versus Placebo for Eradication of Vancomycin-Resistant Enterococcus faecium in Intestinal Carriers: A Systematic Review and Meta-Analysis. Microorganisms 2023; 11:2804. [PMID: 38004815 PMCID: PMC10673360 DOI: 10.3390/microorganisms11112804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The aim of this review was to assess the efficacy and safety of Lacticaseibacillus rhamnosus GG (LGG) (previously known as Lactobacillus rhamnosus GG) for the eradication of vancomycin-resistant Enterococcus faecium (VREfm) in colonized carriers. We searched Cochrane Central, EMBASE, and the PubMed Library from inception to 21 August 2023, for randomized controlled trials (RCTs) investigating the effectiveness of LGG for the eradication of gastrointestinal carriage of VREfm. An initial screening was performed followed by a full-text evaluation of the papers. Out of 4076 articles in the original screening, six RCTs (167 participants) were included in the review. All were placebo-controlled RCTs. The meta-analysis was inconclusive with regard to the effect of LGG for clearing VREfm colonization. The overall quality of the evidence was low due to inconsistency and the small number of patients in the trials. We found insufficient evidence to support the use of LGG for the eradication of VREfm in colonized carriers. There is a need for larger RCTs with a standardized formulation and dosage of LGG in future trials.
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Affiliation(s)
- Ingrid Maria Cecilia Rubin
- Department of Clinical Microbiology, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark; (M.J.S.K.); (C.S.I.); (M.P.); (A.M.P.)
| | - Maja Johanne Søndergaard Knudsen
- Department of Clinical Microbiology, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark; (M.J.S.K.); (C.S.I.); (M.P.); (A.M.P.)
| | - Sofie Ingdam Halkjær
- Gastrounit, Medical Section, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark;
| | - Christian Schaadt Ilsby
- Department of Clinical Microbiology, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark; (M.J.S.K.); (C.S.I.); (M.P.); (A.M.P.)
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark; (M.J.S.K.); (C.S.I.); (M.P.); (A.M.P.)
| | - Andreas Munk Petersen
- Department of Clinical Microbiology, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark; (M.J.S.K.); (C.S.I.); (M.P.); (A.M.P.)
- Gastrounit, Medical Section, Copenhagen University Hospital—Amager and Hvidovre, 2650 Hvidovre, Denmark;
- Department of Clinical Medicine, University of Copenhagen, 1172 Copenhagen, Denmark
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Chanderraj R, Baker JM, Kay SG, Brown CA, Hinkle KJ, Fergle DJ, McDonald RA, Falkowski NR, Metcalf JD, Kaye KS, Woods RJ, Prescott HC, Sjoding MW, Dickson RP. Reply to: Anti-anaerobic antibiotics: indication is key. Eur Respir J 2023; 61:2300492. [PMID: 37169381 DOI: 10.1183/13993003.00492-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/13/2023]
Affiliation(s)
- Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, Veterans Affairs (VA) Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Jennifer M Baker
- Division of Pulmonary and Critical Care Medicine, 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
| | - Stephen G Kay
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel J Fergle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roderick A McDonald
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph D Metcalf
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, Veterans Affairs (VA) Ann Arbor Healthcare System, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hallie C Prescott
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- VA Center for Clinical Management Research, Ann Arbor, MI, USA
| | - Michael W Sjoding
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, 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
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
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7
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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: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [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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8
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Chanderraj R, Baker JM, Kay SG, Brown CA, Hinkle KJ, Fergle DJ, McDonald RA, Falkowski NR, Metcalf JD, Kaye KS, Woods RJ, Prescott HC, Sjoding MW, Dickson RP. In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes. Eur Respir J 2023; 61:13993003.00910-2022. [PMID: 36229047 PMCID: PMC9909213 DOI: 10.1183/13993003.00910-2022] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/16/2022] [Indexed: 01/16/2023]
Abstract
