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Kim J, Kim JS, Kim SH, Yoo S, Lee JK, Kim K. Deep learning-based prediction of Clostridioides difficile infection caused by antibiotics using longitudinal electronic health records. NPJ Digit Med 2024; 7:224. [PMID: 39181992 PMCID: PMC11344761 DOI: 10.1038/s41746-024-01215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024] Open
Abstract
Clostridioides difficile infection (CDI) is a major cause of antibiotic-associated diarrhea and colitis. It is recognized as one of the most significant hospital-acquired infections. Although CDI can develop severe complications and spores of Clostridioides difficile can be transmitted by the fecal-oral route, CDI is occasionally overlooked in clinical settings. Thus, it is necessary to monitor high CDI risk groups, particularly those undergoing antibiotic treatment, to prevent complications and spread. We developed and validated a deep learning-based model to predict the occurrence of CDI within 28 days after starting antibiotic treatment using longitudinal electronic health records. For each patient, timelines of vital signs and laboratory tests with a 35-day monitoring period and a patient information vector consisting of age, sex, comorbidities, and medications were constructed. Our model achieved the prediction performance with an area under the receiver operating characteristic curve of 0.952 (95% CI: 0.932-0.973) in internal validation and 0.972 (95% CI: 0.968-0.975) in external validation. Platelet count and body temperature emerged as the most important features. The risk score, the output value of the model, exhibited a consistent increase in the CDI group, while the risk score in the non-CDI group either maintained its initial value or decreased. Using our CDI prediction model, high-risk patients requiring symptom monitoring can be identified. This could help reduce the underdiagnosis of CDI, thereby decreasing transmission and preventing complications.
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Affiliation(s)
- Junmo Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
| | - Joo Seong Kim
- Division of Gastroenterology, Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Republic of Korea
| | - Sae-Hoon Kim
- Division of Allergy & Clinical Immunology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sooyoung Yoo
- Office of eHealth Research and Businesses, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jun Kyu Lee
- Division of Gastroenterology, Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Republic of Korea.
| | - Kwangsoo Kim
- Department of Transdisciplinary Medicine, Institute of Convergence Medicine with Innovative Technology, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea.
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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 PMCID: PMC11325845 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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Ziaei Chamgordani S, Yadegar A, Ghourchian H. C. difficile biomarkers, pathogenicity and detection. Clin Chim Acta 2024; 558:119674. [PMID: 38621586 DOI: 10.1016/j.cca.2024.119674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy. APPROACH A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods. RESULTS The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected. CONCLUSION To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.
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Affiliation(s)
- Sepideh Ziaei Chamgordani
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedayatollah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
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Bachmann I, Behrmann O, Klingenberg-Ernst M, Rupnik M, Hufert FT, Dame G, Weidmann M. Rapid Isothermal Detection of Pathogenic Clostridioides difficile Using Recombinase Polymerase Amplification. Anal Chem 2024; 96:3267-3275. [PMID: 38358754 DOI: 10.1021/acs.analchem.3c02985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Nosocomial-associated diarrhea due to Clostridioides difficile infection (CDI) is diagnosed after sample precultivation by the detection of the toxins in enzyme immunoassays or via toxin gene nucleic acid amplification. Rapid and direct diagnosis is important for targeted treatment to prevent severe cases and recurrence. We developed two singleplex and a one-pot duplex fluorescent 15 min isothermal recombinase polymerase amplification (RPA) assays targeting the toxin genes A and B (tcdA and tcdB). Furthermore, we adapted the singleplex RPA to a 3D-printed microreactor device. Analytical sensitivity was determined using a DNA standard and DNA extracts of 20 C. difficile strains with different toxinotypes. Nineteen clostridial and gastrointestinal bacteria strains were used to determine analytical specificity. Adaptation of singleplex assays to duplex assays in a 50 μL volume required optimized primer and probe concentrations. A volume reduction by one-fourth (12.4 μL) was established for the 3D-printed microreactor. Mixing of RPA was confirmed as essential for optimal analytical sensitivity. Detection limits (LOD) ranging from 119 to 1411 DNA molecules detected were similar in the duplex tube format and in the singleplex 3D-printed microreactor format. The duplex RPA allows the simultaneous detection of both toxins important for the timely and reliable diagnosis of CDI. The 3D-printed reaction chamber can be developed into a microfluidic lab-on-a-chip system use at the point of care.
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Affiliation(s)
- Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
| | - Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
| | | | - Maja Rupnik
- Center for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food, Prvomajska ulica 1, 2000 Maribor, Slovenia
- Faculty of Medicine, Maribor, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Department of Virology, University Medical Center, Kreuzbergring 57, 37075 Göttingen, Germany
- Brandenburg University of Technology Cottbus - Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Department of Virology, University Medical Center, Kreuzbergring 57, 37075 Göttingen, Germany
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Tikunov AY, Fedorets VA, Shrainer EV, Morozov VV, Bystrova VI, Tikunova NV. Intestinal Microbiome Changes and Clinical Outcomes of Patients with Ulcerative Colitis after Fecal Microbiota Transplantation. J Clin Med 2023; 12:7702. [PMID: 38137770 PMCID: PMC10743744 DOI: 10.3390/jcm12247702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND AND AIMS Ulcerative colitis (UC) is a chronic inflammatory disease that affects many people. One of the possible ways to treat UC is fecal microbiota transplantation (FMT). In this study, changes in the intestinal microbiome and clinical outcomes of 20 patients with UC after FMT were estimated. METHODS FMT enemas were administrated ten times, once a day, and fecal microbiota from three donors was used for each enema. The clinical outcomes were assessed after eight weeks and then via a patient survey. The 16S rRNA profiles of the gut microbiota were compared between three samplings: samples from 20 patients with UC before and after FMT and samples from 18 healthy volunteers. RESULTS Clinical remission was achieved in 19 (95%) patients at week 8. Adverse events occurred in five patients, including one non-responder. A significant increase in average biodiversity was shown in samples after FMT compared to samples before FMT, as well as a decrease in the proportion of some potentially pathogenic bacteria. CONCLUSION The efficacy of FMT for UC treatment was confirmed; however, the duration of remission varied substantially, possibly due to different characteristics of the initial microbiota of patients. Targeted analysis of a patient's microbiome before FMT could increase the treatment efficacy.
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Affiliation(s)
- Artem Y. Tikunov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria A. Fedorets
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Evgenia V. Shrainer
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Vitaliy V. Morozov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria I. Bystrova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Nina V. Tikunova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
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Henderickx JG, Crobach MJ, Terveer EM, Smits WK, Kuijper EJ, Zwittink RD. Fungal and bacterial gut microbiota differ between Clostridioides difficile colonization and infection. MICROBIOME RESEARCH REPORTS 2023; 3:8. [PMID: 38455084 PMCID: PMC10917615 DOI: 10.20517/mrr.2023.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/21/2023] [Accepted: 11/30/2023] [Indexed: 03/09/2024]
Abstract
Aim: The bacterial microbiota is well-recognized for its role in Clostridioides difficile colonization and infection, while fungi and yeasts remain understudied. The aim of this study was to analyze the predictive value of the mycobiota and its interactions with the bacterial microbiota in light of C. difficile colonization and infection. Methods: The mycobiota was profiled by ITS2 sequencing of fecal DNA from C. difficile infection (CDI) patients (n = 29), asymptomatically C. difficile colonization (CDC) patients (n = 38), and hospitalized controls with C. difficile negative stool culture (controls; n = 38). Previously published 16S rRNA gene sequencing data of the same cohort were used additionally for machine learning and fungal-bacterial network analysis. Results: CDI patients were characterized by a significantly higher abundance of Candida spp. (MD 0.270 ± 0.089, P = 0.002) and Candida albicans (MD 0.165 ± 0.082, P = 0.023) compared to controls. Additionally, they were deprived of Aspergillus spp. (MD -0.067 ± 0.026, P = 0.000) and Penicillium spp. (MD -0.118 ± 0.043, P = 0.000) compared to CDC patients. Network analysis revealed a positive association between several fungi and bacteria in CDI and CDC, although the analysis did not reveal a direct association between Clostridioides spp. and fungi. Furthermore, the microbiota machine learning model outperformed the models based on the mycobiota and the joint microbiota-mycobiota model. The microbiota classifier successfully distinguished CDI from CDC [Area Under the Receiver Operating Characteristic (AUROC) = 0.884] and CDI from controls (AUROC = 0.905). Blautia and Bifidobacterium were marker genera associated with CDC patients and controls. Conclusion: The gut mycobiota differs between CDI, CDC, and controls and may affect Clostridioides spp. through indirect interactions. The mycobiota data alone could not successfully discriminate CDC from controls or CDI patients and did not have additional predictive value to the bacterial microbiota data. The identification of bacterial marker genera associated with CDC and controls warrants further investigation.
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Affiliation(s)
- Jannie G.E. Henderickx
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Monique J.T. Crobach
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Elisabeth M. Terveer
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Netherlands Donor Feces Bank, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Wiep Klaas Smits
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Ed J. Kuijper
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Netherlands Donor Feces Bank, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Romy D. Zwittink
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
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Rajack F, Medford S, Naab T. Clostridioides difficile infection leading to fulminant colitis with toxic megacolon. Autops Case Rep 2023; 13:e2023457. [PMID: 38034515 PMCID: PMC10687841 DOI: 10.4322/acr.2023.457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/14/2023] [Indexed: 12/02/2023]
Abstract
Clostridioidesdifficile infection (CDI) is the culprit of millions of nosocomial infections in the United States. Programs that successfully decrease its incidence, therefore, render cost savings for the healthcare system. Toxic megacolon and perforation are two of the most significant complications with increased mortality rates. We report a 23-year-old nursing home resident hospitalized for fever, cough, and green sputum. After 3 days of antibiotic therapy, he developed abdominal distension, diarrhea, and vomiting and underwent a total colectomy. The colon was dilated to a maximum of 11 cm with markedly edematous mucosa and yellow pseudomembranes. Qualitative PCR of the stool detected Clostridioides difficile toxin B gene. While there is no consensus for the required interval between antibiotic treatment and CDI, this presentation 3 days after starting the antibiotic therapy is earlier than most proposed ranges.
