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Markelova NN, Semenova EF, Sineva ON, Sadykova VS. The Role of Cyclomodulins and Some Microbial Metabolites in Bacterial Microecology and Macroorganism Carcinogenesis. Int J Mol Sci 2022; 23:ijms231911706. [PMID: 36233008 PMCID: PMC9570213 DOI: 10.3390/ijms231911706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
A number of bacteria that colonize the human body produce toxins and effectors that cause changes in the eukaryotic cell cycle—cyclomodulins and low-molecular-weight compounds such as butyrate, lactic acid, and secondary bile acids. Cyclomodulins and metabolites are necessary for bacteria as adaptation factors—which are influenced by direct selection—to the ecological niches of the host. In the process of establishing two-way communication with the macroorganism, these compounds cause limited damage to the host, despite their ability to disrupt key processes in eukaryotic cells, which can lead to pathological changes. Possible negative consequences of cyclomodulin and metabolite actions include their potential role in carcinogenesis, in particular, with the ability to cause DNA damage, increase genome instability, and interfere with cancer-associated regulatory pathways. In this review, we aim to examine cyclomodulins and bacterial metabolites as important factors in bacterial survival and interaction with the host organism to show their heterogeneous effect on oncogenesis depending on the surrounding microenvironment, pathological conditions, and host genetic background.
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Affiliation(s)
- Natalia N. Markelova
- Gause Institute of New Antibiotics, ul. Bolshaya Pirogovskaya, 11, 119021 Moscow, Russia
- Correspondence: (N.N.M.); (V.S.S.)
| | - Elena F. Semenova
- Institute of Biochemical Technology, Ecology and Pharmacy, V.I. Vernadsky Crimean Federal University, 295007 Simferopol, Russia
| | - Olga N. Sineva
- Gause Institute of New Antibiotics, ul. Bolshaya Pirogovskaya, 11, 119021 Moscow, Russia
| | - Vera S. Sadykova
- Gause Institute of New Antibiotics, ul. Bolshaya Pirogovskaya, 11, 119021 Moscow, Russia
- Correspondence: (N.N.M.); (V.S.S.)
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52
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Cai J, Rimal B, Jiang C, Chiang JYL, Patterson AD. Bile acid metabolism and signaling, the microbiota, and metabolic disease. Pharmacol Ther 2022; 237:108238. [PMID: 35792223 DOI: 10.1016/j.pharmthera.2022.108238] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022]
Abstract
The diversity, composition, and function of the bacterial community inhabiting the human gastrointestinal tract contributes to host health through its role in producing energy or signaling molecules that regulate metabolic and immunologic functions. Bile acids are potent metabolic and immune signaling molecules synthesized from cholesterol in the liver and then transported to the intestine where they can undergo metabolism by gut bacteria. The combination of host- and microbiota-derived enzymatic activities contribute to the composition of the bile acid pool and thus there can be great diversity in bile acid composition that depends in part on the differences in the gut bacteria species. Bile acids can profoundly impact host metabolic and immunological functions by activating different bile acid receptors to regulate signaling pathways that control a broad range of complex symbiotic metabolic networks, including glucose, lipid, steroid and xenobiotic metabolism, and modulation of energy homeostasis. Disruption of bile acid signaling due to perturbation of the gut microbiota or dysregulation of the gut microbiota-host interaction is associated with the pathogenesis and progression of metabolic disorders. The metabolic and immunological roles of bile acids in human health have led to novel therapeutic approaches to manipulate the bile acid pool size, composition, and function by targeting one or multiple components of the microbiota-bile acid-bile acid receptor axis.
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Affiliation(s)
- Jingwei Cai
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, and the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, PR China
| | - John Y L Chiang
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA.
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53
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Pike CM, Tam J, Melnyk RA, Theriot CM. Tauroursodeoxycholic Acid Inhibits Clostridioides difficile Toxin-Induced Apoptosis. Infect Immun 2022; 90:e0015322. [PMID: 35862710 PMCID: PMC9387233 DOI: 10.1128/iai.00153-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/19/2022] [Indexed: 11/20/2022] Open
Abstract
C. difficile infection (CDI) is a highly inflammatory disease mediated by the production of two large toxins that weaken the intestinal epithelium and cause extensive colonic tissue damage. Antibiotic alternative therapies for CDI are urgently needed as current antibiotic regimens prolong the perturbation of the microbiota and lead to high disease recurrence rates. Inflammation is more closely correlated with CDI severity than bacterial burden, thus therapies that target the host response represent a promising yet unexplored strategy for treating CDI. Intestinal bile acids are key regulators of gut physiology that exert cytoprotective roles in cellular stress, inflammation, and barrier integrity, yet the dynamics between bile acids and host cellular processes during CDI have not been investigated. Here we show that several bile acids are protective against apoptosis caused by C. difficile toxins in Caco-2 cells and that protection is dependent on conjugation of bile acids. Out of 20 tested bile acids, taurine conjugated ursodeoxycholic acid (TUDCA) was the most potent inhibitor, yet unconjugated UDCA did not alter toxin-induced apoptosis. TUDCA treatment decreased expression of genes in lysosome associated and cytokine signaling pathways. TUDCA did not affect C. difficile growth or toxin activity in vitro whereas UDCA significantly reduced toxin activity in a Vero cell cytotoxicity assay and decreased tcdA gene expression. These results demonstrate that bile acid conjugation can have profound effects on C. difficile as well as the host and that conjugated and unconjugated bile acids may exert different therapeutic mechanisms against CDI.
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Affiliation(s)
- Colleen M. Pike
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - John Tam
- Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roman A. Melnyk
- Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- SickKids Proteomics Analytics Robotics Chemical Biology Drug Discovery Facility, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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54
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Schnizlein MK, Young VB. Capturing the environment of the Clostridioides difficile infection cycle. Nat Rev Gastroenterol Hepatol 2022; 19:508-520. [PMID: 35468953 DOI: 10.1038/s41575-022-00610-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/11/2022]
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection is a substantial health and economic burden worldwide. Great strides have been made over the past several years in characterizing the physiology of C. difficile infection, particularly regarding how gut microorganisms and their host work together to provide colonization resistance. As mammalian hosts and their indigenous gut microbiota have co-evolved, they have formed a complex yet stable relationship that prevents invading microorganisms from establishing themselves. In this Review, we discuss the latest advances in our understanding of C. difficile physiology that have contributed to its success as a pathogen, including its versatile survival factors and ability to adapt to unique niches. Using discoveries regarding microorganism-host and microorganism-microorganism interactions that constitute colonization resistance, we place C. difficile within the fiercely competitive gut environment. A comprehensive understanding of these relationships is required to continue the development of precision medicine-based treatments for C. difficile infection.
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Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
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55
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Abstract
The severity of Clostridioides difficile infections (CDI) has increased over the last few decades. Patient age, white blood cell count, and creatinine levels as well as C. difficile ribotype and toxin genes have been associated with disease severity. However, it is unclear whether specific members of the gut microbiota are associated with variations in disease severity. The gut microbiota is known to interact with C. difficile during infection. Perturbations to the gut microbiota are necessary for C. difficile to colonize the gut. The gut microbiota can inhibit C. difficile colonization through bile acid metabolism, nutrient consumption, and bacteriocin production. Here, we sought to demonstrate that members of the gut bacterial communities can also contribute to disease severity. We derived diverse gut communities by colonizing germfree mice with different human fecal communities. The mice were then infected with a single C. difficile ribotype 027 clinical isolate, which resulted in moribundity and histopathologic differences. The variation in severity was associated with the human fecal community that the mice received. Generally, bacterial populations with pathogenic potential, such as Enterococcus, Helicobacter, and Klebsiella, were associated with more-severe outcomes. Bacterial groups associated with fiber degradation and bile acid metabolism, such as Anaerotignum, Blautia, Lactonifactor, and Monoglobus, were associated with less-severe outcomes. These data indicate that, in addition to the host and C. difficile subtype, populations of gut bacteria can influence CDI disease severity.