BACKGROUND Critically ill patients routinely receive antibiotics with activity against anaerobic gut bacteria. However, in other disease states and animal models, gut anaerobes are protective against pneumonia, organ failure and mortality. We therefore designed a translational series of analyses and experiments to determine the effects of anti-anaerobic antibiotics on the risk of adverse clinical outcomes among critically ill patients. METHODS We conducted a retrospective single-centre cohort study of 3032 critically ill patients, comparing patients who did and did not receive early anti-anaerobic antibiotics. We compared intensive care unit outcomes (ventilator-associated pneumonia (VAP)-free survival, infection-free survival and overall survival) in all patients and changes in gut microbiota in a subcohort of 116 patients. In murine models, we studied the effects of anaerobe depletion in infectious (Klebsiella pneumoniae and Staphylococcus aureus pneumonia) and noninfectious (hyperoxia) injury models. RESULTS Early administration of anti-anaerobic antibiotics was associated with decreased VAP-free survival (hazard ratio (HR) 1.24, 95% CI 1.06-1.45), infection-free survival (HR 1.22, 95% CI 1.09-1.38) and overall survival (HR 1.14, 95% CI 1.02-1.28). Patients who received anti-anaerobic antibiotics had decreased initial gut bacterial density (p=0.00038), increased microbiome expansion during hospitalisation (p=0.011) and domination by Enterobacteriaceae spp. (p=0.045). Enterobacteriaceae were also enriched among respiratory pathogens in anti-anaerobic-treated patients (p<2.2×10-16). In murine models, treatment with anti-anaerobic antibiotics increased susceptibility to Enterobacteriaceae pneumonia (p<0.05) and increased the lethality of hyperoxia (p=0.0002). CONCLUSIONS In critically ill patients, early treatment with anti-anaerobic antibiotics is associated with increased mortality. Mechanisms may include enrichment of the gut with respiratory pathogens, but increased mortality is incompletely explained by infections alone. Given consistent clinical and experimental evidence of harm, the widespread use of anti-anaerobic antibiotics should be reconsidered.
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Affiliation(s)
- Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Jennifer M Baker
- Division of Pulmonary and Critical Care Medicine, 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
| | - Stephen G Kay
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel J Fergle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roderick A McDonald
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph D Metcalf
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hallie C Prescott
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- VA Center for Clinical Management Research, Ann Arbor, MI, USA
| | - Michael W Sjoding
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, 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
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
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9
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Mu J, Guo Z, Wang X, Wang X, Fu Y, Li X, Zhu F, Hu G, Ma X. Seaweed polysaccharide relieves hexavalent chromium-induced gut microbial homeostasis. Front Microbiol 2023; 13:1100988. [PMID: 36726569 PMCID: PMC9884827 DOI: 10.3389/fmicb.2022.1100988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023] Open
Abstract
Heavy metals released in the environment pose a huge threat to soil and water quality, food safety and public health. Additionally, humans and other mammals may also be directly exposed to heavy metals or exposed to heavy metals through the food chain, which seriously threatens the health of animals and humans. Chromium, especially hexavalent chromium [Cr (VI)], as a common heavy metal, has been shown to cause serious environmental pollution as well as intestinal damage. Thus, increasing research is devoted to finding drugs to mitigate the negative health effects of hexavalent chromium exposure. Seaweed polysaccharides have been demonstrated to have many pharmacological effects, but whether it can alleviate gut microbial dysbiosis caused by hexavalent chromium exposure has not been well characterized. Here, we hypothesized that seaweed polysaccharides could alleviate hexavalent chromium exposure-induced poor health in mice. Mice in Cr and seaweed polysaccharide treatment group was compulsively receive K2Cr2O7. At the end of the experiment, all mice were euthanized, and colon contents were collected for DNA sequencing analysis. Results showed that seaweed polysaccharide administration can restore the gut microbial dysbiosis and the reduction of gut microbial diversity caused by hexavalent chromium exposure in mice. Hexavalent chromium exposure also caused significant changes in the gut microbial composition of mice, including an increase in some pathogenic bacteria and a decrease in beneficial bacteria. However, seaweed polysaccharides administration could ameliorate the composition of gut microbiota. In conclusion, this study showed that seaweed polysaccharides can restore the negative effects of hexavalent chromium exposure in mice, including gut microbial dysbiosis. Meanwhile, this research also lays the foundation for the application of seaweed polysaccharides.
