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Herrera G, Castañeda S, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile. Microbiol Res 2024; 285:127739. [PMID: 38763016 DOI: 10.1016/j.micres.2024.127739] [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: 12/19/2023] [Revised: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Clostridioides difficile may have a negative impact on gut microbiota composition in terms of diversity and abundance, thereby triggering functional changes supported by the differential presence of genes involved in significant metabolic pathways, such as short-chain fatty acids (SCFA). This work has evaluated shotgun metagenomics data regarding 48 samples from four groups classified according to diarrhea acquisition site (community- and healthcare facility-onset) and positive or negative Clostridioides difficile infection (CDI) result. The metagenomic-assembled genomes (MAGs) obtained from each sample were taxonomically assigned for preliminary comparative analysis concerning differences in composition among groups. The predicted genes involved in metabolism, transport, and signaling remained constant in microbiota members; characteristic patterns were observed in MAGs and genes involved in SCFA butyrate and acetate metabolic pathways for each study group. A decrease in genera and species, as well as relative MAG abundance with the presence of the acetate metabolism-related gene, was evident in the HCFO/- group. Increased antibiotic resistance markers (ARM) were observed in MAGs along with the genes involved in acetate metabolism. The results highlight the need to explore the role of acetate in greater depth as a potential protector of the imbalances produced by CDI, as occurs in other inflammatory intestinal diseases.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia; Semillero de Investigación en Bioinformática - GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia; Grupo de Fundamentos y Enseñanza de la Física y las Sistemas Dinámicas, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E Pérez-Jaramillo
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia; Semillero de Investigación en Bioinformática - GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia; Health Sciences Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Instituto de Biotecnología-UN (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia.
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Okhuysen PC, Ramesh MS, Louie T, Kiknadze N, Torre-Cisneros J, de Oliveira CM, Van Steenkiste C, Stychneuskaya A, Garey KW, Garcia-Diaz J, Li J, Duperchy E, Chang BY, Sukbuntherng J, Montoya JG, Styles L, Clow F, James D, Dubberke ER, Wilcox M. A Randomized, Double-Blind, Phase 3 Safety and Efficacy Study of Ridinilazole Versus Vancomycin for Treatment of Clostridioides difficile Infection: Clinical Outcomes With Microbiome and Metabolome Correlates of Response. Clin Infect Dis 2024; 78:1462-1472. [PMID: 38305378 PMCID: PMC11175683 DOI: 10.1093/cid/ciad792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Exposure to antibiotics predisposes to dysbiosis and Clostridioides difficile infection (CDI) that can be severe, recurrent (rCDI), and life-threatening. Nonselective drugs that treat CDI and perpetuate dysbiosis are associated with rCDI, in part due to loss of microbiome-derived secondary bile acid (SBA) production. Ridinilazole is a highly selective drug designed to treat CDI and prevent rCDI. METHODS In this phase 3 superiority trial, adults with CDI, confirmed with a stool toxin test, were randomized to receive 10 days of ridinilazole (200 mg twice daily) or vancomycin (125 mg 4 times daily). The primary endpoint was sustained clinical response (SCR), defined as clinical response and no rCDI through 30 days after end of treatment. Secondary endpoints included rCDI and change in relative abundance of SBAs. RESULTS Ridinilazole and vancomycin achieved an SCR rate of 73% versus 70.7%, respectively, a treatment difference of 2.2% (95% CI: -4.2%, 8.6%). Ridinilazole resulted in a 53% reduction in recurrence compared with vancomycin (8.1% vs 17.3%; 95% CI: -14.1%, -4.5%; P = .0002). Subgroup analyses revealed consistent ridinilazole benefit for reduction in rCDI across subgroups. Ridinilazole preserved microbiota diversity, increased SBAs, and did not increase the resistome. Conversely, vancomycin worsened CDI-associated dysbiosis, decreased SBAs, increased Proteobacteria abundance (∼3.5-fold), and increased the resistome. CONCLUSIONS Although ridinilazole did not meet superiority in SCR, ridinilazole greatly reduced rCDI and preserved microbiome diversity and SBAs compared with vancomycin. These findings suggest that treatment of CDI with ridinilazole results in an earlier recovery of gut microbiome health. Clinical Trials Registration.Ri-CoDIFy 1 and 2: NCT03595553 and NCT03595566.
