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Yadegar A, Bar-Yoseph H, Monaghan TM, Pakpour S, Severino A, Kuijper EJ, Smits WK, Terveer EM, Neupane S, Nabavi-Rad A, Sadeghi J, Cammarota G, Ianiro G, Nap-Hill E, Leung D, Wong K, Kao D. Fecal microbiota transplantation: current challenges and future landscapes. Clin Microbiol Rev 2024; 37:e0006022. [PMID: 38717124 DOI: 10.1128/cmr.00060-22] [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] [Indexed: 06/14/2024] Open
Abstract
SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.
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Affiliation(s)
- Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haggai Bar-Yoseph
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tanya Marie Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sepideh Pakpour
- School of Engineering, Faculty of Applied Sciences, UBC, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Andrea Severino
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Ed J Kuijper
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisabeth M Terveer
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Sukanya Neupane
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Sadeghi
- School of Engineering, Faculty of Applied Sciences, UBC, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Estello Nap-Hill
- Department of Medicine, Division of Gastroenterology, St Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dickson Leung
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karen Wong
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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Wu P, Lee PC, Chang TE, Hsieh YC, Chiou JJ, Lin CH, Huang YL, Lin YT, Huo TI, Schnabl B, Lee KC, Hou MC. Fecal Carriage of Multidrug-Resistant Organisms Increases the Risk of Hepatic Encephalopathy in Cirrhotic Patients: Insights from Gut Microbiota and Metabolite Features. RESEARCH SQUARE 2024:rs.3.rs-4328129. [PMID: 38766152 PMCID: PMC11100873 DOI: 10.21203/rs.3.rs-4328129/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Impact of fecal colonization by multidrug-resistant organisms (MDROs) on changes in gut microbiota and associated metabolites, as well as its role in cirrhosis-associated outcomes, has not been thoroughly investigated. Methods Eighty-eight cirrhotic patients and 22 healthy volunteers were prospectively enrolled with analysis conducted on plasma metabolites, fecal MDROs, and microbiota. Patients were followed for a minimum of one year. Predictive factors for cirrhosis-associated outcomes were identified using Cox proportional hazards regression models, and risk factors for fecal MDRO carriage were assessed using logistic regression model. Correlations between microbiota and metabolic profiles were evaluated through Spearman's rank test. Results Twenty-nine (33%) cirrhotic patients exhibited MDRO carriage, with a notably higher rate of hepatic encephalopathy (HE) in MDRO carriers (20.7% vs. 3.2%, p = 0.008). Cox regression analysis identified higher serum lipopolysaccharide levels and fecal MDRO carriage as predictors for HE development. Logistic regression analysis showed that MDRO carriage is an independent risk factor for developing HE. Microbiota analysis showed a significant dissimilarity of fecal microbiota between cirrhotic patients with and without MDRO carriage (p = 0.033). Thirty-two metabolites exhibiting significantly different expression levels among healthy controls, cirrhotic patients with and without MDRO carriage were identified. Six of the metabolites showed correlation with specific bacterial taxa expression in MDRO carriers, with isoaustin showing significantly higher levels in MDRO carriers experiencing HE compared to those who did not. Conclusion Fecal MDRO carriage is associated with altered gut microbiota, metabolite modulation, and an elevated risk of HE occurrence within a year.