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Abstract
The nosocomial pathogen Clostridioides difficile is a burden to the healthcare system. Gut microbiome disruption, most commonly by broad-spectrum antibiotic treatment, is well established to generate a state that is susceptible to CDI. A variety of metabolites produced by the host and/or gut microbiota have been shown to interact with C. difficile. Certain bile acids promote/inhibit germination while other cholesterol-derived compounds and amino acids used in the Stickland metabolic pathway affect growth and CDI colonization. Short chain fatty acids maintain intestinal barrier integrity and a myriad of other metabolic compounds are used as nutritional sources or used by C. difficile to inhibit or outcompete other bacteria in the gut. As the move toward non-antibiotic CDI treatment takes place, a deeper understanding of interactions between C. difficile and the host's gut microbiome and metabolites becomes more relevant.
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Affiliation(s)
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX, USA,CONTACT Joseph A. Sorg Department of Biology, Texas A&M University, College Station, TX77843, USA
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Gao Y, Ma L, Su J. Host and microbial-derived metabolites for Clostridioides difficile infection: Contributions, mechanisms and potential applications. Microbiol Res 2022; 263:127113. [PMID: 35841835 DOI: 10.1016/j.micres.2022.127113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/23/2022]
Abstract
Clostridioides difficile infection (CDI), which mostly occurs in hospitalized patients, is the most common and costly health care-associated disease. However, the biology of C. difficile remains incompletely understood. Current therapeutics are still challenged by the frequent recurrence of CDI. Advances in metabolomics facilitate our understanding of the etiology of CDI, which is not merely an alteration in the structure of the gut microbial community but also a dysbiosis metabolic setting promoting the germination, expansion and virulence of C. difficile. Therefore, we summarized the gut microbial and metabolic profiles for CDI under different conditions, such as those of postantibiotic treatment and postfecal microbiota transplantation. The current understanding of the role of host and gut microbial-derived metabolites as well as other nutrients in preventing or alleviating the disease symptoms of CDI will also be provided in this review. We hope that a specific nutrient-centric dietary strategy or the administration of certain nutrients to the colon could serve as an alternate line of investigation for the prophylaxis and mitigation of CDI in the future. Nevertheless, rigorously designed basic studies and randomized controlled trials need to be conducted to assess the functional mechanisms and effects of such therapeutics.
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Affiliation(s)
- Yan Gao
- Department of Clinical Laboratory Diagnostics, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Liyan Ma
- Department of Clinical Laboratory Diagnostics, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jianrong Su
- Department of Clinical Laboratory Diagnostics, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China.
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58
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Ratiner K, Shapiro H, Goldenberg K, Elinav E. Time-limited diets and the gut microbiota in cardiometabolic disease. J Diabetes 2022; 14:377-393. [PMID: 35698246 PMCID: PMC9366560 DOI: 10.1111/1753-0407.13288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, intermittent fasting (IF), including periodic fasting and time-restricted feeding (TRF), has been increasingly suggested to constitute a promising treatment for cardiometabolic diseases (CMD). A deliberate daily pause in food consumption influences the gut microbiome and the host circadian clock, resulting in improved cardiometabolic health. Understanding the molecular mechanisms by which circadian host-microbiome interactions affect host metabolism and immunity may add a potentially important dimension to effective implementation of IF diets. In this review, we discuss emerging evidence potentially linking compositional and functional alterations of the gut microbiome with IF impacts on mammalian metabolism and risk of development of hypertension, type 2 diabetes (T2D), obesity, and their long-term micro- and macrovascular complications. We highlight the challenges and unknowns in causally linking diurnal bacterial signals with dietary cues and downstream metabolic consequences and means of harnessing these signals toward future microbiome integration into precision medicine.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Hagit Shapiro
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Kim Goldenberg
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
| | - Eran Elinav
- Systems Immunology DepartmentWeizmann Institute of ScienceRehovotIsrael
- Microbiome & Cancer Division, DKFZHeidelbergGermany
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59
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Hitch TCA, Hall LJ, Walsh SK, Leventhal GE, Slack E, de Wouters T, Walter J, Clavel T. Microbiome-based interventions to modulate gut ecology and the immune system. Mucosal Immunol 2022; 15:1095-1113. [PMID: 36180583 PMCID: PMC9705255 DOI: 10.1038/s41385-022-00564-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 02/04/2023]
Abstract
The gut microbiome lies at the intersection between the environment and the host, with the ability to modify host responses to disease-relevant exposures and stimuli. This is evident in how enteric microbes interact with the immune system, e.g., supporting immune maturation in early life, affecting drug efficacy via modulation of immune responses, or influencing development of immune cell populations and their mediators. Many factors modulate gut ecosystem dynamics during daily life and we are just beginning to realise the therapeutic and prophylactic potential of microbiome-based interventions. These approaches vary in application, goal, and mechanisms of action. Some modify the entire community, such as nutritional approaches or faecal microbiota transplantation, while others, such as phage therapy, probiotics, and prebiotics, target specific taxa or strains. In this review, we assessed the experimental evidence for microbiome-based interventions, with a particular focus on their clinical relevance, ecological effects, and modulation of the immune system.
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Affiliation(s)
- Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich, UK
- Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Sarah Kate Walsh
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
- APC Microbiome Ireland, School of Microbiology and Department of Medicine, University College Cork, Cork, Ireland
| | | | - Emma Slack
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Jens Walter
- APC Microbiome Ireland, School of Microbiology and Department of Medicine, University College Cork, Cork, Ireland
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany.
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60
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Wu Z, Xu Q, Gu S, Chen Y, Lv L, Zheng B, Wang Q, Wang K, Wang S, Xia J, Yang L, Bian X, Jiang X, Zheng L, Li L. Akkermansia muciniphila Ameliorates Clostridioides difficile Infection in Mice by Modulating the Intestinal Microbiome and Metabolites. Front Microbiol 2022; 13:841920. [PMID: 35663882 PMCID: PMC9159907 DOI: 10.3389/fmicb.2022.841920] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile is a common cause of nosocomial infection. Antibiotic-induced dysbiosis in the intestinal microbiota is a core cause of C. difficile infection (CDI). Akkermansia muciniphila plays an active role in maintaining gastrointestinal balance and might offer the protective effects on CDI as probiotics. Here, we investigated the effects and mechanisms of A. muciniphila on CDI. C57BL/6 mice (n = 29) were administered A. muciniphila Muc T (3 × 109 CFUs, 0.2 mL) or phosphate-buffered saline (PBS) by oral gavage for 2 weeks. Mice were pretreated with an antibiotic cocktail and subsequently challenged with the C. difficile strain VPI 10463. A. muciniphila treatment prevented weight loss in mice and reduced the histological injury of the colon. And it also alleviated inflammation and improved the barrier function of the intestine. The administration effects of A. muciniphila may be associated with an increase in short-chain fatty acid production and the maintenance of bile acids' steady-state. Our results provide evidence that administration of A. muciniphila to CDI mice, with an imbalance in the microbial community structure, lead to a decrease in abundance of members of the Enterobacteriaceae and Enterococcaceae. In short, A. muciniphila shows a potential anti-CDI role by modulating gut microbiota and the metabolome.