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Affiliation(s)
- Fareed Rajack
- Howard University Hospital, Department of Pathology and Laboratory Medicine, Washington, D.C., United States of America
| | - Shawn Medford
- Howard University College of Medicine, Washington, D.C., United States of America
| | - Tammey Naab
- Howard University Hospital, Department of Pathology and Laboratory Medicine, Washington, D.C., United States of America
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Shao T, Hsu R, Hacein-Bey C, Zhang W, Gao L, Kurth MJ, Zhao H, Shuai Z, Leung PSC. The Evolving Landscape of Fecal Microbial Transplantation. Clin Rev Allergy Immunol 2023; 65:101-120. [PMID: 36757537 PMCID: PMC9909675 DOI: 10.1007/s12016-023-08958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 02/10/2023]
Abstract
The human gastrointestinal tract houses an enormous microbial ecosystem. Recent studies have shown that the gut microbiota plays significant physiological roles and maintains immune homeostasis in the human body. Dysbiosis, an imbalanced gut microbiome, can be associated with various disease states, as observed in infectious diseases, inflammatory diseases, autoimmune diseases, and cancer. Modulation of the gut microbiome has become a therapeutic target in treating these disorders. Fecal microbiota transplantation (FMT) from a healthy donor restores the normal gut microbiota homeostasis in the diseased host. Ample evidence has demonstrated the efficacy of FMT in recurrent Clostridioides difficile infection (rCDI). The application of FMT in other human diseases is gaining attention. This review aims to increase our understanding of the mechanisms of FMT and its efficacies in human diseases. We discuss the application, route of administration, limitations, safety, efficacies, and suggested mechanisms of FMT in rCDI, autoimmune diseases, and cancer. Finally, we address the future perspectives of FMT in human medicine.
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Affiliation(s)
- Tihong Shao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
- Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis School of Medicine, Davis, CA, 95616, USA
| | - Ronald Hsu
- Division of Gastroenterology, University of California Davis School of Medicine, Davis, CA, 95616, USA
| | - Camelia Hacein-Bey
- Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis School of Medicine, Davis, CA, 95616, USA
| | - Weici Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Lixia Gao
- Department of Rheumatology and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Mark J Kurth
- Department of Chemistry, University of California Davis, Davis, CA, 95616, USA
| | - Huanhuan Zhao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Zongwen Shuai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Patrick S C Leung
- Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis School of Medicine, Davis, CA, 95616, USA.
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9
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Ivashkin VT, Lyashenko OS, Drapkina OM, Alexeeva OP, Alekseenko SA, Andreev DN, Baranovsky AY, Goloshchapov OV, Zheleznova NV, Zolnikova OY, Kliaritskaia IL, Korochanskaya NV, Lapina TL, Maev IV, Maslennikov RV, Myazin RG, Pavlov PV, Perekalina MV, Pisarenko NA, Povtoreyko AV, Poluektova EA, Sekretareva LA, Tkachev AV, Troshkina YM, Trukhmanov AS, Ulyanin AI, Filatova SG, Tsukanov VV, Shifrin OS. Clinical Practice Guidelines of the Scientific Society for the Clinical Study of Human Microbiome, of the Russian Gastroenterological Association and the Russian Society for the Prevention of Noncommunicable Diseases on the Diagnosis and Treatment of <i>Clostridioides difficile</i> (<i>C. difficile</i>)-associated Disease in Adults. RUSSIAN JOURNAL OF GASTROENTEROLOGY, HEPATOLOGY, COLOPROCTOLOGY 2023; 33:85-119. [DOI: 10.22416/1382-4376-2023-33-3-85-119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2024]
Abstract
Аim: the clinical practice guidelines intended for gastroenterologists, internal medicine specialists, infectious disease specialists, general practitioners (family doctors), coloproctologists, surgeons and endoscopists present modern methods of diagnosis, prevention and treatment of C. difficile-associated disease.Key points. C. difficile-associated disease is a disease that develops when the diversity of the intestinal microbiota decreases and C. difficile excessively colonizes the colon, the toxins of which damage the intestinal muco-epithelial barrier, followed by the development of inflammation in the colon wall, with diarrhea being a characteristic clinical manifestation. The clinical presentation of the disease can vary from asymptomatic carriage, mild to moderate diarrhea that resolves on its own, to profuse watery diarrhea and pseudomembranous colitis with development of life-threatening complications. The diagnosis of C. difficile-associated disease is based on an assessment of the clinical presentation, medical history, an objective examination of the patient and laboratory stool tests. The disease severity is determined by clinical symptoms and laboratory findings. Additional diagnostic methods that are used according to indications and contribute to the assessment of severity include endoscopy of the colon and abdominal cavity imaging methods. Treatment should be initiated in cases of characteristic clinical presentation of C. difficile-associated disease and positive laboratory stool testing. The choice of drug and treatment regimen depends on the severity of the episode, the presence of complications, and whether the episode is initial, recurrent, or reinfection.Conclusion. Determination of target groups of patients for the diagnosis of clostridial infection is important in preventing overdiagnosis and subsequent unnecessary treatment. Timely diagnosis and treatment of C. difficile-associated disease help avoiding the development of life-threatening complications and improve the prognosis and quality of life of patients.
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Affiliation(s)
- V. T. Ivashkin
- I.M. Sechenov First Moscow State University (Sechenov University)
| | - O. S. Lyashenko
- I.M. Sechenov First Moscow State University (Sechenov University)
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
| | | | | | - D. N. Andreev
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry
| | | | | | | | - O. Yu. Zolnikova
- I.M. Sechenov First Moscow State University (Sechenov University)
| | | | | | - T. L. Lapina
- I.M. Sechenov First Moscow State University (Sechenov University)
| | - I. V. Maev
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry
| | | | | | - P. V. Pavlov
- I.M. Sechenov First Moscow State University (Sechenov University)
| | | | | | | | - E. A. Poluektova
- I.M. Sechenov First Moscow State University (Sechenov University)
| | | | | | | | - A. S. Trukhmanov
- I.M. Sechenov First Moscow State University (Sechenov University)
| | - A. I. Ulyanin
- I.M. Sechenov First Moscow State University (Sechenov University)
| | | | - V. V. Tsukanov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”
| | - O. S. Shifrin
- I.M. Sechenov First Moscow State University (Sechenov University)
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10
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Jenior ML, Leslie JL, Kolling GL, Archbald-Pannone L, Powers DA, Petri WA, Papin JA. Systems-ecology designed bacterial consortium protects from severe Clostridioides difficile infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552483. [PMID: 37609255 PMCID: PMC10441344 DOI: 10.1101/2023.08.08.552483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Fecal Microbiota Transplant (FMT) is an emerging therapy that has had remarkable success in treatment and prevention of recurrent Clostridioides difficile infection (rCDI). FMT has recently been associated with adverse outcomes such as inadvertent transfer of antimicrobial resistance, necessitating development of more targeted bacteriotherapies. To address this challenge, we developed a novel systems biology pipeline to identify candidate probiotic strains that would be predicted to interrupt C. difficile pathogenesis. Utilizing metagenomic characterization of human FMT donor samples, we identified those metabolic pathways most associated with successful FMTs and reconstructed the metabolism of encoding species to simulate interactions with C. difficile . This analysis resulted in predictions of high levels of cross-feeding for amino acids in species most associated with FMT success. Guided by these in silico models, we assembled consortia of bacteria with increased amino acid cross-feeding which were then validated in vitro . We subsequently tested the consortia in a murine model of CDI, demonstrating total protection from severe CDI through decreased toxin levels, recovered gut microbiota, and increased intestinal eosinophils. These results support the novel framework that amino acid cross-feeding is likely a critical mechanism in the initial resolution of CDI by FMT. Importantly, we conclude that our predictive platform based on predicted and testable metabolic interactions between the microbiota and C. difficile led to a rationally designed biotherapeutic framework that may be extended to other enteric infections.
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11
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Ciuntu BM, Balan GG, Buna-Arvinte M, Abdulan IM, Papancea A, Toma ȘL, Veliceasa B, Bădulescu OV, Ghiga G, Fătu AM, Vascu MB, Moldovanu A, Vintilă D, Vasilescu AM. Clostridium difficile Infections in an Emergency Surgical Unit from North-East Romania. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59050830. [PMID: 37241061 DOI: 10.3390/medicina59050830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023]
Abstract
Background and Objectives: Colitis with Clostridium difficile is an important health problem that occurs with an intensity that varies between mild and severe. Surgical interventions are required only in fulminant forms. There is little evidence regarding the best surgical intervention in these cases. Materials and Methods: Patients with C. difficile infection were identified from the two surgery clinics from the 'Saint Spiridon' Emergency Hospital Iași, Romania. Data regarding the presentation, indication for surgery, antibiotic therapy, type of toxins, and post-operative outcomes were collected over a 3-year period. Results: From a total of 12,432 patients admitted for emergency or elective surgery, 140 (1.12%) were diagnosed with C. difficile infection. The mortality rate was 14% (20 cases). Non-survivors had higher rates of lower-limb amputations, bowel resections, hepatectomy, and splenectomy. Additional surgery was necessary in 2.8% of cases because of the complications of C. difficile colitis. In three cases, terminal colostomy was performed and as well as one case with subtotal colectomy with ileostomy. All patients who required the second surgery died within the 30-day mortality period. Conclusions: In our prospective study, the incidence was increased both in cases of patients with interventions on the colon and in those requiring limb amputations. Surgical interventions are rarely required in patients with C. difficile colitis.
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Affiliation(s)
- Bogdan Mihnea Ciuntu
- Department of General Surgery, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street, No. 16, 700115 Iasi, Romania
| | - Gheorghe G Balan
- Department of Gastroenterology, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street, No. 16, 700115 Iasi, Romania
| | - Mihaela Buna-Arvinte
- Department of General Surgery, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street, No. 16, 700115 Iasi, Romania
| | - Irina Mihaela Abdulan
- Department of Medical Specialties I, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adelina Papancea
- Department of General Surgery, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street, No. 16, 700115 Iasi, Romania
| | - Ștefan Lucian Toma
- Department of Materials Engineering and Industrial Security, Faculty of Materials Science and Engineering, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania
| | - Bogdan Veliceasa
- Department of Traumatology and Orthopaedics, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Oana Viola Bădulescu
- Department of Haematholohy, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Gabriela Ghiga
- Department of Mother and Child Medicine, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ana Maria Fătu
- Department of Implantology Removable Denture Technology, Discipline of Ergonomy, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Mihai Bogdan Vascu
- Department of Odontology, Periodontology and Fixed Prosthesis, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Antonia Moldovanu
- Department of Odontology, Periodontology and Fixed Prosthesis, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Dan Vintilă
- Department of General Surgery, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street, No. 16, 700115 Iasi, Romania
| | - Alin Mihai Vasilescu
- Department of General Surgery, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street, No. 16, 700115 Iasi, Romania
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12
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Amamoto R, Shimamoto K, Suwa T, Park S, Matsumoto H, Shimizu K, Katto M, Makino H, Matsubara S, Aoyagi Y. Relationships between dietary diversity and gut microbial diversity in the elderly. Benef Microbes 2022; 13:453-464. [PMID: 36377581 DOI: 10.3920/bm2022.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Diet is considered as a major driver of gut microbiota composition. However, little is known about the relationship between overall dietary balance and gut microbiota, especially in the elderly. Here, using the Quantitative Index for Dietary Diversity (QUANTIDD), we analysed the relationships between dietary diversity and gut microbiota diversity in 445 Japanese subjects aged 65-90 years. We also examined the effect of age by comparing the young-old group aged 65 to 74 years (<75 years group; n=246) and the old-old group aged 75 years and older (≥75 years group; n=199). QUANTIDD showed significant positive relationships with Pielou's evenness and Shannon indices, two α-diversity indices related to the uniformity of species distribution. This suggests that a more diverse diet is associated with a more uniform abundance of various bacterial groups, rather than a greater variety of gut bacteria. QUANTIDD also showed significant positive associations with the abundance of Anaerostipes, Eubacterium eligens group, and Eubacterium ventriosum group, which produce short-chain fatty acids (SCFAs) and are beneficial to health. Negative association was found with the abundance of Ruminococcus gnavus group, which produces inflammatory polysaccharides. Positive associations between QUANTIDD and α-diversity indices or the abundance of specific bacterial groups were identified among all subjects and in the <75 years group, but not in the ≥75 years group. Our results suggest that dietary diversity contributes to the diversity of the gut microbiota and increases the abundance of SCFAs-producing bacteria, but only up to a certain age. These findings help to understand the complex relationship between diet and gut microbiota, and provide hints for specific dietary interventions to promote beneficial gut microbiota in the elderly.