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Affiliation(s)
- Jinghao Mu
- Department of Urology, Chinese PLA General Hospital, Beijing, China,Department of Urology, The Seventh Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhenhuan Guo
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China,*Correspondence: Zhenhuan Guo, ✉
| | - Xiujun Wang
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Xuefei Wang
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Yunxing Fu
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Xianghui Li
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Fuli Zhu
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Guangyuan Hu
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Xia Ma
- Zhengzhou Key Laboratory of Immunopharmacology of Traditional Chinese Veterinary Medicines, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China,Xia Ma, ✉
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10
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Efficacy and Safety of Fecal Microbiota Transplantation for Clearance of Multidrug-Resistant Organisms under Multiple Comorbidities: A Prospective Comparative Trial. Biomedicines 2022; 10:biomedicines10102404. [PMID: 36289668 PMCID: PMC9598999 DOI: 10.3390/biomedicines10102404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Fecal microbiota transplantation (FMT) could decolonize multidrug-resistant organisms. We investigated FMT effectiveness and safety in the eradication of carbapenem-resistant Enterobacteriaceae (CRE) and vancomycin-resistant enterococci (VRE) intestinal colonization. A prospective non-randomized comparative study was performed with 48 patients. FMT material (60 g) was obtained from a healthy donor, frozen, and administered via endoscopy. The primary endpoint was 1-month decolonization, and secondary endpoints were 3-month decolonization and adverse events. Microbiota analysis of fecal samples was performed using 16S rRNA sequencing. Intention-to-treat analysis revealed overall negative conversion between the FMT and control groups at 1 (26% vs. 10%, p = 0.264) and 3 (52% vs. 24%, p = 0.049) months. The 1-month and 3-month CRE clearance did not differ significantly by group (36% vs. 10%, p = 0.341; and 71% vs. 30%, p = 0.095, respectively). Among patients with VRE, FMT was ineffective for 1-month or 3-month negative conversion (13% vs. 9%, p > 0.999; and 36% vs. 18%, p = 0.658, respectively) However, cumulative overall negative-conversion rate was significantly higher in the FMT group (p = 0.037). Enterococcus abundance in patients with VRE significantly decreased following FMT. FMT may be effective at decolonizing multidrug-resistant organisms in the intestinal tract.
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11
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Kuzma J, Palcová L, Timko J, Bastová V, Janošcová V, Chmelař D. Detection and molecular characterization of VRE isolates in Slovakia from stool samples positive for Clostridioides difficile toxins. Folia Microbiol (Praha) 2022; 67:975-984. [PMID: 35997873 PMCID: PMC9395909 DOI: 10.1007/s12223-022-01002-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/10/2022] [Indexed: 12/04/2022]
Abstract
The study aimed to identify colonized patients as a possible source of eventual VRE (vancomycin-resistant enterococci) infection from stool samples positive for glutamate dehydrogenase antigen, as well as for Clostridioides difficile toxins A and B. The study was carried out from 7/2020 to 9/2021. Stool samples were grown in a brain heart infusion medium with a gram-positive non-spore-forming bacteria supplement under aerobic conditions. The samples for VRE identification were grown on CHROMID® VRE agar, and the MICs for vancomycin and teicoplanin were also estimated. The presence of the vanA/vanB genes was tested using the PCR method. The total number of 113 stool samples positive for Clostridioides difficile toxins was analyzed. Of these samples, 44 isolates with VRE characters were identified. The most prevalent isolates in our set of isolates were Enterococcus faecium (27 isolates, 62%), Enterococcus faecalis (9 isolates, 21%), Enterococcus solitarius (4 isolates, 9%), Enterococcus durans (2 isolates, 4%), 1 isolate Enterococcus sulfurous (2%), and Enterococcus raffinosus (2%). In total, 26 isolates were detected in the study in the presence of vanA genes (24 isolates E. faecium, 2 isolates E. faecalis) and 18 isolates detected in the presence of vanB genes (7 isolates E. faecalis, 4 isolates E. solitarius, 3 isolates E. faecium, 2 isolates E. durans, 1 isolate E. sulfurous, and E. raffinosus). The results of this study showed the local dominance character of the vanA gene of hospital VRE isolates that were carriers of genes associated with high resistance to vancomycin, teicoplanin, and occasionally linezolid.