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Affiliation(s)
- Zhengjie Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiangqiang Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kaicen Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liya Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyuan Bian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianwan Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisi Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Bacterial Research Platform, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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Cruz KCP, Enekegho LO, Stuart DT. Bioengineered Probiotics: Synthetic Biology Can Provide Live Cell Therapeutics for the Treatment of Foodborne Diseases. Front Bioeng Biotechnol 2022; 10:890479. [PMID: 35656199 PMCID: PMC9152101 DOI: 10.3389/fbioe.2022.890479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/29/2022] [Indexed: 11/15/2022] Open
Abstract
The rising prevalence of antibiotic resistant microbial pathogens presents an ominous health and economic challenge to modern society. The discovery and large-scale development of antibiotic drugs in previous decades was transformational, providing cheap, effective treatment for what would previously have been a lethal infection. As microbial strains resistant to many or even all antibiotic drug treatments have evolved, there is an urgent need for new drugs or antimicrobial treatments to control these pathogens. The ability to sequence and mine the genomes of an increasing number of microbial strains from previously unexplored environments has the potential to identify new natural product antibiotic biosynthesis pathways. This coupled with the power of synthetic biology to generate new production chassis, biosensors and “weaponized” live cell therapeutics may provide new means to combat the rapidly evolving threat of drug resistant microbial pathogens. This review focuses on the application of synthetic biology to construct probiotic strains that have been endowed with functionalities allowing them to identify, compete with and in some cases kill microbial pathogens as well as stimulate host immunity. Weaponized probiotics may have the greatest potential for use against pathogens that infect the gastrointestinal tract: Vibrio cholerae, Staphylococcus aureus, Clostridium perfringens and Clostridioides difficile. The potential benefits of engineered probiotics are highlighted along with the challenges that must still be met before these intriguing and exciting new therapeutic tools can be widely deployed.
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62
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Abstract
The gastrointestinal ecosystem is formed from interactions between the host, indigenous gut microbiota, and external world. When colonizing the gut, bacteria must overcome barriers imposed by the intestinal environment, such as host immune responses and microbiota-mediated nutrient limitation. Thus, understanding bacterial colonization requires determining how the gut landscape interacts with microbes attempting to establish within the ecosystem. However, the complicated network of interactions between elements of the intestinal environment makes it challenging to uncover emergent properties of the system using only reductionist methods. A systems biology approach, which aims to investigate complex systems by examining the behavior and relationships of all elements of the system, may afford a more holistic perspective of the colonization process. Here, we examine the confluence between the gut landscape and bacterial colonization through the lens of systems biology. We offer an overview of the conceptual and methodological underpinnings of systems biology, followed by a discussion of key elements of the gut ecosystem as they pertain to bacterial establishment and growth. We conclude by reintegrating these elements to guide future comprehensive investigations of the ecosystem in the context of bacterial intestinal colonization.
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Affiliation(s)
- Madeline R. Barron
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
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63
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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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64
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The Stickland Reaction Precursor trans-4-Hydroxy-l-Proline Differentially Impacts the Metabolism of Clostridioides difficile and Commensal Clostridia. mSphere 2022; 7:e0092621. [PMID: 35350846 PMCID: PMC9044972 DOI: 10.1128/msphere.00926-21] [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: 02/07/2023] Open
Abstract
An intact gut microbiota confers colonization resistance against Clostridioides difficile through a variety of mechanisms, likely including competition for nutrients. Recently, proline was identified as an important environmental amino acid that C. difficile uses to support growth and cause significant disease. A posttranslationally modified form, trans-4-hydroxyproline, is highly abundant in collagen, which is degraded by host proteases in response to C. difficile toxin activity. The ability to dehydrate trans-4-hydroxyproline via the HypD glycyl radical enzyme is widespread among gut microbiota, including C. difficile and members of the commensal Clostridia, suggesting that this amino acid is an important nutrient in the host environment. Therefore, we constructed a C. difficile ΔhypD mutant and found that it was modestly impaired in fitness in a mouse model of infection, and was associated with an altered microbiota when compared to mice challenged with the wild-type strain. Changes in the microbiota between the two groups were largely driven by members of the Lachnospiraceae family and the Clostridium genus. We found that C. difficile and type strains of three commensal Clostridia had significant alterations to their metabolic gene expression in the presence of trans-4-hydroxyproline in vitro. The proline reductase (prd) genes were elevated in C. difficile, consistent with the hypothesis that trans-4-hydroxyproline is used by C. difficile to supply proline for energy metabolism. Similar transcripts were also elevated in some commensal Clostridia tested, although each strain responded differently. This suggests that the uptake and utilization of other nutrients by the commensal Clostridia may be affected by trans-4-hydroxyproline metabolism, highlighting how a common nutrient may be a signal to each organism to adapt to a unique niche. Further elucidation of the differences between them in the presence of hydroxyproline and other key nutrients will be important in determining their role in nutrient competition against C. difficile. IMPORTANCE Proline is an essential environmental amino acid that C. difficile uses to support growth and cause significant disease. A posttranslationally modified form, hydroxyproline, is highly abundant in collagen, which is degraded by host proteases in response to C. difficile toxin activity. The ability to dehydrate hydroxyproline via the HypD glycyl radical enzyme is widespread among gut microbiota, including C. difficile and members of the commensal Clostridia, suggesting that this amino acid is an important nutrient in the host environment. We found that C. difficile and three commensal Clostridia strains had significant, but different, alterations to their metabolic gene expression in the presence of hydroxyproline in vitro. This suggests that the uptake and utilization of other nutrients by the commensal Clostridia may be affected by hydroxyproline metabolism, highlighting how a common nutrient may be a signal to each organism to adapt to a unique niche. Further elucidation of the differences between them in the presence of hydroxyproline and other key nutrients will be important to determining their role in nutrient competition against C. difficile.
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Metzendorf NG, Lange LM, Lainer N, Schlüter R, Dittmann S, Paul LS, Troitzsch D, Sievers S. Destination and Specific Impact of Different Bile Acids in the Intestinal Pathogen Clostridioides difficile. Front Microbiol 2022; 13:814692. [PMID: 35401433 PMCID: PMC8989276 DOI: 10.3389/fmicb.2022.814692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/09/2022] [Indexed: 01/05/2023] Open
Abstract
The anaerobic bacterium Clostridioides difficile represents one of the most problematic pathogens, especially in hospitals. Dysbiosis has been proven to largely reduce colonization resistance against this intestinal pathogen. The beneficial effect of the microbiota is closely associated with the metabolic activity of intestinal microbes such as the ability to transform primary bile acids into secondary ones. However, the basis and the molecular action of bile acids (BAs) on the pathogen are not well understood. We stressed the pathogen with the four most abundant human bile acids: cholic acid (CA), chenodeoxycholic acid (CDCA), deoxycholic acid (DCA) and lithocholic acid (LCA). Thin layer chromatography (TLC), confocal laser scanning microscopy (CLSM), and electron microscopy (EM) were employed to track the enrichment and destination of bile acids in the bacterial cell. TLC not only revealed a strong accumulation of LCA in C. difficile, but also indicated changes in the composition of membrane lipids in BA-treated cells. Furthermore, morphological changes induced by BAs were determined, most pronounced in the virtually complete loss of flagella in LCA-stressed cells and a flagella reduction after DCA and CDCA challenge. Quantification of both, protein and RNA of the main flagella component FliC proved the decrease in flagella to originate from a change in gene expression on transcriptional level. Notably, the loss of flagella provoked by LCA did not reduce adhesion ability of C. difficile to Caco-2 cells. Most remarkably, extracellular toxin A levels in the presence of BAs showed a similar pattern as flagella expression. That is, CA did not affect toxin expression, whereas lower secretion of toxin A was determined in cells stressed with LCA, DCA or CDCA. In summary, the various BAs were shown to differentially modify virulence determinants, such as flagella expression, host cell adhesion and toxin synthesis. Our results indicate differences of BAs in cellular localization and impact on membrane composition, which could be a reason of their diverse effects. This study is a starting point in the elucidation of the molecular mechanisms underlying the differences in BA action, which in turn can be vital regarding the outcome of a C. difficile infection.