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Affiliation(s)
- R Amamoto
- Food Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - K Shimamoto
- Food Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - T Suwa
- Food Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - S Park
- Exercise Sciences Research Group, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo 173-0015, Japan
| | - H Matsumoto
- Microbiological Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - K Shimizu
- Basic Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - M Katto
- Basic Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - H Makino
- Food Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - S Matsubara
- Food Research Department, Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Y Aoyagi
- Exercise Sciences Research Group, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo 173-0015, Japan
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13
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Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile. Genes (Basel) 2022; 13:genes13122200. [PMID: 36553467 PMCID: PMC9778335 DOI: 10.3390/genes13122200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile.
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14
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Wei S, Jespersen ML, Baunwall SMD, Myers PN, Smith EM, Dahlerup JF, Rasmussen S, Nielsen HB, Licht TR, Bahl MI, Hvas CL. Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report. MICROBIOME 2022; 10:193. [PMID: 36352460 PMCID: PMC9647999 DOI: 10.1186/s40168-022-01394-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but potential further transfer to other sites, including the vertical transmission of donor-specific strains to future generations, has not been investigated. Here, we report, for the first time, the cross-generational transmission of specific bacterial strains from an FMT donor to a pregnant patient with CDI and further to her child, born at term, 26 weeks after the FMT treatment. METHODS A pregnant woman (gestation week 12 + 5) with CDI was treated with FMT via colonoscopy. She gave vaginal birth at term to a healthy baby. Fecal samples were collected from the feces donor, the mother (before FMT, and 1, 8, 15, 22, 26, and 50 weeks after FMT), and the infant (meconium at birth and 3 and 6 months after birth). Fecal samples were profiled by deep metagenomic sequencing for strain-level analysis. The microbial transfer was monitored using single nucleotide variants in metagenomes and further compared to a collection of metagenomic samples from 651 healthy infants and 58 healthy adults. RESULTS The single FMT procedure led to an uneventful and sustained clinical resolution in the patient, who experienced no further CDI-related symptoms up to 50 weeks after treatment. The gut microbiota of the patient with CDI differed considerably from the healthy donor and was characterized as low in alpha diversity and enriched for several potential pathogens. The FMT successfully normalized the patient's gut microbiota, likely by donor microbiota transfer and engraftment. Importantly, our analysis revealed that some specific strains were transferred from the donor to the patient and then further to the infant, thus demonstrating cross-generational microbial transfer. CONCLUSIONS The evidence for cross-generational strain transfer following FMT provides novel insights into the dynamics and engraftment of bacterial strains from healthy donors. The data suggests FMT treatment of pregnant women as a potential strategy to introduce beneficial strains or even bacterial consortia to infants, i.e., neonatal seeding. Video Abstract.
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Affiliation(s)
- Shaodong Wei
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Mark Dahl Baunwall
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Emilie Milton Smith
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark.
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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15
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Canine Fecal Microbiota Transplantation: Current Application and Possible Mechanisms. Vet Sci 2022; 9:vetsci9080396. [PMID: 36006314 PMCID: PMC9413255 DOI: 10.3390/vetsci9080396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is an emerging therapeutic option for a variety of diseases, and is characterized as the transfer of fecal microorganisms from a healthy donor into the intestinal tract of a diseased recipient. In human clinics, FMT has been used for treating diseases for decades, with promising results. In recent years, veterinary specialists adapted FMT in canine patients; however, compared to humans, canine FMT is more inclined towards research purposes than practical applications in most cases, due to safety concerns. Therefore, in order to facilitate the application of fecal transplant therapy in dogs, in this paper, we review recent applications of FMT in canine clinical treatments, as well as possible mechanisms that are involved in the process of the therapeutic effect of FMT. More research is needed to explore more effective and safer approaches for conducting FMT in dogs.
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16
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Trunfio M, Scabini S, Rugge W, Bonora S, Di Perri G, Calcagno A. Concurrent and Subsequent Co-Infections of Clostridioides difficile Colitis in the Era of Gut Microbiota and Expanding Treatment Options. Microorganisms 2022; 10:microorganisms10071275. [PMID: 35888994 PMCID: PMC9317215 DOI: 10.3390/microorganisms10071275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
We narratively reviewed the physiopathology, epidemiology, and management of co-infections in Clostridioides difficile colitis (CDI) by searching the following keywords in Embase, MedLine, and PubMed: “Clostridium/Clostridioides difficile”, “co-infection”, “blood-stream infection” (BSI), “fungemia”, “Candida”, “Cytomegalovirus”, “probiotics”, “microbial translocation” (MT). Bacterial BSIs (mainly by Enterobacteriaceae and Enterococcus) and fungemia (mainly by Candida albicans) may occur in up to 20% and 9% of CDI, increasing mortality and length of hospitalization. Up to 68% of the isolates are multi-drug-resistant bacteria. A pivotal role is played by gut dysbiosis, intestinal barrier leakage, and MT. Specific risk factors are represented by CDI-inducing broad-spectrum antibiotics, oral vancomycin use, and CDI severity. Probiotics administration (mainly Saccharomyces and Lactobacillus) during moderate/severe CDI may favor probiotics superinfection. Other co-infections (such as Cytomegalovirus or protozoa) can complicate limited and specific cases. There is mounting evidence that fidaxomicin, bezlotoxumab, and fecal microbiota transplantation can significantly reduce the rate of co-infections compared to historical therapies by interrupting the vicious circle between CDI, treatments, and MT. Bacterial BSIs and candidemia represent the most common co-infections in CDI. Physicians should be aware of this complication to promptly diagnose and treat it and enforce preventive strategies that include a more comprehensive consideration of newer treatment options.
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Affiliation(s)
- Mattia Trunfio
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
- Correspondence: ; Tel.: +39-0114393884
| | - Silvia Scabini
- Unit of Infectious Diseases, AOU “Città della Salute e della Scienza”, Department of Medical Sciences, University of Turin, 10149 Torino, Italy;
| | - Walter Rugge
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
| | - Stefano Bonora
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
| | - Giovanni Di Perri
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
| | - Andrea Calcagno
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
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17
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Facciotti F. Modulation of intestinal immune cell responses by eubiotic or dysbiotic microbiota in inflammatory bowel diseases. PHARMANUTRITION 2022. [DOI: 10.1016/j.phanu.2022.100303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Zhang Y, Saint Fleur A, Feng H. The development of live biotherapeutics against Clostridioides difficile infection towards reconstituting gut microbiota. Gut Microbes 2022; 14:2052698. [PMID: 35319337 PMCID: PMC8959509 DOI: 10.1080/19490976.2022.2052698] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile is the most prevalent pathogen of nosocomial diarrhea. In the United States, over 450,000 cases of C. difficile infection (CDI), responsible for more than 29,000 deaths, are reported annually in recent years. Because of the emergence of hypervirulent strains and strains less susceptible to vancomycin and fidaxomicin, new therapeutics other than antibiotics are urgently needed. The gut microbiome serves as one of the first-line defenses against C. difficile colonization. The use of antibiotics causes gut microbiota dysbiosis and shifts the status from colonization resistance to infection. Hence, novel CDI biotherapeutics capable of reconstituting normal gut microbiota have become a focus of drug development in this field.
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Affiliation(s)
- Yongrong Zhang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201, United States
| | - Ashley Saint Fleur
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201, United States
| | - Hanping Feng
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201, United States,CONTACT Hanping Feng Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201United States
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Lee JC, Chiu CW, Tsai PJ, Lee CC, Huang IH, Ko WC, Hung YP. Clostridium butyricum therapy for mild-moderate Clostridioides difficile infection and the impact of diabetes mellitus. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2022; 41:37-44. [PMID: 35433161 PMCID: PMC8970652 DOI: 10.12938/bmfh.2021-049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/19/2021] [Indexed: 01/26/2023]
Abstract
The therapeutic effect of Clostridium butyricum for adults with
Clostridioides difficile infection (CDI) was investigated. A
retrospective study was conducted in medical wards of Tainan Hospital, Ministry of Health
and Welfare, between January 2013 and April 2020. The disease severity of CDI was scored
based on the Clinical Practice Guidelines of the IDSA/SHEA. Treatment success was defined
as the resolution of diarrhea within six days of a therapeutic intervention without the
need to modify the therapeutic regimen. In total, 241 patients developed CDI during
hospitalization in the study period. The treatment success rates for the 99 patients with
mild-moderate CDI among them were as follows: metronidazole, 69.4%; C.
butyricum, 68.2%; metronidazole plus C. butyricum, 66.7%; and
oral vancomycin, 66.7% (p=1.00). Patients with treatment success were less likely to have
diabetes mellitus than those with treatment failure (38.2% vs. 61.3%, p=0.05). Patients
treated with C. butyricum alone or in combination with metronidazole had
shorter durations of diarrhea than those treated with metronidazole alone (3.1 ± 2.0 days
or 3.5 ± 2.4 days vs. 4.2 ± 3.5 days; p=0.43 or 0.71), although the differences were not
statistically significant. In conclusion, the treatment success rate of C.
butyricum alone or in combination with metronidazole for patients with CDI was
non inferior to that of metronidazole alone. The presence of diabetes mellitus in affected
individuals is a risk factor for treatment failure.