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Affiliation(s)
- Jozef Kuzma
- Faculty of Medicine, Institute of Laboratory Medicine, University of Ostrava, Ostrava, Czech Republic. .,Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Lenka Palcová
- Science and Research Department, Faculty Hospital, Central Military Hospital, Ružomberok, Slovakia.,St. Elizabeth University in Bratislava, Catholic University, Ružomberok, Slovakia
| | - Jaroslav Timko
- Laboratory of Clinical Microbiology, Faculty Hospital, Central Military Hospital, Ružomberok, Slovakia.,Catholic University, Ružomberok, Slovakia
| | - Veronika Bastová
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | | | - Dittmar Chmelař
- Czech Anaerobic Bacteria Reference Laboratory, Faculty of Medicine, Institute of Laboratory Medicine, University of Ostrava, Ostrava, Czech Republic
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12
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Antibiotic resistance in the commensal human gut microbiota. Curr Opin Microbiol 2022; 68:102150. [DOI: 10.1016/j.mib.2022.102150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 12/24/2022]
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13
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No Effect of Lactobacillus rhamnosus GG on Eradication of Colonization by Vancomycin-Resistant Enterococcus faecium or Microbiome Diversity in Hospitalized Adult Patients. Microbiol Spectr 2022; 10:e0234821. [PMID: 35475684 PMCID: PMC9241610 DOI: 10.1128/spectrum.02348-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The purpose of this trial was to evaluate the efficacy of a 4-week supplementation of Lactobacillus rhamnosus GG (LGG) in eliminating the gastrointestinal carrier state of vancomycin-resistant Enterococcus faecium (VREfm) in hospitalized adults. The primary outcome of the study was the number of patients with cleared VREfm colonization after the 4-week intervention. Secondary outcomes were clearance of VREfm colonization at weeks 8, 16, and 24, number of VREfm infections (isolated from nonintestinal foci), and changes in fecal microbiome diversity after the intervention. The trial was a multicenter, randomized, double-blind, placebo-controlled trial in hospitalized adult VREfm carriers. Patients were enrolled and randomized to receive 60 billion CFU of LGG daily or placebo for 4 weeks. For a subgroup of patients, rectal swabs for VREfm were collected also at 8, 16, and 24 weeks and analyzed using shotgun metagenomics. Patients ingesting a minimum of 50% of the probiotic during the 4-week intervention were included in subsequent outcome analyses (48 of 81 patients). Twelve of 21 patients in the LGG group (57%) compared to 15 of 27 patients in the placebo group (56%) cleared their VREfm carriage. Eighteen patients completed the entire 24-week intervention with the same minimum compliancy. Of these, almost 90% in both groups cleared their VREfm carriage. We found a statistically significant difference between VREfm clearers and nonclearers regarding metronidazole and vancomycin usage as well as length of hospitalization after inclusion. The microbiome analyses revealed no significant difference in alpha diversity between the LGG and the placebo group. Beta diversity differed between the groups and the different time points. This study did not show an effect of LGG in eradication of VREfm after a 4-week intervention. IMPORTANCE Whereas other studies exploring the effect of L. rhamnosus in clearing VREfm from the intestine included children and adults, with a wider age range, our study consisted of a geriatric patient cohort. The natural clearance of VREfm in this study was almost 60% after 4 weeks, thus much higher than described previously. Also, this study characterizes the microbiome of VREfm patients in detail. This article showed no effect of the probiotic L. rhamnosus in clearing VREfm from the intestine of patients.