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Affiliation(s)
| | - Lena Melanie Lange
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Nina Lainer
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Silvia Dittmann
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Lena-Sophie Paul
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Daniel Troitzsch
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
- *Correspondence: Susanne Sievers,
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Łukawska A, Mulak A. Impact of Primary and Secondary Bile Acids on Clostridioides difficile Infection. Pol J Microbiol 2022; 71:11-18. [PMID: 35635171 PMCID: PMC9152914 DOI: 10.33073/pjm-2022-007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/31/2022] [Indexed: 11/05/2022] Open
Abstract
Primary bile acids (BAs), synthesized from cholesterol in the liver, after their secretion with bile into the intestinal lumen, are transformed by gut microbiota to secondary BAs. As natural detergents, BAs play a key role in the digestion and absorption of lipids and liposoluble vitamins. However, they have also been recognized as important signaling molecules involved in numerous metabolic processes. The close bidirectional interactions between BAs and gut microbiota occur since BAs influence microbiota composition, whereas microbiota determines BA metabolism. In particular, it is well established that BAs modulate Clostridioides difficile life cycle in vivo. C. difficile is a cause of common nosocomial infections that have become a growing concern. The aim of this review is to summarize the current knowledge regarding the impact of BAs on the pathogenesis, prevention, and treatment of C. difficile infection. ![]()
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Affiliation(s)
- Agata Łukawska
- Department of Gastroenterology and Hepatology , Wroclaw Medical University , Wroclaw , Poland
| | - Agata Mulak
- Department of Gastroenterology and Hepatology , Wroclaw Medical University , Wroclaw , Poland
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Novel Developments on Stimuli-Responsive Probiotic Encapsulates: From Smart Hydrogels to Nanostructured Platforms. FERMENTATION 2022. [DOI: 10.3390/fermentation8030117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Biomaterials engineering and biotechnology have advanced significantly towards probiotic encapsulation with encouraging results in assuring sufficient bioactivity. However, some major challenges remain to be addressed, and these include maintaining stability in different compartments of the gastrointestinal tract (GIT), favoring adhesion only at the site of action, and increasing residence times. An alternative to addressing such challenges is to manufacture encapsulates with stimuli-responsive polymers, such that controlled release is achievable by incorporating moieties that respond to chemical and physical stimuli present along the GIT. This review highlights, therefore, such emerging delivery matrices going from a comprehensive description of addressable stimuli in each GIT compartment to novel synthesis and functionalization techniques to currently employed materials used for probiotic’s encapsulation and achieving multi-modal delivery and multi-stimuli responses. Next, we explored the routes for encapsulates design to enhance their performance in terms of degradation kinetics, adsorption, and mucus and gut microbiome interactions. Finally, we present the clinical perspectives of implementing novel probiotics and the challenges to assure scalability and cost-effectiveness, prerequisites for an eventual niche market penetration.
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Khan I, Bai Y, Zha L, Ullah N, Ullah H, Shah SRH, Sun H, Zhang C. Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection. Front Cell Infect Microbiol 2022; 11:716299. [PMID: 35004340 PMCID: PMC8733563 DOI: 10.3389/fcimb.2021.716299] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022] Open
Abstract
The mammalian gut microbial community, known as the gut microbiota, comprises trillions of bacteria, which co-evolved with the host and has an important role in a variety of host functions that include nutrient acquisition, metabolism, and immunity development, and more importantly, it plays a critical role in the protection of the host from enteric infections associated with exogenous pathogens or indigenous pathobiont outgrowth that may result from healthy gut microbial community disruption. Microbiota evolves complex mechanisms to restrain pathogen growth, which included nutrient competition, competitive metabolic interactions, niche exclusion, and induction of host immune response, which are collectively termed colonization resistance. On the other hand, pathogens have also developed counterstrategies to expand their population and enhance their virulence to cope with the gut microbiota colonization resistance and cause infection. This review summarizes the available literature on the complex relationship occurring between the intestinal microbiota and enteric pathogens, describing how the gut microbiota can mediate colonization resistance against bacterial enteric infections and how bacterial enteropathogens can overcome this resistance as well as how the understanding of this complex interaction can inform future therapies against infectious diseases.
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Affiliation(s)
- Israr Khan
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Yanrui Bai
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Lajia Zha
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Naeem Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
| | - Habib Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Syed Rafiq Hussain Shah
- Department of Microecology, School of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hui Sun
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Chunjiang Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China
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Mutai WC, Mureithi M, Anzala O, Kullin B, Ofwete R, Kyany' A C, Odoyo E, Musila L, Revathi G. Assessment of independent comorbidities and comorbidity measures in predicting healthcare facility-onset Clostridioides difficile infection in Kenya. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000090. [PMID: 36962261 PMCID: PMC10022263 DOI: 10.1371/journal.pgph.0000090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Clostridioides difficile is primarily associated with hospital-acquired diarrhoea. The disease burden is aggravated in patients with comorbidities due to increased likelihood of polypharmacy, extended hospital stays and compromised immunity. The study aimed to investigate comorbidity predictors of healthcare facility-onset C. difficile infection (HO-CDI) in hospitalized patients. METHODOLOGY We performed a cross sectional study of 333 patients who developed diarrhoea during hospitalization. The patients were tested for CDI. Data on demographics, admission information, medication exposure and comorbidities were collected. The comorbidities were also categorised according to Charlson Comorbidity Index (CCI) and Elixhauser Comorbidity Index (ECI). Comorbidity predictors of HO-CDI were identified using multiple logistic regression analysis. RESULTS Overall, 230/333 (69%) patients had comorbidities, with the highest proportion being in patients aged over 60 years. Among the patients diagnosed with HO-CDI, 63/71(88.7%) reported comorbidities. Pairwise comparison between HO-CDI patients and comparison group revealed significant differences in hypertension, anemia, tuberculosis, diabetes, chronic kidney disease and chronic obstructive pulmonary disease. In the multiple logistic regression model significant predictors were chronic obstructive pulmonary disease (odds ratio [OR], 9.51; 95% confidence interval [CI], 1.8-50.1), diabetes (OR, 3.56; 95% CI, 1.11-11.38), chronic kidney disease (OR, 3.88; 95% CI, 1.57-9.62), anemia (OR, 3.67; 95% CI, 1.61-8.34) and hypertension (OR, 2.47; 95% CI, 1.-6.07). Among the comorbidity scores, CCI score of 2 (OR 6.67; 95% CI, 2.07-21.48), and ECI scores of 1 (OR, 4.07; 95% CI, 1.72-9.65), 2 (OR 2.86; 95% CI, 1.03-7.89), and ≥ 3 (OR, 4.87; 95% CI, 1.40-16.92) were significantly associated with higher odds of developing HO-CDI. CONCLUSION Chronic obstructive pulmonary disease, chronic kidney disease, anemia, diabetes, and hypertension were associated with an increased risk of developing HO-CDI. Besides, ECI proved to be a better predictor for HO-CDI. Therefore, it is imperative that hospitals should capitalize on targeted preventive approaches in patients with these underlying conditions to reduce the risk of developing HO-CDI and limit potential exposure to other patients.
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Affiliation(s)
- Winnie C Mutai
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Marianne Mureithi
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Brian Kullin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Robert Ofwete
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Cecilia Kyany' A
- US Army Medical Research Directorate-Africa, Kenya, Nairobi, Kenya
| | - Erick Odoyo
- US Army Medical Research Directorate-Africa, Kenya, Nairobi, Kenya
| | - Lillian Musila
- US Army Medical Research Directorate-Africa, Kenya, Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Division of Medical Microbiology, Aga Khan University Hospital, Nairobi, Kenya
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Antimicrobial Properties of Chitosan and Chitosan Derivatives in the Treatment of Enteric Infections. Molecules 2021; 26:molecules26237136. [PMID: 34885715 PMCID: PMC8659174 DOI: 10.3390/molecules26237136] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Antibiotics played an important role in controlling the development of enteric infection. However, the emergence of antibiotic resistance and gut dysbiosis led to a growing interest in the use of natural antimicrobial agents as alternatives for therapy and disinfection. Chitosan is a nontoxic natural antimicrobial polymer and is approved by GRAS (Generally Recognized as Safe by the United States Food and Drug Administration). Chitosan and chitosan derivatives can kill microbes by neutralizing negative charges on the microbial surface. Besides, chemical modifications give chitosan derivatives better water solubility and antimicrobial property. This review gives an overview of the preparation of chitosan, its derivatives, and the conjugates with other polymers and nanoparticles with better antimicrobial properties, explains the direct and indirect mechanisms of action of chitosan, and summarizes current treatment for enteric infections as well as the role of chitosan and chitosan derivatives in the antimicrobial agents in enteric infections. Finally, we suggested future directions for further research to improve the treatment of enteric infections and to develop more useful chitosan derivatives and conjugates.