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Affiliation(s)
- Jen-Chieh Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, North Dist., Tainan 704, Taiwan
| | - Chun-Wei Chiu
- Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, No. 125, Jhongshan Rd., West Central Dist., Tainan 70043, Taiwan
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, No.1, University Road, Tainan 701, Taiwan.,Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 1, Dasyue Rd, East District, Tainan 701, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, No.138, Sheng Li Road, North Dist., Tainan 704, Taiwan
| | - Ching-Chi Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, North Dist., Tainan 704, Taiwan.,Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 1, Dasyue Rd, East District, Tainan 701, Taiwan
| | - I-Hsiu Huang
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, 1111 W. 17th Street Tulsa, OK 74107, USA
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, North Dist., Tainan 704, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, 1 University Road, Tainan City 70101, Taiwan
| | - Yuan-Pin Hung
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, North Dist., Tainan 704, Taiwan.,Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, No. 125, Jhongshan Rd., West Central Dist., Tainan 70043, Taiwan
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20
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Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers. Cell Host Microbe 2022; 30:583-598.e8. [PMID: 35421353 DOI: 10.1016/j.chom.2022.03.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/22/2021] [Accepted: 03/10/2022] [Indexed: 11/20/2022]
Abstract
Manipulation of the gut microbiota via fecal microbiota transplantation (FMT) has shown clinical promise in diseases such as recurrent Clostridioides difficile infection (rCDI). However, the variable nature of this approach makes it challenging to describe the relationship between fecal strain colonization, corresponding microbiota changes, and clinical efficacy. Live biotherapeutic products (LBPs) consisting of defined consortia of clonal bacterial isolates have been proposed as an alternative therapeutic class because of their promising preclinical results and safety profile. We describe VE303, an LBP comprising 8 commensal Clostridia strains under development for rCDI, and its early clinical development in healthy volunteers (HVs). In a phase 1a/b study in HVs, VE303 is determined to be safe and well-tolerated at all doses tested. VE303 strains optimally colonize HVs if dosed over multiple days after vancomycin pretreatment. VE303 promotes the establishment of a microbiota community known to provide colonization resistance.
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21
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Clostridioides difficile Phosphoproteomics Shows an Expansion of Phosphorylated Proteins in Stationary Growth Phase. mSphere 2022; 7:e0091121. [PMID: 34986318 PMCID: PMC8730811 DOI: 10.1128/msphere.00911-21] [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] [Indexed: 12/19/2022] Open
Abstract
Phosphorylation is a posttranslational modification that can affect both housekeeping functions and virulence characteristics in bacterial pathogens. In the Gram-positive enteropathogen Clostridioides difficile, the extent and nature of phosphorylation events are poorly characterized, though a protein kinase mutant strain demonstrates pleiotropic phenotypes. Here, we used an immobilized metal affinity chromatography strategy to characterize serine, threonine, and tyrosine phosphorylation in C. difficile. We find limited protein phosphorylation in the exponential growth phase but a sharp increase in the number of phosphopeptides after the onset of the stationary growth phase. Our approach identifies expected targets and phosphorylation sites among the more than 1,500 phosphosites, including the protein kinase PrkC, the anti-sigma-F factor antagonist (SpoIIAA), the anti-sigma-B factor antagonist (RsbV), and HPr kinase/phosphorylase (HprK). Analysis of high-confidence phosphosites shows that phosphorylation on serine residues is most common, followed by threonine and tyrosine phosphorylation. This work forms the basis for a further investigation into the contributions of individual kinases to the overall phosphoproteome of C. difficile and the role of phosphorylation in C. difficile physiology and pathogenesis. IMPORTANCE In this paper, we present a comprehensive analysis of protein phosphorylation in the Gram-positive enteropathogen Clostridioides difficile. To date, only limited evidence on the role of phosphorylation in the regulation of this organism has been published; the current study is expected to form the basis for research on this posttranslational modification in C. difficile.
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22
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Romo JA, Kumamoto CA. Characterization of the Effects of Candida Gastrointestinal Colonization on Clostridioides difficile Infection in a Murine Model. Methods Mol Biol 2022; 2542:271-285. [PMID: 36008672 DOI: 10.1007/978-1-0716-2549-1_20] [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: 06/15/2023]
Abstract
The role of fungal colonizers of the gastrointestinal tract during disease states is not well understood. Antibiotic treatment renders patients highly susceptible to infection by the bacterial pathogen C. difficile while also leading to blooms in fungal commensals, setting the stage for trans-kingdom interactions. Here, we describe a murine model of Candida gastrointestinal colonization coupled to a C. difficile infection (CDI) model, the measurement of CFU of both organisms, and collection of cecum and colon contents for the purpose of quantifying C. difficile toxin production. Additionally, we describe how to induce and purify C. difficile spores.
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Affiliation(s)
- Jesús A Romo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Carol A Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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23
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Strati F, Lattanzi G, Amoroso C, Facciotti F. Microbiota-targeted therapies in inflammation resolution. Semin Immunol 2022; 59:101599. [PMID: 35304068 DOI: 10.1016/j.smim.2022.101599] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/24/2022] [Accepted: 02/15/2022] [Indexed: 02/07/2023]
Abstract
Gut microbiota has been shown to systemically shape the immunological landscape, modulate homeostasis and play a role in both health and disease. Dysbiosis of gut microbiota promotes inflammation and contributes to the pathogenesis of several major disorders in gastrointestinal tract, metabolic, neurological and respiratory diseases. Much effort is now focused on understanding host-microbes interactions and new microbiota-targeted therapies are deeply investigated as a means to restore health or prevent disease. This review details the immunoregulatory role of the gut microbiota in health and disease and discusses the most recent strategies in manipulating individual patient's microbiota for the management and prevention of inflammatory conditions.
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Affiliation(s)
- Francesco Strati
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Georgia Lattanzi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Amoroso
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Facciotti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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24
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Bernard R, Hourigan SK, Nicholson MR. Fecal Microbiota Transplantation and Microbial Therapeutics for the Treatment of Clostridioides difficile Infection in Pediatric Patients. J Pediatric Infect Dis Soc 2021; 10:S58-S63. [PMID: 34791396 PMCID: PMC8600035 DOI: 10.1093/jpids/piab056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clostridioides difficile infection (CDI) is the most common cause of antibiotic-associated diarrhea and has high rates of recurrent disease. As a disease associated with intestinal dysbiosis, gastrointestinal microbiome manipulation and fecal microbiota transplantation (FMT) have evolved as effective, although relatively unregulated therapeutics and not without safety concerns. FMT for the treatment of CDI has been well studied in adults with increasing data reported in children. In this review, we discuss the current body of literature on the use of FMT in children including effectiveness, safety, risk factors for a failed FMT, and the role of FMT in children with comorbidities. We also review emerging microbial therapeutics for the treatment of rCDI.
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Affiliation(s)
- Rachel Bernard
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Monroe Carell Jr. Vanderbilt Children’s Hospital, Nashville, Tennessee, USA,Corresponding Author: Rachel Bernard, DO MS, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Monroe Carell Jr. Vanderbilt Children’s Hospital, 2200 Children’s Way, Suite 11226 Doctors’ Office Tower, Nashville, TN 38201, USA. E-mail:
| | - Suchitra K Hourigan
- Division of Pediatric Gastroenterology, Pediatric Specialists of Virginia, Fairfax, Virginia, USA
| | - Maribeth R Nicholson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Monroe Carell Jr. Vanderbilt Children’s Hospital, Nashville, Tennessee, USA
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25
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Yadav M, Chauhan NS. Microbiome therapeutics: exploring the present scenario and challenges. Gastroenterol Rep (Oxf) 2021; 10:goab046. [PMID: 35382166 PMCID: PMC8972995 DOI: 10.1093/gastro/goab046] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/11/2022] Open
Abstract
Human gut-microbiome explorations have enriched our understanding of microbial colonization, maturation, and dysbiosis in health-and-disease subsets. The enormous metabolic potential of gut microbes and their role in the maintenance of human health is emerging, with new avenues to use them as therapeutic agents to overcome human disorders. Microbiome therapeutics are aimed at engineering the gut microbiome using additive, subtractive, or modulatory therapy with an application of native or engineered microbes, antibiotics, bacteriophages, and bacteriocins. This approach could overcome the limitation of conventional therapeutics by providing personalized, harmonized, reliable, and sustainable treatment. Its huge economic potential has been shown in the global therapeutics market. Despite the therapeutic and economical potential, microbiome therapeutics is still in the developing stage and is facing various technical and administrative issues that require research attention. This review aims to address the current knowledge and landscape of microbiome therapeutics, provides an overview of existing health-and-disease applications, and discusses the potential future directions of microbiome modulations.
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Affiliation(s)
- Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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26
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Girinathan BP, DiBenedetto N, Worley JN, Peltier J, Arrieta-Ortiz ML, Immanuel SRC, Lavin R, Delaney ML, Cummins CK, Hoffman M, Luo Y, Gonzalez-Escalona N, Allard M, Onderdonk AB, Gerber GK, Sonenshein AL, Baliga NS, Dupuy B, Bry L. In vivo commensal control of Clostridioides difficile virulence. Cell Host Microbe 2021; 29:1693-1708.e7. [PMID: 34637781 DOI: 10.1016/j.chom.2021.09.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/26/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022]
Abstract
Leveraging systems biology approaches, we illustrate how metabolically distinct species of Clostridia protect against or worsen Clostridioides difficile infection in mice by modulating the pathogen's colonization, growth, and virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenter Paraclostridium bifermentans survive infection with reduced disease severity, while mice colonized with the butyrate-producer, Clostridium sardiniense, succumb more rapidly. Systematic in vivo analyses revealed how each commensal alters the gut-nutrient environment to modulate the pathogen's metabolism, gene regulatory networks, and toxin production. Oral administration of P. bifermentans rescues conventional, clindamycin-treated mice from lethal C. difficile infection in a manner similar to that of monocolonized animals, thereby supporting the therapeutic potential of this commensal species. Our findings lay the foundation for mechanistically informed therapies to counter C. difficile disease using systems biology approaches to define host-commensal-pathogen interactions in vivo.
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Affiliation(s)
- Brintha P Girinathan
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas DiBenedetto
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; National Center of Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, 25-28 Rue du Dr. Roux, Institut Pasteur, 75015 Paris Cedex, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-yvette Cedex, France
| | | | | | - Richard Lavin
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mary L Delaney
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Clinical Microbiology Laboratory, Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Christopher K Cummins
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Maria Hoffman
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Microbiology, College Park, MD 20740, USA
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Microbiology, College Park, MD 20740, USA
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Microbiology, College Park, MD 20740, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Microbiology, College Park, MD 20740, USA
| | - Andrew B Onderdonk
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Clinical Microbiology Laboratory, Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Health Sciences & Technology, Cambridge, MA 02139, USA
| | - Abraham L Sonenshein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | | | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, 25-28 Rue du Dr. Roux, Institut Pasteur, 75015 Paris Cedex, France
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Clinical Microbiology Laboratory, Department of Pathology, Brigham & Women's Hospital, Boston, MA 02115, USA.