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Affiliation(s)
| | | | | | | | | | | | - Yi-Long Huang
- National Yang Ming Chiao Tung University - Yangming Campus
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3
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Decker BK. Primum Non Nocere: Time to Rethink Probiotic Therapy. Crit Care Med 2023; 51:1592-1593. [PMID: 37902343 DOI: 10.1097/ccm.0000000000005977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Affiliation(s)
- Brooke K Decker
- Infectious Diseases/Deputy Chief of Staff, Chief of Staff Office, VA Pittsburgh, Pittsburgh, PA
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4
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Gupta U, Dey P. Rise of the guardians: Gut microbial maneuvers in bacterial infections. Life Sci 2023; 330:121993. [PMID: 37536616 DOI: 10.1016/j.lfs.2023.121993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
AIMS Bacterial infections are one of the major causes of mortality globally. The gut microbiota, primarily comprised of the commensals, performs an important role in maintaining intestinal immunometabolic homeostasis. The current review aims to provide a comprehensive understanding of how modulation of the gut microbiota influences opportunistic bacterial infections. MATERIALS AND METHODS Primarily centered around mechanisms related to colonization resistance, nutrient, and metabolite-associated factors, mucosal immune response, and commensal-pathogen reciprocal interactions, we discuss how gut microbiota can promote or prevent bacterial infections. KEY FINDINGS Opportunistic infections can occur directly due to obligate pathogens or indirectly due to the overgrowth of opportunistic pathobionts. Gut microbiota-centered mechanisms of altered intestinal immunometabolic and metabolomic homeostasis play a significant role in infection promotion and prevention. Depletion in the population of commensals, increased abundance of pathobionts, and overall decrease in gut microbial diversity and richness caused due to prolonged antibiotic use are risk factors of opportunistic bacterial infections, including infections from multidrug-resistant spp. Gut commensals can limit opportunistic infections by mechanisms including the production of antimicrobials, short-chain fatty acids, bile acid metabolism, promoting mucin formation, and maintaining immunological balance at the mucosa. Gut microbiota-centered strategies, including the administration of probiotics and fecal microbiota transplantation, could help attenuate opportunistic bacterial infections. SIGNIFICANCE The current review discussed the gut microbial population and function-specific aspects contributing to bacterial infection susceptibility and prophylaxis. Collectively, this review provides a comprehensive understanding of the mechanisms related to the dual role of gut microbiota in bacterial infections.
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Affiliation(s)
- Upasana Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India.
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5
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Araos R, Smith RM, Styczynski A, Sánchez F, Acevedo J, Maureira L, Paredes C, González M, Rivas L, Spencer-Sandino M, Peters A, Khan A, Sepulveda D, Wettig LR, Rioseco ML, Usedo P, Soto PR, Huidobro LA, Ferreccio C, Park BJ, Undurraga E, D'Agata EMC, Jara A, Munita JM. High Burden of Intestinal Colonization With Antimicrobial-Resistant Bacteria in Chile: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study. Clin Infect Dis 2023; 77:S75-S81. [PMID: 37406045 DOI: 10.1093/cid/ciad283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Antimicrobial resistance is a global threat, heavily impacting low- and middle-income countries. This study estimated antimicrobial-resistant gram-negative bacteria (GNB) fecal colonization prevalence in hospitalized and community-dwelling adults in Chile before the coronavirus disease 2019 pandemic. METHODS From December 2018 to May 2019, we enrolled hospitalized adults in 4 public hospitals and community dwellers from central Chile, who provided fecal specimens and epidemiological information. Samples were plated onto MacConkey agar with ciprofloxacin or ceftazidime added. All recovered morphotypes were identified and characterized according to the following phenotypes: fluoroquinolone-resistant (FQR), extended-spectrum cephalosporin-resistant (ESCR), carbapenem-resistant (CR), or multidrug-resistant (MDR; as per Centers for Disease Control and Prevention criteria) GNB. Categories were not mutually exclusive. RESULTS A total of 775 hospitalized adults and 357 community dwellers were enrolled. Among hospitalized subjects, the prevalence of colonization with FQR, ESCR, CR, or MDR-GNB was 46.4% (95% confidence interval [CI], 42.9-50.0), 41.2% (95% CI, 37.7-44.6), 14.5% (95% CI, 12.0-16.9), and 26.3% (95% CI, 23.2-29.4). In the community, the prevalence of FQR, ESCR, CR, and MDR-GNB colonization was 39.5% (95% CI, 34.4-44.6), 28.9% (95% CI, 24.2-33.6), 5.6% (95% CI, 3.2-8.0), and 4.8% (95% CI, 2.6-7.0), respectively. CONCLUSIONS A high burden of antimicrobial-resistant GNB colonization was observed in this sample of hospitalized and community-dwelling adults, suggesting that the community is a relevant source of antibiotic resistance. Efforts are needed to understand the relatedness between resistant strains circulating in the community and hospitals.