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Monaghan TM, Duggal NA, Rosati E, Griffin R, Hughes J, Roach B, Yang DY, Wang C, Wong K, Saxinger L, Pučić-Baković M, Vučković F, Klicek F, Lauc G, Tighe P, Mullish BH, Blanco JM, McDonald JAK, Marchesi JR, Xue N, Dottorini T, Acharjee A, Franke A, Li Y, Wong GKS, Polytarchou C, Yau TO, Christodoulou N, Hatziapostolou M, Wang M, Russell LA, Kao DH. A Multi-Factorial Observational Study on Sequential Fecal Microbiota Transplant in Patients with Medically Refractory Clostridioides difficile Infection. Cells 2021; 10:cells10113234. [PMID: 34831456 PMCID: PMC8624539 DOI: 10.3390/cells10113234] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is highly effective in recurrent Clostridioides difficile infection (CDI); increasing evidence supports FMT in severe or fulminant Clostridioides difficile infection (SFCDI). However, the multifactorial mechanisms that underpin the efficacy of FMT are not fully understood. Systems biology approaches using high-throughput technologies may help with mechanistic dissection of host-microbial interactions. Here, we have undertaken a deep phenomics study on four adults receiving sequential FMT for SFCDI, in which we performed a longitudinal, integrative analysis of multiple host factors and intestinal microbiome changes. Stool samples were profiled for changes in gut microbiota and metabolites and blood samples for alterations in targeted epigenomic, metabonomic, glycomic, immune proteomic, immunophenotyping, immune functional assays, and T-cell receptor (TCR) repertoires, respectively. We characterised temporal trajectories in gut microbial and host immunometabolic data sets in three responders and one non-responder to sequential FMT. A total of 562 features were used for analysis, of which 78 features were identified, which differed between the responders and the non-responder. The observed dynamic phenotypic changes may potentially suggest immunosenescent signals in the non-responder and may help to underpin the mechanisms accompanying successful FMT, although our study is limited by a small sample size and significant heterogeneity in patient baseline characteristics. Our multi-omics integrative longitudinal analytical approach extends the knowledge regarding mechanisms of efficacy of FMT and highlights preliminary novel signatures, which should be validated in larger studies.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham NG7 2UH, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK;
- Correspondence: (T.M.M.); (M.W.); (L.A.R.); (D.H.K.); Tel.: +115-8231090 (T.M.M.)
| | - Niharika A. Duggal
- MRC-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK;
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Christian-Albrecht University of Kiel, 24105 Kiel, Germany; (E.R.); (A.F.)
| | - Ruth Griffin
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK;
- Synthetic Biology Research Centre, The University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Jamie Hughes
- Synthetic Biology Research Centre, The University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Brandi Roach
- Division of Gastroenterology, Department of Medicine, University of Alberta; Edmonton, Alberta, AB T6G 2G3, Canada; (B.R.); (D.Y.Y.); (C.W.); (K.W.)
| | - David Y. Yang
- Division of Gastroenterology, Department of Medicine, University of Alberta; Edmonton, Alberta, AB T6G 2G3, Canada; (B.R.); (D.Y.Y.); (C.W.); (K.W.)
| | - Christopher Wang
- Division of Gastroenterology, Department of Medicine, University of Alberta; Edmonton, Alberta, AB T6G 2G3, Canada; (B.R.); (D.Y.Y.); (C.W.); (K.W.)
| | - Karen Wong
- Division of Gastroenterology, Department of Medicine, University of Alberta; Edmonton, Alberta, AB T6G 2G3, Canada; (B.R.); (D.Y.Y.); (C.W.); (K.W.)
| | - Lynora Saxinger
- Division of Infectious Diseases, Department of Medicine, University of Alberta; Edmonton, Alberta, AB T6G 2G3, Canada;
| | - Maja Pučić-Baković
- Glycoscience Research Laboratory, Genos Ltd., Borongajska cesta 83H, 10000 Zagreb, Croatia; (M.P.-B.); (F.V.); (F.K.); (G.L.)
| | - Frano Vučković
- Glycoscience Research Laboratory, Genos Ltd., Borongajska cesta 83H, 10000 Zagreb, Croatia; (M.P.-B.); (F.V.); (F.K.); (G.L.)
| | - Filip Klicek
- Glycoscience Research Laboratory, Genos Ltd., Borongajska cesta 83H, 10000 Zagreb, Croatia; (M.P.-B.); (F.V.); (F.K.); (G.L.)
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd., Borongajska cesta 83H, 10000 Zagreb, Croatia; (M.P.-B.); (F.V.); (F.K.); (G.L.)
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Paddy Tighe
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Benjamin H. Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (B.H.M.); (J.M.B.); (J.A.K.M.); (J.R.M.)
| | - Jesus Miguens Blanco
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (B.H.M.); (J.M.B.); (J.A.K.M.); (J.R.M.)
| | - Julie A. K. McDonald
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (B.H.M.); (J.M.B.); (J.A.K.M.); (J.R.M.)
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julian R. Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (B.H.M.); (J.M.B.); (J.A.K.M.); (J.R.M.)
| | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2UH, UK; (N.X.); (T.D.)
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2UH, UK; (N.X.); (T.D.)
| | - Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK;
| | - Andre Franke
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Christian-Albrecht University of Kiel, 24105 Kiel, Germany; (E.R.); (A.F.)
| | - Yingrui Li
- Shenzhen Digital Life Institute, Shenzhen 518016, China;
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Christos Polytarchou
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK; (C.P.); (T.O.Y.); (N.C.); (M.H.)
| | - Tung On Yau
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK; (C.P.); (T.O.Y.); (N.C.); (M.H.)
| | - Niki Christodoulou
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK; (C.P.); (T.O.Y.); (N.C.); (M.H.)
| | - Maria Hatziapostolou
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Health Aging and Understanding Disease, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK; (C.P.); (T.O.Y.); (N.C.); (M.H.)
| | - Minkun Wang
- Shenzhen Digital Life Institute, Shenzhen 518016, China;
- Innovation Lab, Innovent Biologics, Inc., Suzhou 215011, China
- Correspondence: (T.M.M.); (M.W.); (L.A.R.); (D.H.K.); Tel.: +115-8231090 (T.M.M.)
| | - Lindsey A. Russell
- Division of Gastroenterology, Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Correspondence: (T.M.M.); (M.W.); (L.A.R.); (D.H.K.); Tel.: +115-8231090 (T.M.M.)
| | - Dina H. Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta; Edmonton, Alberta, AB T6G 2G3, Canada; (B.R.); (D.Y.Y.); (C.W.); (K.W.)
- Correspondence: (T.M.M.); (M.W.); (L.A.R.); (D.H.K.); Tel.: +115-8231090 (T.M.M.)