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27
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Hotinger JA, Morris ST, May AE. The Case against Antibiotics and for Anti-Virulence Therapeutics. Microorganisms 2021; 9:2049. [PMID: 34683370 PMCID: PMC8537500 DOI: 10.3390/microorganisms9102049] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
Although antibiotics have been indispensable in the advancement of modern medicine, there are downsides to their use. Growing resistance to broad-spectrum antibiotics is leading to an epidemic of infections untreatable by first-line therapies. Resistance is exacerbated by antibiotics used as growth factors in livestock, over-prescribing by doctors, and poor treatment adherence by patients. This generates populations of resistant bacteria that can then spread resistance genes horizontally to other bacterial species, including commensals. Furthermore, even when antibiotics are used appropriately, they harm commensal bacteria leading to increased secondary infection risk. Effective antibiotic treatment can induce bacterial survival tactics, such as toxin release and increasing resistance gene transfer. These problems highlight the need for new approaches to treating bacterial infection. Current solutions include combination therapies, narrow-spectrum therapeutics, and antibiotic stewardship programs. These mediate the issues but do not address their root cause. One emerging solution to these problems is anti-virulence treatment: preventing bacterial pathogenesis instead of using bactericidal agents. In this review, we discuss select examples of potential anti-virulence targets and strategies that could be developed into bacterial infection treatments: the bacterial type III secretion system, quorum sensing, and liposomes.
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Affiliation(s)
| | | | - Aaron E. May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA; (J.A.H.); (S.T.M.)
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28
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Sahra S, Abureesh M, Amarnath S, Alkhayyat M, Badran R, Jahangir A, Gumaste V. Clostridioides difficile infection in liver cirrhosis patients: A population-based study in United States. World J Hepatol 2021; 13:926-938. [PMID: 34552699 PMCID: PMC8422922 DOI: 10.4254/wjh.v13.i8.926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/11/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Clostridioides (formerly Clostridium) difficile infection (CDI) is an increasingly frequent cause of morbidity and mortality in hospitalized patients. Multiple risk factors are documented in the literature that includes, but are not limited to, antibiotics use, advanced age, and gastric acid suppression. Several epidemiological studies have reported an increased incidence of CDI in advanced liver disease patients. Some have also demonstrated a higher prevalence of nosocomial infections in cirrhotic patients.
AIM To use a large nationwide database, we sought to determine CDI’s risk among liver cirrhosis patients in the United States.
METHODS We queried a commercial database (Explorys IncTM, Cleveland, OH, United States), and obtained an aggregate of electronic health record data from 26 major integrated United States healthcare systems comprising 360 hospitals in the United States from 2018 to 2021. Diagnoses were organized into the Systematized Nomenclature of Medicine Clinical Terms (SNOMED–CT) hierarchy. Statistical analysis for the multivariable model was performed using Statistical Package for Social Sciences (SPSS version 25, IBM CorpTM). For all analyses, a two-sided P value of < 0.05 was considered statistically significant.
RESULTS There were a total of 19387760 patients in the database who were above 20 years of age between the years 2018-2021. Of those, 133400 were diagnosed with liver cirrhosis. The prevalence of CDI amongst the liver cirrhosis population was 134.93 per 100.000 vs 19.06 per 100.000 in non-cirrhotic patients (P < 0.0001). The multivariate analysis model uncovered that cirrhotic patients were more likely to develop CDI (OR: 1.857; 95%CI: 1.665-2.113, P < 0.0001) compared to those without any prior history of liver cirrhosis.
CONCLUSION In this large database study, we uncovered that cirrhotic patients have a significantly higher CDI prevalence than those without cirrhosis. Liver cirrhosis may be an independent risk factor for CDI. Further prospective studies are needed to clarify this possible risk association that may lead to the implementation of screening methods in this high-risk population.
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Affiliation(s)
- Syeda Sahra
- Department of Internal Medicine, Staten Island University Hospital, Staten Island, NY 10305, United States
| | - Mohammad Abureesh
- Department of Internal Medicine, Staten Island University Hospital, Staten Island, NY 10305, United States
| | - Shivantha Amarnath
- Department of Internal Medicine, Staten Island University Hospital, Staten Island, NY 10305, United States
| | - Motasem Alkhayyat
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Rawan Badran
- Department of Internal Medicine, Staten Island University Hospital, Staten Island, NY 10305, United States
| | - Abdullah Jahangir
- Department of Internal Medicine, Staten Island University Hospital, Staten Island, NY 10305, United States
| | - Vivek Gumaste
- Department of Gastroenterology, Staten Island University Hospital, Staten Island, NY 10305, United States
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29
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Influence of Cultivation pH on Composition, Diversity, and Metabolic Production in an In Vitro Human Intestinal Microbiota. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7030156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fecal microbiota transplantation, an alternative treatment method for gastrointestinal diseases, has a high recovery rate, but comes with disadvantages, such as high donor requirements and the low storability of stool. A solution to overcome these problems is the cultivation of an in vitro microbiota. However, the influence of cultivation conditions on the pH are yet unknown. In this study, the influence of the cultivation pH (6.0–7.0) on the system’s behavior and characteristics, including cell count, metabolism, and microbial composition, was investigated. With an increasing cultivation pH, an increase in cell count, total amount of SCFAs, acetate, propionate, and the abundance of Bacteroidetes and Verrucomicrobia were observed. For the concentration of butyrate and the abundance of Actinobacteria and Firmicutes, a decrease with increasing pH was determined. For the concentration of isovalerate, the abundance of Proteobacteria and diversity (richness and Shannon effective), no effect of the pH was observed. Health-promoting genera were more abundant at lower pH levels. When cultivating an in vitro microbiota, all investigated pH values created a diverse and stable system. Ultimately, therefore, the choice of pH creates significant differences in the established in vitro microbiota, but no clear recommendations for a special value can be made.
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30
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Boekhoud IM, Sidorov I, Nooij S, Harmanus C, Bos-Sanders IMJG, Viprey V, Spittal W, Clark E, Davies K, Freeman J, Kuijper EJ, Smits WK. Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile. J Antimicrob Chemother 2021; 76:1731-1740. [PMID: 33876817 PMCID: PMC8212768 DOI: 10.1093/jac/dkab097] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Background Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Objectives To identify factors that contribute to plasmid-independent metronidazole resistance of C. difficile. Methods Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile using a combination of antimicrobial susceptibility testing on different solid agar media and WGS of selected isolates. Results We find that nearly all isolates demonstrate a haem-dependent increase in the MIC of metronidazole, which in some cases leads to isolates qualifying as resistant (MIC >2 mg/L). Moreover, we find an SNP in the haem-responsive gene hsmA, which defines a metronidazole-resistant lineage of PCR ribotype 010/MLST ST15 isolates that also includes pCD-METRO-containing strains. Conclusions Our data demonstrate that haem is crucial for medium-dependent metronidazole resistance in C. difficile.
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Affiliation(s)
- Ilse M Boekhoud
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, 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
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Virginie Viprey
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - William Spittal
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Emma Clark
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kerrie Davies
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Jane Freeman
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
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31
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Haindl R, Engel J, Kulozik U. Establishment of an In Vitro System of the Human Intestinal Microbiota: Effect of Cultivation Conditions and Influence of Three Donor Stool Samples. Microorganisms 2021; 9:1049. [PMID: 34068085 PMCID: PMC8152740 DOI: 10.3390/microorganisms9051049] [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: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 11/16/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is an alternative method for the treatment of gastrointestinal diseases with a high recovery rate. Disadvantages are ethical concerns, high donor requirements and the low storability of stool samples. The cultivation of an in vitro microbiota in a continuous bioreactor was established as an alternative to FMT to overcome these problems. In this study, the influence of the system parameters and donor stool characteristics was investigated. Each continuous colonic fermentation system was inoculated with feces from three different donors until a stable state was established. The influence of the fermentation conditions on the system's behavior regarding cell count, metabolic activity, short-chain fatty acid profile and microbiota composition as well as richness and diversity was assessed. Cultivation conditions were found to affect the microbial system: the number of cells and the production of short-chain fatty acids increased. The abundance of Actinobacteria and Firmicutes decreased, Bacteroidetes increased, while Proteobacteria and Verrucomicrobia remained largely unaffected. Diversity in the in vitro system decreased, but richness was unaffected. The cultivation of stool from different donors revealed that the performance of the created in vitro system was similar and comparable, but unique characteristics of the composition of the original stool remained.
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Affiliation(s)
- Regina Haindl
- Chair of Food and Bioprocess Engineering, ZIEL—Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 1, 85354 Freising, Germany; (J.E.); (U.K.)
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32
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Immunosuppressive Effects of Myeloid-Derived Suppressor Cells in Cancer and Immunotherapy. Cells 2021; 10:cells10051170. [PMID: 34065010 PMCID: PMC8150533 DOI: 10.3390/cells10051170] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The primary function of myeloid cells is to protect the host from infections. However, during cancer progression or states of chronic inflammation, these cells develop into myeloid-derived suppressor cells (MDSCs) that play a prominent role in suppressing anti-tumor immunity. Overcoming the suppressive effects of MDSCs is a major hurdle in cancer immunotherapy. Therefore, understanding the mechanisms by which MDSCs promote tumor growth is essential for improving current immunotherapies and developing new ones. This review explores mechanisms by which MDSCs suppress T-cell immunity and how this impacts the efficacy of commonly used immunotherapies.
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Fujimoto K, Kimura Y, Allegretti JR, Yamamoto M, Zhang YZ, Katayama K, Tremmel G, Kawaguchi Y, Shimohigoshi M, Hayashi T, Uematsu M, Yamaguchi K, Furukawa Y, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation. Gastroenterology 2021; 160:2089-2102.e12. [PMID: 33577875 PMCID: PMC8684800 DOI: 10.1053/j.gastro.2021.02.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI). However, the overall mechanisms underlying FMT success await comprehensive elucidation, and the safety of FMT has recently become a serious concern because of the occurrence of drug-resistant bacteremia transmitted by FMT. We investigated whether functional restoration of the bacteriomes and viromes by FMT could be an indicator of successful FMT. METHODS The human intestinal bacteriomes and viromes from 9 patients with rCDI who had undergone successful FMT and their donors were analyzed. Prophage-based and CRISPR spacer-based host bacteria-phage associations in samples from recipients before and after FMT and in donor samples were examined. The gene functions of intestinal microorganisms affected by FMT were evaluated. RESULTS Metagenomic sequencing of both the viromes and bacteriomes revealed that FMT does change the characteristics of intestinal bacteriomes and viromes in recipients after FMT compared with those before FMT. In particular, many Proteobacteria, the fecal abundance of which was high before FMT, were eliminated, and the proportion of Microviridae increased in recipients. Most temperate phages also behaved in parallel with the host bacteria that were altered by FMT. Furthermore, the identification of bacterial and viral gene functions before and after FMT revealed that some distinctive pathways, including fluorobenzoate degradation and secondary bile acid biosynthesis, were significantly represented. CONCLUSIONS The coordinated action of phages and their host bacteria restored the recipients' intestinal flora. These findings show that the restoration of intestinal microflora functions reflects the success of FMT.