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Affiliation(s)
- Rafael Araos
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research in Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Rachel M Smith
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashley Styczynski
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Felipe Sánchez
- Instituto de Sociología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Johanna Acevedo
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Centro de Control y Prevención del Cáncer (CECAN) FONDAP 152220002, Santiago, Chile
| | - Lea Maureira
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Catalina Paredes
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Maite González
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Lina Rivas
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research in Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Maria Spencer-Sandino
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research in Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Anne Peters
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research in Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Ayesha Khan
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Dino Sepulveda
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Loreto Rojas Wettig
- Hospital Puerto Montt, Facultad de Medicina, Universidad San Sebastián, Chile
| | - María Luisa Rioseco
- Hospital Puerto Montt, Facultad de Medicina, Universidad San Sebastián, Chile
| | - Pedro Usedo
- Hospital Regional de Antofagasta, Universidad de Antofagasta, Chile
| | | | - Laura Andrea Huidobro
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Catterina Ferreccio
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Facultad de Medicina, Departamento de Salud Pública, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Benjamin J Park
- US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eduardo Undurraga
- Multidisciplinary Initiative for Collaborative Research in Bacterial Resistance (MICROB-R), Santiago, Chile
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago, Chile
- Research Center for Integrated Disaster Risk Management (CIGIDEN), Santiago, Chile
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada
| | - Erika M C D'Agata
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island, USA
| | - Alejandro Jara
- Facultad de Matemáticas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jose M Munita
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research in Bacterial Resistance (MICROB-R), Santiago, Chile
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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: 1.0] [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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Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol 2022; 30:853-865. [DOI: 10.1016/j.tim.2022.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
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8
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Changes in the gut microbiota and risk of colonization by multidrug-resistant bacteria, infection and death in critical care patients. Clin Microbiol Infect 2022; 28:975-982. [DOI: 10.1016/j.cmi.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/22/2022]
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9
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Bilsen MP, Lambregts MM, van Prehn J, Kuijper EJ. Faecal microbiota replacement to eradicate antimicrobial resistant bacteria in the intestinal tract - a systematic review. Curr Opin Gastroenterol 2022; 38:15-25. [PMID: 34636363 PMCID: PMC8654246 DOI: 10.1097/mog.0000000000000792] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Antimicrobial resistance is a rising threat to global health and is associated with increased mortality. Intestinal colonisation with multidrug-resistant organisms (MDRO) can precede invasive infection and facilitates spread within communities and hospitals. Novel decolonisation strategies, such as faecal microbiota transplantation (FMT), are being explored. The purpose of this review is to provide an update on how the field of FMT for MDRO decolonisation has developed during the past year and to assess the efficacy of FMT for intestinal MDRO decolonisation. RECENT FINDINGS Since 2020, seven highly heterogenous, small, nonrandomised cohort studies and five case reports have been published. In line with previous literature, decolonisation rates ranged from 20 to 90% between studies and were slightly higher for carbapenem-resistant Enterobacteriaceae than vancomycin-resistant Enterococcus. Despite moderate decolonisation rates in two studies, a reduction in MDRO bloodstream and urinary tract infections was observed. SUMMARY AND IMPLICATIONS Although a number of smaller cohort studies show some effect of FMT for MDRO decolonisation, questions remain regarding the true efficacy of FMT (taking spontaneous decolonisation into account), the optimal route of administration, the role of antibiotics pre and post-FMT and the efficacy in different patient populations. The observed decrease in MDRO infections post-FMT warrants further research.
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Affiliation(s)
| | | | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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10
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Ducarmon QR, Terveer EM, Nooij S, Bloem MN, Vendrik KEW, Caljouw MAA, Sanders IMJG, van Dorp SM, Wong MC, Zwittink RD, Kuijper EJ. Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home. Genome Med 2021; 13:54. [PMID: 33827686 PMCID: PMC8028076 DOI: 10.1186/s13073-021-00869-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00869-z.