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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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Monaghan TM, Seekatz AM, Mullish BH, Moore-Gillon CCER, Dawson LF, Ahmed A, Kao D, Chan WC. Clostridioides difficile: innovations in target discovery and potential for therapeutic success. Expert Opin Ther Targets 2021; 25:949-963. [PMID: 34793686 DOI: 10.1080/14728222.2021.2008907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Clostridioides difficile infection (CDI) remains a worldwide clinical problem. Increased incidence of primary infection, occurrence of hypertoxigenic ribotypes, and more frequent occurrence of drug resistant, recurrent, and non-hospital CDI, emphasizes the urgent unmet need of discovering new therapeutic targets. AREAS COVERED We searched PubMed and Web of Science databases for articles identifying novel therapeutic targets or treatments for C. difficile from 2001 to 2021. We present an updated review on current preclinical efforts on designing inhibitory compounds against these drug targets and indicate how these could become the focus of future therapeutic approaches. We also evaluate the increasing exploitability of gut microbial-derived metabolites and host-derived therapeutics targeting VEGF-A, immune targets and pathways, ion transporters, and microRNAs as anti-C. difficile therapeutics, which have yet to reach clinical trials. Our review also highlights the therapeutic potential of re-purposing currently available agents . We conclude by considering translational hurdles and possible strategies to mitigate these problems. EXPERT OPINION Considerable progress has been made in the development of new anti-CDI drug candidates. Nevertheless, a greater comprehension of CDI pathogenesis and host-microbe interactions is beginning to uncover potential novel therapeutic targets, which can be exploited to plug gaps in the CDI drug discovery pipeline.
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Affiliation(s)
- Tanya M Monaghan
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Anna M Seekatz
- Biological Sciences, Clemson University, Clemson, SC, USA
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Claudia C E R Moore-Gillon
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ammar Ahmed
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Dina Kao
- Department of Gastroenterology, Zeidler Ledcor Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Weng C Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, UK
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74
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Aguirre AM, Yalcinkaya N, Wu Q, Swennes A, Tessier ME, Roberts P, Miyajima F, Savidge T, Sorg JA. Bile acid-independent protection against Clostridioides difficile infection. PLoS Pathog 2021; 17:e1010015. [PMID: 34665847 PMCID: PMC8555850 DOI: 10.1371/journal.ppat.1010015] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/29/2021] [Accepted: 10/07/2021] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile infections occur upon ecological / metabolic disruptions to the normal colonic microbiota, commonly due to broad-spectrum antibiotic use. Metabolism of bile acids through a 7α-dehydroxylation pathway found in select members of the healthy microbiota is regarded to be the protective mechanism by which C. difficile is excluded. These 7α-dehydroxylated secondary bile acids are highly toxic to C. difficile vegetative growth, and antibiotic treatment abolishes the bacteria that perform this metabolism. However, the data that supports the hypothesis that secondary bile acids protect against C. difficile infection is supported only by in vitro data and correlative studies. Here we show that bacteria that 7α-dehydroxylate primary bile acids protect against C. difficile infection in a bile acid-independent manner. We monoassociated germ-free, wildtype or Cyp8b1-/- (cholic acid-deficient) mutant mice and infected them with C. difficile spores. We show that 7α-dehydroxylation (i.e., secondary bile acid generation) is dispensable for protection against C. difficile infection and provide evidence that Stickland metabolism by these organisms consumes nutrients essential for C. difficile growth. Our findings indicate secondary bile acid production by the microbiome is a useful biomarker for a C. difficile-resistant environment but the microbiome protects against C. difficile infection in bile acid-independent mechanisms. Secondary bile acid production by the colonic microbiome strongly correlates with an environment that is resistant to C. difficile invasion. However, it remained unclear if these bile acids provided in vivo protection. Here, we show that members of the microbiome that generate secondary bile acids (e.g., C. scindens) protect against C. difficile disease independently of secondary bile acid generation. These results are important because efforts to restore colonization resistance (e.g., FMT or precision bacterial therapy) focus on restoring secondary bile acid generation. Instead, restoring the organisms that produce 5-aminovalerate or consume proline / glycine are more important.
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Affiliation(s)
- Andrea Martinez Aguirre
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Nazli Yalcinkaya
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Qinglong Wu
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Alton Swennes
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Mary Elizabeth Tessier
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Paul Roberts
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, United Kingdom
| | - Fabio Miyajima
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, United Kingdom
- Oswaldo Cruz Foundation, Ceara branch, Fortaleza, Brazil
| | - Tor Savidge
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Sánchez-Pellicer P, Navarro-López V, González-Tamayo R, Llopis-Ruiz C, Núñez-Delegido E, Ruzafa-Costas B, Navarro-Moratalla L, Agüera-Santos J. Descriptive Study of Gut Microbiota in Infected and Colonized Subjects by Clostridiodes difficile. Microorganisms 2021; 9:microorganisms9081727. [PMID: 34442805 PMCID: PMC8401824 DOI: 10.3390/microorganisms9081727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Clostridiodes difficile can lead to a range of situations from the absence of symptoms (colonization) to severe diarrhea (infection). Disruption of gut microbiota provides an ideal environment for infection to occur. Comparison of gut microbiota of infected and colonized subjects could provide relevant information on susceptible groups or protectors to the development of infection, since the presence of certain genera could be related to the inhibition of transition from a state of colonization to infection. Through high-throughput sequencing of 16S rDNA gene, we performed alpha and beta diversity and composition studies on 15 infected patients (Group CDI), 15 colonized subjects (Group P), and 15 healthy controls (Group CTLR). A loss of alpha diversity and richness and a different structure have been evidenced in the CDI and P groups with respect to the CTRL group, but without significant differences between the first two. In CDI and P groups, there was a strong decrease in phylum Firmicutes and an expansion of potential pathogens. Likewise, there was a loss of inhibitory genus of C. difficile germination in infected patients that were partially conserved in colonized subjects. Therefore, infected and colonized subjects presented a gut microbiota that was completely different from that of healthy controls, although similar to each other. It is in composition where we found that colonized subjects, especially in minority genera, presented differences with respect to those infected.
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Affiliation(s)
- Pedro Sánchez-Pellicer
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
- Correspondence: (P.S.-P.); (V.N.-L.)
| | - Vicente Navarro-López
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
- Infectious Diseases Unit, University Hospital of Vinalopó, Carrer Tonico Sansano Mora, 14, 03293 Elche, Spain
- Correspondence: (P.S.-P.); (V.N.-L.)
| | - Ruth González-Tamayo
- Biochemistry Laboratory, Vega Baja Hospital, Carretera Orihuela-Almoradí s/n, 03314 San Bartolomé, Spain;
| | - Coral Llopis-Ruiz
- Microbiology Laboratory, University Hospital of Vinalopó, Carrer Tonico Sansano Mora, 14, 03293 Elche, Spain;
| | - Eva Núñez-Delegido
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Beatriz Ruzafa-Costas
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Laura Navarro-Moratalla
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Juan Agüera-Santos
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
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76
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Listening in on the conversation between the human gut microbiome and its host. Curr Opin Microbiol 2021; 63:150-157. [PMID: 34352595 DOI: 10.1016/j.mib.2021.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host's mechanisms to sense and respond to the microbial ecosystem for its own benefit. We can listen in on the host-microbiome 'conversation' in the simultaneous responses of the microbiome and the host to strong perturbations. In laboratory animals a perturbation can be done for research; in human patients a perturbation can be caused by disease or therapy. Advances in metagenomics, metabolomics and computation amplify our means to listen in on the conversation between the gut microbiome and its host.