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Affiliation(s)
- Kosuke Fujimoto
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan,Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan,Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yasumasa Kimura
- Division of Systems Immunology, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Jessica R. Allegretti
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mako Yamamoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yao-zhong Zhang
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kotoe Katayama
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Georg Tremmel
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yunosuke Kawaguchi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Masaki Shimohigoshi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Tetsuya Hayashi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Miho Uematsu
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yutaka Akiyama
- Department of Computer Science, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Rui Yamaguchi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sheila E. Crowe
- Department of Medicine, University of California, San Diego, La Jolla, California
| | - Peter B. Ernst
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California San Diego, San Diego, La Jolla, California,Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, San Diego, La Jolla, California,Center for Veterinary Sciences and Comparative Medicine, University of California, San Diego, La Jolla, California
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Hiroshi Kiyono
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California San Diego, San Diego, La Jolla, California,Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, San Diego, La Jolla, California,Department of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan,International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan; Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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Wu W, Shen N, Luo L, Deng Z, Chen J, Tao Y, Mo X, Cao Q. Fecal microbiota transplantation before hematopoietic stem cell transplantation in a pediatric case of chronic diarrhea with a FOXP3 mutation. Pediatr Neonatol 2021; 62:172-180. [PMID: 33358585 DOI: 10.1016/j.pedneo.2020.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/23/2020] [Accepted: 11/27/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a rare disorder caused by mutation of the forkhead box protein 3 (FOXP3) gene, often leading to intractable and life-threatening diarrhea. Fecal microbiota transplantation (FMT), has been regarded in recent years as an available approach to reconstruct disrupted gut microbiome and successfully used to attenuates diarrhea induced by different underlying diseases. Therefore, FMT may have curative potential on the symptoms of enteropathy in patients with IPEX syndrome. METHODS Physical and laboratory examinations were performed, and clinical data were collected. FMT was administered via frozen fecal microbial solution, and the fecal microbiota composition was analyzed using 16S rDNA sequencing before and after FMT. RESULTS The patient was diagnosed with IPEX syndrome with a mutation detected in the FOXP3 gene, which was identified as c.767T > C (p.M256T). He presented with recurrent watery diarrhea and respiratory infections after birth and developed a significant failure to thrive. Disturbances in the gut microbiota composition and marked decreased bacterial diversity were observed to be involved in the persistent and refractory diarrhea. After receiving FMT treatment, the patient responded with remission of the diarrhea without apparent side effects. His stool output significantly decreased, corresponding to increased microbial diversity and modification of his microbiota composition. The patient finally achieved full recovery after hematopoietic stem cell transplantation (HSCT). CONCLUSION Our data suggest an association between the gut microbiota and clinical symptoms of patient with IPEX syndrome and demonstrate FMT as an alternative therapy for severe diarrhea unresponsive to routine therapy in these patients.
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Affiliation(s)
- Wenyan Wu
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nan Shen
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijuan Luo
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaohui Deng
- Department of Gastroenterology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Chen
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Qing Cao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Al-Ali D, Ahmed A, Shafiq A, McVeigh C, Chaari A, Zakaria D, Bendriss G. Fecal microbiota transplants: A review of emerging clinical data on applications, efficacy, and risks (2015-2020). Qatar Med J 2021; 2021:5. [PMID: 34604008 PMCID: PMC8475724 DOI: 10.5339/qmj.2021.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022] Open
Abstract
As the importance of the gut microbiota in health and disease is a subject of growing interest, fecal microbiota transplantation (FMT) was suggested as an attractive therapeutic strategy to restore homeostasis of the gut microbiota, thereby treating diseases that were associated with alteration of the gut microbiota. FMT involves the administration of fresh, frozen, or dried fecal microorganisms from the gut of a healthy donor into the intestinal tract of a patient. This rediscovery of the potential benefits of an ancient practice was accompanied by a rapid progression of our understanding of the roles and mechanisms of gut microbes in the pathogenesis of disease. With a growing number of diseases being associated with dysbiosis or the alteration of gut microbiota, FMT was suggested as an attractive therapeutic strategy to "reset the gut" and initiate clinical resolutions or remissions. The number of FMT clinical trials is increasing worldwide, but no trials are registered in the Gulf region; this suggested the need for raising awareness of the latest studies on FMT. This review presented the emergent preclinical and clinical data to give an overview of the potential clinical applications, the benefits, and inconveniences that were worth considering for eventual future testing of fecal transplants in Qatar and the Middle East. This study highlighted the diversity of methods tested and commented on the variables that can affect the assessment of the effectiveness of FMT in specific diseases. The risks associated with FMT and the threat of antimicrobial resistance for this therapeutic approach were reviewed. From gastrointestinal diseases to neurodevelopmental disorders, understanding the roles of the gut microbiota in health and disease should be at the heart of developing novel, standardized, yet personalized, methods for this ancient therapeutic approach.
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Affiliation(s)
- Dana Al-Ali
- Premedical Division Weill Cornell Medicine-Qatar, Premedical Division, PO Box 24144 Doha, Qatar E-mail:
| | | | - Ameena Shafiq
- Premedical Division Weill Cornell Medicine-Qatar, Premedical Division, PO Box 24144 Doha, Qatar E-mail:
| | - Clare McVeigh
- Premedical Division Weill Cornell Medicine-Qatar, Premedical Division, PO Box 24144 Doha, Qatar E-mail:
| | - Ali Chaari
- Premedical Division Weill Cornell Medicine-Qatar, Premedical Division, PO Box 24144 Doha, Qatar E-mail:
| | - Dalia Zakaria
- Premedical Division Weill Cornell Medicine-Qatar, Premedical Division, PO Box 24144 Doha, Qatar E-mail:
| | - Ghizlane Bendriss
- Premedical Division Weill Cornell Medicine-Qatar, Premedical Division, PO Box 24144 Doha, Qatar E-mail:
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Cao Y, Liu J, Zhu W, Qin N, Ren X, Zhu B, Xia X. Impact of dietary components on enteric infectious disease. Crit Rev Food Sci Nutr 2021; 62:4010-4035. [PMID: 33455435 DOI: 10.1080/10408398.2021.1871587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Diets impact host health in multiple ways and an unbalanced diet could contribute to the initiation or progression of a variety of diseases. Although a wealth of information exists on the connections between diet and chronic metabolic diseases such as cardiovascular disease, diabetes mellitus, etc., how diet influences enteric infectious disease still remain underexplored. The review summarizes the current findings on the link between various dietary components and diverse enteric infectious diseases. Dietary ingredients discussed include macronutrients (carbohydrates, lipids, proteins), micronutrients (vitamins, minerals), and other dietary ingredients (phytonutrients and probiotic supplements). We first describe the importance of enteric infectious diseases and the direct and indirect relationship between diet and enteric infectious diseases. Then we discuss the effects of different dietary components on the susceptibility to or progression of enteric infectious disease. Finally, we delineate current knowledge gap and highlighted future research directions. The literature review revealed that different dietary components affect host resistance to enteric infections through a variety of mechanisms. Dietary components may directly inhibit or bind to enteric pathogens, or indirectly influence enteric infections through modulating immune function and gut microbiota. Elucidating the unique repercussions of different diets on enteric infections in this review may help provide dietary guidelines or design dietary interventions to prevent or alleviate enteric infectious diseases.
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Affiliation(s)
- Yu Cao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Jiaxiu Liu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Wenxiu Zhu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Ningbo Qin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Xiaomeng Ren
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Beiwei Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Xiaodong Xia
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
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Utay NS, Monczor AN, Somasunderam A, Lupo S, Jiang ZD, Alexander AS, Finkelman M, Vigil KJ, Lake JE, Hanson B, DuPont HL, Arduino RC. Evaluation of Six Weekly Oral Fecal Microbiota Transplants in People with HIV. Pathog Immun 2020; 5:364-381. [PMID: 33501400 PMCID: PMC7815055 DOI: 10.20411/pai.v5i1.388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background Reduced microbiota diversity (dysbiosis) in people with HIV (PWH) likely contributes to inflammation, a driver of morbidity and mortality. We aimed to evaluate the safety and tolerability of 6 weekly oral fecal microbiota transplants (FMT) administered to reverse this dysbiosis. Methods Six PWH on suppressive antiretroviral therapy (ART) received 6 weekly doses of lyophilized fecal microbiota product from healthy donors. Shotgun sequencing on stool before, after last FMT, and 20 weeks thereafter was performed. Inflammation and gut permeability biomarkers were measured. Results Median age at week 0 was 39 years, CD4+ T cell count 496 cells/mm3, HIV RNA levels <20 copies/mL. FMT was safe and well-tolerated. α diversity increased in 4 participants from weeks 0 to 6, including the 3 with the lowest α diversity at week 0. At week 26, α diversity more closely resembled week 0 than week 6 in these 4 participants. Metagenomic analysis showed no consistent changes across all participants. One participant had high gut permeability and inflammation biomarker levels and low α diversity that improved between weeks 0 and 6 with a shift in distribution. Conclusions Weekly FMT was safe and well-tolerated. α diversity increased in participants with the lowest baseline α diversity during the treatment period. Future randomized, controlled trials of FMT should consider evaluating PWH with greater inflammation, gut damage, or dysbiosis as this population may be most likely to show a significant response.ClinicalTrials.gov Identifier: NCT03329560.
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Affiliation(s)
- Netanya S Utay
- Division of General Medicine, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas.,Kelsey Research Foundation, Houston, Texas
| | - Ana N Monczor
- Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Anoma Somasunderam
- Division of General Medicine, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Sofia Lupo
- Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Zhi-Dong Jiang
- School of Public Health at The University of Texas Health Science Center at Houston, Houston, Texas
| | | | | | - Karen J Vigil
- Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Jordan E Lake
- Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Blake Hanson
- School of Public Health at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Herbert L DuPont
- Kelsey Research Foundation, Houston, Texas.,School of Public Health at The University of Texas Health Science Center at Houston, Houston, Texas
| | - Roberto C Arduino
- Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas
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Kelly VW, Liang BK, Sirk SJ. Living Therapeutics: The Next Frontier of Precision Medicine. ACS Synth Biol 2020; 9:3184-3201. [PMID: 33205966 DOI: 10.1021/acssynbio.0c00444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Modern medicine has long studied the mechanism and impact of pathogenic microbes on human hosts, but has only recently shifted attention toward the complex and vital roles that commensal and probiotic microbes play in both health and dysbiosis. Fueled by an enhanced appreciation of the human-microbe holobiont, the past decade has yielded countless insights and established many new avenues of investigation in this area. In this review, we discuss advances, limitations, and emerging frontiers for microbes as agents of health maintenance, disease prevention, and cure. We highlight the flexibility of microbial therapeutics across disease states, with special consideration for the rational engineering of microbes toward precision medicine outcomes. As the field advances, we anticipate that tools of synthetic biology will be increasingly employed to engineer functional living therapeutics with the potential to address longstanding limitations of traditional drugs.