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Affiliation(s)
- Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands. .,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle N Bloem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Monique A A Caljouw
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sofie M van Dorp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Internal Medicine and Geriatrics, Onze Lieve Vrouwe Gasthuis (OLVG Hospital), Amsterdam, The Netherlands
| | - Man C Wong
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Romy D Zwittink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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11
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Abstract
Fecal microbiota transplantation (FMT) has been recommended in clinical guidelines for the treatment of recurrent Clostridioides difficile infection (CDI). However, it is considered investigational by most regulatory agencies. As the adoption of FMT has increased from a small group of CDI experts alone to more widespread use, there has been a corresponding increase in concern regarding potential risk. FMT is largely considered a safe procedure although risks described range from mild gastrointestinal symptoms to serious infection. Currently, there is variability in how "FMT" is characterized specifically regarding testing approach, which, in turn, impacts the risk profile. This has been highlighted by the rare cases of multidrug-resistant organisms, Shiga toxin-producing Escherichia and enteropathogenic E. coli, recently reported, where these organisms were not screened. These cases have prompted additional screening mandates from the US Food and Drug Administration (FDA), which has maintained its policy of enforcement discretion for the use of FMT for CDI not responding to standard therapy. Here, we examine the evolving risk landscape of FMT.
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12
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Abstract
The human microbiome participates in numerous aspects of human physiology and disease states. Recently, studies have begun to explore the role of the microbiome in colonization, infection and transmission of pathogens. This review provides a summary of the methodological principles used in microbiome studies and the published evidence of the impact of microbiome dysbiosis in infection prevention.
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Seekatz AM, Bassis CM, Fogg L, Moore NM, Rhee Y, Lolans K, Weinstein RA, Lin MY, Young VB, Hayden MK. Gut Microbiota and Clinical Features Distinguish Colonization With Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae at the Time of Admission to a Long-term Acute Care Hospital. Open Forum Infect Dis 2018; 5:ofy190. [PMID: 30151415 PMCID: PMC6101546 DOI: 10.1093/ofid/ofy190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/27/2018] [Indexed: 12/29/2022] Open
Abstract
Background Identification of gut microbiota features associated with antibiotic-resistant bacterial colonization may reveal new infection prevention targets. Methods We conducted a matched, case–control study of long-term acute care hospital (LTACH) patients to identify gut microbiota and clinical features associated with colonization by Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp), an urgent antibiotic resistance threat. Fecal or rectal swab specimens were collected and tested for KPC-Kp; 16S rRNA gene-based sequencing was performed. Comparisons were made between cases and controls in calibration and validation subsamples using microbiota similarity indices, logistic regression, and unit-weighted predictive models. Results Case (n = 32) and control (n = 99) patients had distinct fecal microbiota communities, but neither microbiota diversity nor inherent clustering into community types distinguished case and control specimens. Comparison of differentially abundant operational taxonomic units (OTUs) revealed 1 OTU associated with case status in both calibration (n = 51) and validation (n = 80) subsamples that matched the canonical KPC-Kp strain ST258. Permutation analysis using the presence or absence of OTUs and hierarchical logistic regression identified 2 OTUs (belonging to genus Desulfovibrio and family Ruminococcaceae) associated with KPC-Kp colonization. Among clinical variables, the presence of a decubitus ulcer alone was independently and consistently associated with case status. Combining the presence of the OTUs Desulfovibrio and Ruminococcaceae with decubitus ulcer increased the likelihood of KPC-Kp colonization to >38% in a unit-weighted predictive model. Conclusions We identified microbiota and clinical features that distinguished KPC-Kp gut colonization in LTACH patients, a population particularly susceptible to KPC-Kp infection. These features may warrant further investigation as markers of risk for KPC-Kp colonization.
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Affiliation(s)
- Anna M Seekatz
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christine M Bassis
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Louis Fogg
- Department of Nursing, Rush College of Nursing, Chicago, Illinois
| | | | - Yoona Rhee
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, Illinois
| | | | - Robert A Weinstein
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, Illinois.,Cook County Health and Hospitals System, Chicago, Illinois
| | - Michael Y Lin
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, Illinois
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mary K Hayden
- Department of Pathology.,Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, Illinois
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