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Affiliation(s)
- Pablo C Okhuysen
- Department of Infectious Diseases, Infection Control, and Employee Heatlh, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Thomas Louie
- Foothills Medical Center and University of Calgary, Calgary, Canada
| | | | - Julian Torre-Cisneros
- Reina Sofia University Hospital-IMIBIC, University of Córdoba, CIBERINFEC, Cordoba, Spain
| | | | | | | | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, Texas, USA
| | | | - Jianling Li
- Summit Therapeutics, Menlo Park, California, USA
| | | | | | | | - Jose G Montoya
- Summit Therapeutics, Menlo Park, California, USA
- Dr. Jack S. Remington Laboratory for Specialty Diagnostics, Palo Alto Medical Foundation, Palo Alto, California, USA
| | - Lori Styles
- Summit Therapeutics, Menlo Park, California, USA
| | - Fong Clow
- Summit Therapeutics, Menlo Park, California, USA
| | | | - Erik R Dubberke
- Washington University School of Medicine, St.Louis, Missouri, USA
| | - Mark Wilcox
- Leeds Teaching Hospitals and University of Leeds, School of Medicine, Leeds, United Kingdom
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Herrera G, Vega L, Camargo A, Patarroyo MA, Ramírez JD, Muñoz M. Acquisition site-based remodelling of Clostridium perfringens- and Clostridioides difficile-related gut microbiota. Comp Immunol Microbiol Infect Dis 2023; 102:102074. [PMID: 37832162 DOI: 10.1016/j.cimid.2023.102074] [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: 08/07/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
INTRODUCTION Clostridium perfringens is a gram-positive, anaerobic sporulating bacillus which can infect several hosts, thereby being considered the causative agent of many gut illnesses. Some studies have suggested that C. perfringens's virulence factors may negatively affect gut microbiota homeostasis by decreasing beneficial bacteria; however, studies have failed to evaluate the simultaneous presence of other pathogenic bacteria, such as C. difficile (another sporulating bacillus known to play a role in gut microbiota imbalance). Conscious of the lack of compelling data, this work has ascertained how such microorganisms' coexistence can be associated with a variation in gut microbiota composition, compared to that of C. perfringens colonisation. METHODS PCR was thus used for identifying C. perfringens and C. difficile in 98 samples. Amplicon-based sequencing of 16S- and 18S-rRNA genes' V4 hypervariable region from such samples was used for determining the microbiota's taxonomical composition and diversity. RESULTS Small differences were observed in bacterial communities' taxonomic composition and diversity; such imbalance was mainly associated with groups having hospital-acquired diarrhoea. CONCLUSION The alterations reported herein may have been influenced by C. difficile and diarrhoea acquisition site, despite C. perfringens' ability to cause alterations in microbiota due to its virulence factors. Our findings highlight the need for a holistic view of gut microbiota.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Laura Vega
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Anny Camargo
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C. 111321, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia; Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá D.C. 110231, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia.
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Herrera G, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection. Microbiol Spectr 2022; 10:e0050222. [PMID: 36154277 PMCID: PMC9602525 DOI: 10.1128/spectrum.00502-22] [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] [Received: 02/08/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E. Pérez-Jaramillo
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Chen Y, Lv T, Yan D, Zheng L, Zheng B, Wang J, Gu S, Li L. Disordered Intestinal Microbial Communities During Clostridioides difficile Colonization and Subsequent Infection of Hepatic Cirrhosis Patients in a Tertiary Care Hospital in China. Front Cell Infect Microbiol 2022; 12:825189. [PMID: 35433508 PMCID: PMC9010725 DOI: 10.3389/fcimb.2022.825189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Patients with hepatic cirrhosis are more susceptible to Clostridioides difficile infection (CDI) and colonization with Clostridioides difficile (C. difficile). Asymptomatic C. difficile colonization is thought to predispose to subsequent CDI. However, the dynamic gut microbiota changes remain unclear. In this study, we used 16S rRNA gene sequencing to longitudinally monitor alterations in the intestinal microbiota of 22 hepatic cirrhosis patients with toxigenic C. difficile colonization at admission (pre-CDI) and developed CDI during hospitalization, subdivided into pre-CDI and CDI. 21 hospitalized cirrhotic patients without C. difficile colonization served as controls (HC). Compared with HC, pre-CDI and CDI samples had significantly decreased microbial richness and diversity, a significantly higher relative abundance of opportunistic pathogen Enterococcus, and a lower relative abundance of beneficial symbionts, such as Faecalibacterium, Dorea, and Roseburia. Three biomarkers showed high accuracy for distinguishing pre-CDI samples from HC with an area under the curve (AUC) up to 0.81. In conclusion, our study explored the changes of the gut microbiome before and after CDI. The gut microbial richness as well as diversity in CDI patients were notably reduced, relative to controls. Imbalance of the intestinal flora may be related to the risk for development of CDI. Identifying key members of the gut microbiota and illustrating their roles and mechanisms of action in CDI development are important avenues for future research.
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Affiliation(s)
- Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tao Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lisi Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jingxia Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Silan Gu,
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Bacterial Research Platform, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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