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Affiliation(s)
- Vince W. Kelly
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Benjamin K. Liang
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors. Sci Rep 2020; 10:17608. [PMID: 33077744 PMCID: PMC7573688 DOI: 10.1038/s41598-020-74090-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Objective was to analyse bacterial composition and abundance of Clostridioides difficile in gut microbiome of patients with C. difficile infection (CDI) in association with clinical characteristics. Whole metagenome sequencing of gut microbiome of 26 CDI patients was performed, and the relative abundance of C. difficile and its toxin genes was measured. Clinical characteristics of the patients were obtained through medical records. A strong correlation between the abundance of C. difficile and tcdB genes in CDI patients was found. The relative abundance of C. difficile in the gut microbiome ranged from undetectable to 2.8% (median 0.089). Patients with fever exhibited low abundance of C. difficile in their gut, and patients with fewer C. difficile organisms required long-term anti-CDI treatment. Abundance of Bifidobacterium and Bacteroides negatively correlated with that of C. difficile at the genus level. CDI patients were clustered using the bacterial composition of the gut: one with high population of Enterococcus (cluster 1, n = 12) and another of Bacteroides or Lactobacillus (cluster 2, n = 14). Cluster1 showed significantly lower bacterial diversity and clinical cure at the end of treatment. Additionally, patients with CDI exhibited increased ARGs; notably, blaTEM, blaSHV and blaCTX-M were enriched. C. difficile existed in variable proportion of the gut microbiome in CDI patients. CDI patients with Enterococcus-rich microbiome in the gut had lower bacterial diversity and poorer clinical cure.
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Reygner J, Charrueau C, Delannoy J, Mayeur C, Robert V, Cuinat C, Meylheuc T, Mauras A, Augustin J, Nicolis I, Modoux M, Joly F, Waligora-Dupriet AJ, Thomas M, Kapel N. Freeze-dried fecal samples are biologically active after long-lasting storage and suited to fecal microbiota transplantation in a preclinical murine model of Clostridioides difficile infection. Gut Microbes 2020; 11:1405-1422. [PMID: 32501140 PMCID: PMC7524285 DOI: 10.1080/19490976.2020.1759489] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Fecal microbiota transplantation is now recommended for treating recurrent forms of Clostridioides difficile infection. Recent studies have reported protocols using capsules of either frozen or freeze-dried stool allowing oral administration in in- and out-patient settings. However, a central question remains the viability, engraftment, and efficacy of the microbiome over time during storage life. This study shows that both the freeze-drying and freezing procedures for fecal samples allowed preserving viability, short-chain fatty acids concentration, and anti-Clostridioides difficile properties of microbiota without significant alteration after storage for 12 months. Fecal transplantation with freeze-dried microbiota allowed engraftment of microbiota leading to clearance of Clostridioides difficile infection in a preclinical murine model with a survival rate of 70% versus 53-60% in mice treated with frozen inocula, and 20% in the untreated group. Moreover, the freeze-dried powder can be used to fill oral hard capsules using a very low amount (0.5%) of glidant excipient, allowing oral formulation. Altogether, this study showed that freeze-dried inocula can be used for the treatment of Clostridioides difficile infection with long-lasting stability of the fecal microbiota. This formulation facilitates biobanking and allows the use of hard capsules, an essential step to simplify patient access to treatment.
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Affiliation(s)
- Julie Reygner
- INSERM UMR-S1139, Université de Paris, Paris, France
| | - Christine Charrueau
- INSERM U1267 CNRS UMR 8258, Chimie ParisTech, PSL Research University, Université de Paris, Paris, France
| | | | - Camille Mayeur
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Véronique Robert
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Cuinat
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Jérémy Augustin
- Department of Pathology, APHP Sorbonne Université, Pitie-Salpetriere Hospital, Paris, France
| | | | | | - Francisca Joly
- Department of Gastroenterology and Nutrition Support, APHP, Beaujon Hospital, Clichy, France
| | | | - Muriel Thomas
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nathalie Kapel
- INSERM UMR-S1139, Université de Paris, Paris, France,Department of Coprology, APHP Sorbonne Université, Pitie-Salpetriere Hospital, Paris, France,CONTACT Nathalie Kapel Laboratoire de Coprologie Fonctionnelle, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, 47-83 Boulevard de l’Hôpital, Paris75013, France
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Fecal microbiota transplantation improves metabolic syndrome parameters: systematic review with meta-analysis based on randomized clinical trials. Nutr Res 2020; 83:1-14. [PMID: 32987284 DOI: 10.1016/j.nutres.2020.06.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/02/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023]
Abstract
Obesity and metabolic syndrome are important health problems that can lead to significant morbidity/mortality as well as subsequent health concerns. Alterations in the gut microbiota have been implicated in both obesity and metabolic syndrome. Fecal Microbiota Transplantation (FMT) has emerged as a new promising therapeutic approach aimed at manipulating the gut microbiota in various chronic diseases. Randomized clinical trials assessing the use of FMT in obese and metabolic syndrome patients have been reported. The purpose of this systematic review with meta-analysis using randomized clinical trials (RCT) is to evaluate the role of FMT for the treatment of obesity and metabolic syndrome and its impact on clinically relevant parameters. We searched the main databases, as well as the gray literature, to identify RCTs comparing FMT from lean donor(s) vs placebo for obese/metabolic syndrome patients. We included all studies that utilized any form of placebo (sham, saline, autologous FMT, or placebo capsules). Six studies met the inclusion criteria and were included for final analysis with a total of 154 patients. We looked for clinically significant parameters related to obesity and metabolic syndrome and organized the findings into early (2-6 weeks after intervention) and late (12 weeks after intervention) outcomes. Two to 6 weeks after intervention, mean HbA1c was lower in the FMT group (MD = -1.69 mmol/L, CI [-2.88, -0.56], P = .003) and mean HDL cholesterol was higher in the FMT group (MD = 0.09 mmol/L, CI [0.02, 0.15], P = .008). There was no difference in obesity parameters 6 to 12 weeks after intervention. No serious adverse events were reported. The findings for this meta-analysis show that FMT may have a role for the treatment of metabolic syndrome, but there is currently not enough evidence to support its use in clinical practice. High-quality well-powered RCTS with longer follow-up are necessary to clarify the role of FMT in this patient cohort.
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Berg G, Rybakova D, Fischer D, Cernava T, Vergès MCC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran GS, Selvin J, Souza RSCD, van Overbeek L, Singh BK, Wagner M, Walsh A, Sessitsch A, Schloter M. Microbiome definition re-visited: old concepts and new challenges. MICROBIOME 2020; 8:103. [PMID: 32605663 PMCID: PMC7329523 DOI: 10.1186/s40168-020-00875-0] [Citation(s) in RCA: 710] [Impact Index Per Article: 177.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/22/2020] [Indexed: 05/03/2023]
Abstract
The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.
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Affiliation(s)
- Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Daria Rybakova
- Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Tomislav Cernava
- Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Trevor Charles
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Metagenom Bio, 550 Parkside Drive, Unit A9, Waterloo, ON, N2L 5 V4, Canada
| | - Xiaoyulong Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Luca Cocolin
- European Food Information Council, Brussels, Belgium
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Summit, Lee, MO, 's, USA
| | | | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lene Lange
- BioEconomy, Research, & Advisory, Valby, Denmark
| | - Nelson Lima
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Alexander Loy
- Department of Microbial Ecology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Emmanuelle Maguin
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Tim Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, UK
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Birgit Mitter
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Inga Sarand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | | | - G Seghal Kiran
- Dept of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Leo van Overbeek
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michael Wagner
- Department of Microbial Ecology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Aaron Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
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Merrick B, Allen L, Masirah M Zain N, Forbes B, Shawcross DL, Goldenberg SD. Regulation, risk and safety of Faecal Microbiota Transplant. Infect Prev Pract 2020; 2:100069. [PMID: 34316559 PMCID: PMC7280140 DOI: 10.1016/j.infpip.2020.100069] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/03/2020] [Indexed: 02/06/2023] Open
Abstract
From its origins as a left-field, experimental, and even “maverick” intervention, faecal microbiota transplantation (FMT) is now a well-recognised, accepted, and potentially life-saving therapeutic strategy, for the management of recurrent Clostridiodes difficile infection (rCDI). It is being investigated as a treatment for a growing number of diseases including hepatic encephalopathy and eradication of antimicrobial resistant organisms, and the list of indications will likely expand in the future. There is no universally accepted definition of what FMT is, and its mechanism of action remains incompletely understood; this has likely contributed to the breadth of approaches to regulation depending on interpretation. In the UK FMT is considered a medicinal product, in North America, a biological product, whereas in parts of Europe, it is considered a human cell/tissue product. Regulation seeks to improve quality and safety, however, lack of standardisation creates confusion, and overly restrictive regulation may hamper widespread access and discourage research using FMT. FMT is generally considered safe, especially if rigorous donor screening and testing is conducted. Most short-term risks are associated with the delivery method (e.g. colonoscopy). Longer term risks are less well described but longitudinal follow-up of treated cohorts is in place to assess for this, and no signal towards harm has been found to date. Rarely it has been associated with adverse outcomes including the transmission of antibiotic resistant bacteria, and even death. It is vital patients undergoing FMT are well informed to the currently appreciated risks and benefits before proceeding.
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Affiliation(s)
- Blair Merrick
- Centre for Clinical Infection and Diagnostics Research (CIDR), King's College, London and Guy's & St. Thomas' NHS Foundation Trust, UK
| | - Liz Allen
- Early Clinical Development Centre of Excellence, IQVIA, Reading, UK.,Department of Pharmacy, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Nur Masirah M Zain
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College, London, UK
| | - Ben Forbes
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College, London, UK
| | - Debbie L Shawcross
- Institute of Liver Studies, Inflammation Biology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research (CIDR), King's College, London and Guy's & St. Thomas' NHS Foundation Trust, UK
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44
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Ramalho R, Rao M, Zhang C, Agrati C, Ippolito G, Wang FS, Zumla A, Maeurer M. Immunometabolism: new insights and lessons from antigen-directed cellular immune responses. Semin Immunopathol 2020; 42:279-313. [PMID: 32519148 PMCID: PMC7282544 DOI: 10.1007/s00281-020-00798-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
Abstract
Modulation of immune responses by nutrients is an important area of study in cellular biology and clinical sciences in the context of cancer therapies and anti-pathogen-directed immune responses in health and disease. We review metabolic pathways that influence immune cell function and cellular persistence in chronic infections. We also highlight the role of nutrients in altering the tissue microenvironment with lessons from the tumor microenvironment that shapes the quality and quantity of cellular immune responses. Multiple layers of biological networks, including the nature of nutritional supplements, the genetic background, previous exposures, and gut microbiota status have impact on cellular performance and immune competence against molecularly defined targets. We discuss how immune metabolism determines the differentiation pathway of antigen-specific immune cells and how these insights can be explored to devise better strategies to strengthen anti-pathogen-directed immune responses, while curbing unwanted, non-productive inflammation.