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14
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Chanderraj R, Brown CA, Hinkle K, Falkowski N, Woods RJ, Dickson RP. The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection. MICROBIOME 2022; 10:2. [PMID: 34991717 PMCID: PMC8734160 DOI: 10.1186/s40168-021-01190-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/18/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND In ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for microbiome analysis, yet variation in their bacterial density-and the clinical and methodologic significance of this variation-remains undetermined. We used an ultra-sensitive quantification approach-droplet digital PCR (ddPCR)-to quantify bacterial density in rectal swabs from 118 hospitalized patients. We compared bacterial density with bacterial community composition (via 16S rRNA amplicon sequencing) and clinical data to determine if variation in bacterial density has methodological, clinical, and prognostic significance. RESULTS Bacterial density in rectal swab specimens was highly variable, spanning five orders of magnitude (1.2 × 104-3.2 × 109 16S rRNA gene copies/sample). Low bacterial density was strongly correlated with the detection of sequencing contamination (Spearman ρ = - 0.95, p < 10-16). Low-density rectal swab communities were dominated by peri-rectal skin bacteria and sequencing contaminants (p < 0.01), suggesting that some variation in bacterial density is explained by sampling variation. Yet bacterial density was also associated with important clinical exposures, conditions, and outcomes. Bacterial density was lower among patients who had received piperacillin-tazobactam (p = 0.017) and increased among patients with multiple medical comorbidities (Charlson score, p = 0.0040) and advanced age (p = 0.043). Bacterial density at the time of hospital admission was independently associated with subsequent extraintestinal infection (p = 0.0028), even when controlled for severity of illness and comorbidities. CONCLUSIONS The bacterial density of rectal swabs is highly variable, and this variability is of methodological, clinical, and prognostic significance. Microbiome studies using rectal swabs are vulnerable to sequencing contamination and should include appropriate negative sequencing controls. Among hospitalized patients, gut bacterial density is associated with clinical exposures (antibiotics, comorbidities) and independently predicts infection risk. Bacterial density is an important and under-studied feature of gut microbiome community analysis. Video abstract.
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Affiliation(s)
- Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, 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.
- Weil Institute for Critical Care Research & Innovation, MI, Ann Arbor, USA.
- Pulmonary and Critical Care Medicine, University of Michigan Health System, 6220 MSRB III / SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA.
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15
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Le Guern R, Stabler S, Gosset P, Pichavant M, Grandjean T, Faure E, Karaca Y, Faure K, Kipnis E, Dessein R. Colonization resistance against multi-drug-resistant bacteria: a narrative review. J Hosp Infect 2021; 118:48-58. [PMID: 34492304 DOI: 10.1016/j.jhin.2021.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Colonization resistance by gut microbiota is a fundamental phenomenon in infection prevention and control. Hospitalized patients may be exposed to multi-drug-resistant bacteria when hand hygiene compliance among healthcare workers is not adequate. An additional layer of defence is provided by the healthy gut microbiota, which helps clear the exogenous bacteria and acts as a safety net when hand hygiene procedures are not followed. This narrative review focuses on the role of the gut microbiota in colonization resistance against multi-drug-resistant bacteria, and its implications for infection control. The review discusses the underlying mechanisms of colonization resistance (direct or indirect), the concept of resilience of the gut microbiota, the link between the antimicrobial spectrum and gut dysbiosis, and possible therapeutic strategies. Antimicrobial stewardship is crucial to maximize the effects of colonization resistance. Avoiding unnecessary antimicrobial therapy, shortening the antimicrobial duration as much as possible, and favouring antibiotics with low anti-anaerobe activity may decrease the acquisition and expansion of multi-drug-resistant bacteria. Even after antimicrobial therapy, the resilience of the gut microbiota often occurs spontaneously. Spontaneous resilience explains the existence of a window of opportunity for colonization of multi-drug-resistant bacteria during or just after antimicrobial therapy. Strategies favouring resilience of the gut microbiota, such as high-fibre diets or precision probiotics, should be evaluated.
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Affiliation(s)
- R Le Guern
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France.
| | - S Stabler
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - P Gosset
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - M Pichavant
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - T Grandjean
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - E Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - Y Karaca
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - K Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - E Kipnis
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Réanimation Chirurgicale, CHU Lille, Lille, France
| | - R Dessein
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France
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