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Secondary (iso)BAs cooperate with endogenous ligands to activate FXR under physiological and pathological conditions. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166153. [PMID: 33895309 PMCID: PMC8177068 DOI: 10.1016/j.bbadis.2021.166153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 12/30/2022]
Abstract
IsoBAs, stereoisomers of primary and secondary BAs, are found in feces and plasma of human individuals. BA signaling via the nuclear receptor FXR is crucial for regulation of hepatic and intestinal physiology/pathophysiology. AIM Investigate the ability of BA-stereoisomers to bind and modulate FXR under physiological/pathological conditions. METHODS Expression-profiling, luciferase-assays, fluorescence-based coactivator-association assays, administration of (iso)-BAs to WT and cholestatic mice. RESULTS Compared to CDCA/isoCDCA, administration of DCA/isoDCA, UDCA/isoUDCA only slightly increased mRNA expression of FXR target genes; the induction was more evident looking at pre-mRNAs. Notably, almost 50% of isoBAs were metabolized to 3-oxo-BAs within 4 h in cell-based assays, making it difficult to study their actions. FRET-based real-time monitoring of FXR activity revealed that isoCDCA>CDCA stimulated FXR, and isoDCA and isoUDCA allowed fully activated FXR to be re-stimulated by a second dose of GW4064. In vivo co-administration of a single dose of isoBAs followed by GW4064 cooperatively activated FXR, as did feeding of UDCA in a background of endogenous FXR ligands. However, in animals with biliary obstruction and concomitant loss of intestinal BAs, UDCA was unable to increase intestinal Fgf15. In contrast, mice with an impaired enterohepatic circulation of BAs (Asbt-/-, Ostα-/-), administration of UDCA was still able to induce ileal Fgf15 and repress hepatic BA-synthesis, arguing that UDCA is only effective in the presence of endogenous FXR ligands. CONCLUSION Secondary (iso)BAs cooperatively activate FXR in the presence of endogenous BAs, which is important to consider in diseases linked to disturbances in BA enterohepatic cycling.
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78
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Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature 2021; 599:458-464. [PMID: 34325466 DOI: 10.1038/s41586-021-03832-5] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/16/2021] [Indexed: 11/09/2022]
Abstract
Centenarians have a decreased susceptibility to ageing-associated illnesses, chronic inflammation and infectious diseases1-3. Here we show that centenarians have a distinct gut microbiome that is enriched in microorganisms that are capable of generating unique secondary bile acids, including various isoforms of lithocholic acid (LCA): iso-, 3-oxo-, allo-, 3-oxoallo- and isoallolithocholic acid. Among these bile acids, the biosynthetic pathway for isoalloLCA had not been described previously. By screening 68 bacterial isolates from the faecal microbiota of a centenarian, we identified Odoribacteraceae strains as effective producers of isoalloLCA both in vitro and in vivo. Furthermore, we found that the enzymes 5α-reductase (5AR) and 3β-hydroxysteroid dehydrogenase (3β-HSDH) were responsible for the production of isoalloLCA. IsoalloLCA exerted potent antimicrobial effects against Gram-positive (but not Gram-negative) multidrug-resistant pathogens, including Clostridioides difficile and Enterococcus faecium. These findings suggest that the metabolism of specific bile acids may be involved in reducing the risk of infection with pathobionts, thereby potentially contributing to the maintenance of intestinal homeostasis.
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Shen A. Clostridioides difficile Spore Formation and Germination: New Insights and Opportunities for Intervention. Annu Rev Microbiol 2021; 74:545-566. [PMID: 32905755 DOI: 10.1146/annurev-micro-011320-011321] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spore formation and germination are essential for the bacterial pathogen Clostridioides difficile to transmit infection. Despite the importance of these developmental processes to the infection cycle of C. difficile, the molecular mechanisms underlying how this obligate anaerobe forms infectious spores and how these spores germinate to initiate infection were largely unknown until recently. Work in the last decade has revealed that C. difficile uses a distinct mechanism for sensing and transducing germinant signals relative to previously characterized spore formers. The C. difficile spore assembly pathway also exhibits notable differences relative to Bacillus spp., where spore formation has been more extensively studied. For both these processes, factors that are conserved only in C. difficile or the related Peptostreptococcaceae family are employed, and even highly conserved spore proteins can have differential functions or requirements in C. difficile compared to other spore formers. This review summarizes our current understanding of the mechanisms controlling C. difficile spore formation and germination and describes strategies for inhibiting these processes to prevent C. difficile infection and disease recurrence.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA;
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80
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Li Y, Honda K. Towards the development of defined microbial therapeutics. Int Immunol 2021; 33:761-766. [PMID: 34232990 DOI: 10.1093/intimm/dxab038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
The collection of microorganisms living in the mammalian gastrointestinal tract, termed the gut microbiota, has been shown to have profound impacts on host health and increasingly is regarded as a viable therapeutic target. Clinical studies of fecal microbiota transplantation (FMT) have demonstrated potential efficacy of microbiota-based therapies for diseases including Clostridioides difficile infections, inflammatory bowel disease, graft-versus-host disease and cancer. However, the lack of understanding of the active ingredients and potential risks of such therapies pose challenges for clinical application. Meanwhile, efforts are being made to identify effector microbes directly associated with a given phenotype, to establish causality and to devise well-characterized microbial therapeutics for clinical use. Strategies based on defined microbial components will likely enhance the potential of microbiota-targeted therapies.
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Affiliation(s)
- Youxian Li
- RIKEN Center for Integrative Medical Sciences, Suehirocho, Tsurumi, Yokohama, Kanagawa, Japan
| | - Kenya Honda
- RIKEN Center for Integrative Medical Sciences, Suehirocho, Tsurumi, Yokohama, Kanagawa, Japan.,Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
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81
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Mullish BH, Allegretti JR. The contribution of bile acid metabolism to the pathogenesis of Clostridioides difficile infection. Therap Adv Gastroenterol 2021; 14:17562848211017725. [PMID: 34104212 PMCID: PMC8165815 DOI: 10.1177/17562848211017725] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 04/26/2021] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile infection (CDI) remains a major global cause of gastrointestinal infection, with significant associated morbidity, mortality and impact upon healthcare system resources. Recent antibiotic use is a key risk factor for the condition, with the marked antibiotic-mediated perturbations in gut microbiome diversity and composition that underpin the pathogenesis of CDI being well-recognised. However, only relatively recently has further insight been gained into the specific mechanistic links between these gut microbiome changes and CDI, with alteration of gut microbial metabolites - in particular, bile acid metabolism - being a particular area of focus. A variety of in vitro, ex vivo, animal model and human studies have now demonstrated that loss of gut microbiome members with bile-metabolising capacity (including bile salt hydrolases, and 7-α-dehydroxylase) - with a resulting alteration of the gut bile acid milieu - contributes significantly to the disease process in CDI. More specifically, this microbiome disruption results in the enrichment of primary conjugated bile acids (including taurocholic acid, which promotes the germination of C. difficile spores) and loss of secondary bile acids (which inhibit the growth of C. difficile, and may bind to and limit activity of toxins produced by C. difficile). These bile acid changes are also associated with reduced activity of the farnesoid X receptor pathway, which may exacerbate C. difficile colitis throughout its impact upon gut barrier function and host immune/inflammatory response. Furthermore, a key mechanism of efficacy of faecal microbiota transplant (FMT) in treating recurrent CDI has been shown to be restoration of gut microbiome bile metabolising functionality; ensuring the presence of this functionality among defined microbial communities (and other 'next generation' FMT products) designed to treat CDI may be critical to their success.