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Affiliation(s)
- Renata Ramalho
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM, U4585 FCT), Applied Nutrition Studies Group G.E.N.A.-IUEM), Instituto Universitário Egas Moniz, Egas Moniz Higher Education School, Monte de Caparica, Portugal
| | - Martin Rao
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Chao Zhang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | | | | | - Fu-Sheng Wang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal.
- I Medizinische Klinik, Johannes Gutenberg University Mainz, Mainz, Germany.
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45
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Amoroso C, Perillo F, Strati F, Fantini M, Caprioli F, Facciotti F. The Role of Gut Microbiota Biomodulators on Mucosal Immunity and Intestinal Inflammation. Cells 2020; 9:cells9051234. [PMID: 32429359 PMCID: PMC7291275 DOI: 10.3390/cells9051234] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
Alterations of the gut microbiota may cause dysregulated mucosal immune responses leading to the onset of inflammatory bowel diseases (IBD) in genetically susceptible hosts. Restoring immune homeostasis through the normalization of the gut microbiota is now considered a valuable therapeutic approach to treat IBD patients. The customization of microbe-targeted therapies, including antibiotics, prebiotics, live biotherapeutics and faecal microbiota transplantation, is therefore considered to support current therapies in IBD management. In this review, we will discuss recent advancements in the understanding of host−microbe interactions in IBD and the basis to promote homeostatic immune responses through microbe-targeted therapies. By considering gut microbiota dysbiosis as a key feature for the establishment of chronic inflammatory events, in the near future it will be suitable to design new cost-effective, physiologic, and patient-oriented therapeutic strategies for the treatment of IBD that can be applied in a personalized manner.
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Affiliation(s)
- Chiara Amoroso
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.A.); (F.P.); (F.S.)
| | - Federica Perillo
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.A.); (F.P.); (F.S.)
| | - Francesco Strati
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.A.); (F.P.); (F.S.)
| | - Massimo Fantini
- Gastroenterology Unit, Duilio Casula Hospital, AOU Cagliari, 09042 Cagliari, Italy;
- Department of Medical Science and Public Health, University of Cagliari, 09124 Cagliari, Italy
| | - Flavio Caprioli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20135 Milan, Italy;
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20135 Milan, Italy
| | - Federica Facciotti
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.A.); (F.P.); (F.S.)
- Correspondence:
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46
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Fadda HM. The Route to Palatable Fecal Microbiota Transplantation. AAPS PharmSciTech 2020; 21:114. [PMID: 32296975 DOI: 10.1208/s12249-020-1637-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
The community of symbiotic microorganisms that reside in our gastrointestinal tract is integral to human health. Fecal microbiota transplantation (FMT) has been shown to be highly effective in treating recurrent Clostridioides difficile infection (rCDI) and is now recommended by medical societies for patients suffering from rCDI who have failed to respond to conventional therapy. The main challenges with FMT are its accessibility, acceptability, lack of standardization, and regulatory complexity, which will be discussed in this review. Access to FMT is being addressed through the development of frozen and lyophilized FMT preparations that can be prepared at stool banks and shipped to the point of care. Both access and patient acceptance would be enhanced by oral FMT capsules, and there is potential to reduce capsule burden by utilizing colonic release capsules, targeting the site of disease. This review compares the efficacy of different FMT routes of administration: capsules, nasal feeding tubes, enemas, and colonoscopic infusions. FMT is considered investigational by the Food and Drug Administration. In effort to improve access to FMT, physicians may perform FMT outside of an investigational new drug application for treating CDI infections not responsive to standard therapies. The majority of FMT studies report only minor adverse effects; however, there is risk of transmission of infections.
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47
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Sullivan MH, Boggiano VL, Smith KL. Management of difficult-to-treat Clostridioides difficile in a patient with chronic osteomyelitis. BMJ Case Rep 2020; 13:13/3/e233095. [PMID: 32229549 PMCID: PMC7167421 DOI: 10.1136/bcr-2019-233095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A 61-year-old male patient being treated with intravenous antibiotics for left foot osteomyelitis presented to the hospital septic, with several days of worsening abdominal pain, bloating and watery bowel movements. Investigation revealed that the patient had severe, treatment-resistant Clostridioides difficile colitis. He was initially treated with oral vancomycin and intravenous metronidazole, which was switched to oral fidaxomicin. After no improvement in the patient's symptoms, he was treated with two faecal microbiota transplants. He was offered a third faecal microbiota transplant but declined. The patient was placed back on oral fidaxomicin and saw ultimate resolution of his symptoms. This case provides an example of a treatment pathway for refractory C. difficile infection.
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Affiliation(s)
| | | | - Kelly Lacy Smith
- Department of Family Medicine, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
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48
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Chen YT, Hsieh PS, Ho HH, Hsieh SH, Kuo YW, Yang SF, Lin CW. Antibacterial activity of viable and heat-killed probiotic strains against oral pathogens. Lett Appl Microbiol 2020; 70:310-317. [PMID: 31955445 DOI: 10.1111/lam.13275] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 12/16/2022]
Abstract
Probiotics can stabilize gut flora, regulate intestinal immunity and protect the host from enteric diseases; however, their roles in oral health have received little attention compared to their roles in gut health. Nowadays, the prevalence of sugar-sweetened foods and abuse of antibiotics contribute towards dysbiosis of oral microbiota and drug resistance development in oral pathogens, resulting in various intractable oral diseases. We screened the antibacterial activities of viable and heat-killed probiotic strains against the oral pathogens Streptococcus mutans, Porphyromonas gingivalis, Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans. The probiotic strains Lactobacillus salivarius subsp. salicinius AP-32, L. rhamnosus CT-53, L. paracasei ET-66 and Bifidobacterium animalis subsp. lactis CP-9 displayed strong antipathogenic activities, whereas heat-killed AP-32, CT-53 and ET-66 displayed high levels of pathogen inhibition. The antibacterial activities of these probiotics were not associated with their H2 O2 production; L. acidophilus TYCA02 produced high levels of H2 O2 but merely exhibited moderate antibacterial activities. Oral tablets containing probiotics showed positive inhibitory effects against oral pathogens, particularly those containing viable probiotics. Our results indicate that probiotics prevent the growth of oral pathogens and improve oral health, providing insights into the antipathogenic efficacy of different probiotic species and their potential role in functional foods that improve oral health. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study provides insights into the antipathogenic efficacy of different probiotic species and their potential roles in developing functional foods to improve oral health. We showed that the probiotic strains Lactobacillus salivarius subsp. salicinius AP-32, L. rhamnosus CT-53, L. paracasei ET-66 and Bifidobacterium animalis subsp. lactis CP-9 have great potential for use in the development of functional foods to improve oral health. Since active probiotics may provide strong and long-term protection, the development of functional food products should favour the use of viable bacteria.
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Affiliation(s)
- Y-T Chen
- School of Dentistry, Chung Shan Medical University, Taichung, Taiwan.,Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - P-S Hsieh
- Glac Biotech Co. Ltd, Tainan, Taiwan
| | - H-H Ho
- Glac Biotech Co. Ltd, Tainan, Taiwan
| | - S-H Hsieh
- Glac Biotech Co. Ltd, Tainan, Taiwan
| | - Y-W Kuo
- Glac Biotech Co. Ltd, Tainan, Taiwan
| | - S-F Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - C-W Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
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49
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Plasmid-mediated metronidazole resistance in Clostridioides difficile. Nat Commun 2020; 11:598. [PMID: 32001686 PMCID: PMC6992631 DOI: 10.1038/s41467-020-14382-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
Metronidazole was until recently used as a first-line treatment for potentially life-threatening Clostridioides difficile (CD) infection. Although cases of metronidazole resistance have been documented, no clear mechanism for metronidazole resistance or a role for plasmids in antimicrobial resistance has been described for CD. Here, we report genome sequences of seven susceptible and sixteen resistant CD isolates from human and animal sources, including isolates from a patient with recurrent CD infection by a PCR ribotype (RT) 020 strain, which developed resistance to metronidazole over the course of treatment (minimal inhibitory concentration [MIC] = 8 mg L−1). Metronidazole resistance correlates with the presence of a 7-kb plasmid, pCD-METRO. pCD-METRO is present in toxigenic and non-toxigenic resistant (n = 23), but not susceptible (n = 563), isolates from multiple countries. Introduction of a pCD-METRO-derived vector into a susceptible strain increases the MIC 25-fold. Our finding of plasmid-mediated resistance can impact diagnostics and treatment of CD infections. Cases of C. difficile (CD) resistant to metronidazole have been reported but the mechanism remains enigmatic. Here the authors identify a plasmid, which correlates with metronidazole resistance status in a large international collection of CD isolates, and demonstrate that the plasmid can confer metronidazole resistance.
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50
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DUPONT HERBERTL, JIANG ZHIDONG, DUPONT ANDREWW, UTAY NETANYAS. THE INTESTINAL MICROBIOME IN HUMAN HEALTH AND DISEASE. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2020; 131:178-197. [PMID: 32675857 PMCID: PMC7358474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Human Microbiome Initiative of NIH, begun in 2007, has opened the door to the power of the intestinal microbiome in health and disease. The 100 trillion gut microbes influence body function through three pathways: (1) via the neural route where 500 million neurons of the enteric nervous system (the body's second brain) connect to the brain and spinal cord, (2) via the immune route where the gut-immune capacity prevents infection and elicits immune response to vaccines, and (3) by the hormonal route wherein biologically active chemicals are released from enteroendocrine cells to control mood and body functions. Through research, the identification of diseases and disorders associated with abnormal microbiome ("dysbiosis") has increased in number with potential for reversibility. Our team has developed an orally administered fecal microbiota transplantation product that is effective in reversing dysbiosis in recurrent Clostridioides difficile (C. difficile) and is being used to reverse abnormal microbiomes in chronic dysbiotic disorders.
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Affiliation(s)
- HERBERT L. DUPONT
- Correspondence and reprint requests: Herbert L. DuPont, MD, MACP, 1200 Pressler Street, Houston, Texas 77030713-500-9366
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