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Affiliation(s)
- Benjamin H. Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jessica R. Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, 850 Boylston Street, Suite 201, Chestnut Hill, MA 02467, USA
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA
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Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes. mSphere 2021; 6:6/3/e01238-20. [PMID: 33952668 PMCID: PMC8103992 DOI: 10.1128/msphere.01238-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing Clostridioides difficile colonization across different community perturbations. However, those bacteria alone have been unable to clear C. difficile colonization. To elucidate the changes necessary to clear colonization, we compared differences in bacterial abundance between communities able and unable to clear C. difficile colonization. We treated mice with titrated doses of antibiotics prior to C. difficile challenge, resulting in no colonization, colonization and clearance, or persistent colonization. Previously, we observed that clindamycin-treated mice were susceptible to colonization but spontaneously cleared C. difficile. Therefore, we investigated whether other antibiotics would show the same result. We found that reduced doses of cefoperazone and streptomycin permitted colonization and clearance of C. difficile. Mice that cleared colonization had antibiotic-specific community changes and predicted interactions with C. difficile. Clindamycin treatment led to a bloom in populations related to Enterobacteriaceae. Clearance of C. difficile was concurrent with the reduction of those blooming populations and the restoration of community members related to the Porphyromonadaceae and Bacteroides. Cefoperazone created a susceptible community characterized by drastic reductions in the community diversity and interactions and a sustained increase in the abundance of many facultative anaerobes. Lastly, clearance in streptomycin-treated mice was associated with the recovery of multiple members of the Porphyromonadaceae, with little overlap in the specific Porphyromonadaceae observed in the clindamycin treatment. Further elucidation of how C. difficile colonization is cleared from different gut bacterial communities will improve C. difficile infection treatments. IMPORTANCE The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The recurrent infection cycle often ends when the fecal microbiota from a presumed resistant person is transplanted into the susceptible person. Although this treatment is highly effective, we do not understand the mechanism. We hope to improve the treatment of CDI through elucidating how the bacterial community eliminates CDI. We found that C. difficile colonized susceptible mice but was spontaneously eliminated in an antibiotic treatment-specific manner. These data indicate that each community had different requirements for clearing colonization. Understanding how different communities clear colonization will reveal targets to improve CDI treatments.
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Grier JT, Arivett BA, Ramírez MS, Chosed RJ, Bigner JA, Ohneck EJ, Metz ML, Wood CR, Arce S, Tartaro A, Relich RF, Actis LA, Fiester SE. Two Acinetobacter baumannii Isolates Obtained From a Fatal Necrotizing Fasciitis Infection Display Distinct Genomic and Phenotypic Characteristics in Comparison to Type Strains. Front Cell Infect Microbiol 2021; 11:635673. [PMID: 33912474 PMCID: PMC8072282 DOI: 10.3389/fcimb.2021.635673] [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: 11/30/2020] [Accepted: 03/11/2021] [Indexed: 11/23/2022] Open
Abstract
Acinetobacter baumannii has been recognized as a critical pathogen that causes severe infections worldwide not only because of the emergence of extensively drug-resistant (XDR) derivatives, but also because of its ability to persist in medical environments and colonize compromised patients. While there are numerous reports describing the mechanisms by which this pathogen acquires resistance genes, little is known regarding A. baumannii’s virulence functions associated with rare manifestations of infection such as necrotizing fasciitis, making the determination and implementation of alternative therapeutic targets problematic. To address this knowledge gap, this report describes the analysis of the NFAb-1 and NFAb-2 XDR isolates, which were obtained at two time points during a fatal case of necrotizing fasciitis, at the genomic and functional levels. The comparative genomic analysis of these isolates with the ATCC 19606T and ATCC 17978 strains showed that the NFAb-1 and NFAb-2 isolates are genetically different from each other as well as different from the ATCC 19606T and ATCC 17978 clinical isolates. These genomic differences could be reflected in phenotypic differences observed in these NFAb isolates. Biofilm, cell viability and flow cytometry assays indicate that all tested strains caused significant decreases in A549 human alveolar epithelial cell viability with ATCC 17978, NFAb-1 and NFAb-2 producing significantly less biofilm and significantly more hemolysis and capacity for intracellular invasion than ATCC 19606T. NFAb-1 and NFAb-2 also demonstrated negligible surface motility but significant twitching motility compared to ATCC 19606T and ATCC 17978, likely due to the presence of pili exceeding 2 µm in length, which are significantly longer and different from those previously described in the ATCC 19606T and ATCC 17978 strains. Interestingly, infection with cells of the NFAb-1 isolate, which were obtained from a premortem blood sample, lead to significantly higher mortality rates than NFAb-2 bacteria, which were obtained from postmortem tissue samples, when tested using the Galleria mellonella in vivo infection model. These observations suggest potential changes in the virulence phenotype of the A. baumannii necrotizing fasciitis isolates over the course of infection by mechanisms and cell processes that remain to be identified.
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Affiliation(s)
- Jennifer T Grier
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States
| | - Brock A Arivett
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Maria S Ramírez
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
| | - Renee J Chosed
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States
| | - Jessica A Bigner
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States
| | - Emily J Ohneck
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Maeva L Metz
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Cecily R Wood
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Sergio Arce
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States.,Cancer Institute, Prisma Health, Greenville, SC, United States
| | - Andrea Tartaro
- Computer Science Department, Furman University, Greenville, SC, United States
| | - Ryan F Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Luis A Actis
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Steven E Fiester
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States.,Department of Pathology, Prisma Health, Greenville, SC, United States
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84
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Leslie JL, Jenior ML, Vendrov KC, Standke AK, Barron MR, O'Brien TJ, Unverdorben L, Thaprawat P, Bergin IL, Schloss PD, Young VB. Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant. mBio 2021; 12:e00522-21. [PMID: 33785619 PMCID: PMC8092246 DOI: 10.1128/mbio.00522-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile, a Gram-positive, spore-forming bacterium, is the primary cause of infectious nosocomial diarrhea. Antibiotics are a major risk factor for C. difficile infection (CDI), as they disrupt the gut microbial community, enabling increased germination of spores and growth of vegetative C. difficile To date, the only single-species bacterial preparation that has demonstrated efficacy in reducing recurrent CDI in humans is nontoxigenic C. difficile Using multiple infection models, we determined that precolonization with a less virulent strain is sufficient to protect from challenge with a lethal strain of C. difficile, surprisingly even in the absence of adaptive immunity. Additionally, we showed that protection is dependent on high levels of colonization by the less virulent strain and that it is mediated by exclusion of the invading strain. Our results suggest that reduction of amino acids, specifically glycine following colonization by the first strain of C. difficile, is sufficient to decrease germination of the second strain, thereby limiting colonization by the lethal strain.IMPORTANCE Antibiotic-associated colitis is often caused by infection with the bacterium Clostridioides difficile In this study, we found that reduction of the amino acid glycine by precolonization with a less virulent strain of C. difficile is sufficient to decrease germination of a second strain. This finding demonstrates that the axis of competition for nutrients can include multiple life stages. This work is important, as it is the first to identify a possible mechanism through which precolonization with C. difficile, a current clinical therapy, provides protection from reinfection. Furthermore, our work suggests that targeting nutrients utilized by all life stages could be an improved strategy for bacterial therapeutics that aim to restore colonization resistance in the gut.
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Affiliation(s)
- Jhansi L Leslie
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Matthew L Jenior
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kimberly C Vendrov
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexandra K Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Madeline R Barron
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tricia J O'Brien
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lavinia Unverdorben
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Pariyamon Thaprawat
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid L Bergin
- The Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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85
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Dissecting Individual Interactions between Pathogenic and Commensal Bacteria within a Multispecies Gut Microbial Community. mSphere 2021; 6:6/2/e00013-21. [PMID: 33762315 PMCID: PMC8546675 DOI: 10.1128/msphere.00013-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro models to monitor community responses to pathogens at a single-species level. We have developed a multispecies community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a quantitative PCR (qPCR)-based approach. Introduction of the major nosocomial gut pathogen, Clostridioides difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp. in prevention of C. difficile colonization. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community. IMPORTANCE Studying interactions between bacterial species that reside in the human gut is crucial for gaining a better insight into how they provide protection from pathogen colonization. In vitro models of multispecies bacterial communities wherein behaviors of single species can be accurately tracked are key to such studies. Here, we have developed a synthetic, trackable, gut microbiota community which reduces growth of the human gut pathogen Clostridioides difficile. We report that Bacteroides spp. within this community respond by multiplying in the presence of this pathogen, resulting in reduction of C. difficile growth. Defined in vitro communities that can be tailored to include different species are well suited to functional genomic approaches and are valuable tools for understanding interbacterial interactions.
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86
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Jose S, Mukherjee A, Horrigan O, Setchell KDR, Zhang W, Moreno-Fernandez ME, Andersen H, Sharma D, Haslam DB, Divanovic S, Madan R. Obeticholic acid ameliorates severity of Clostridioides difficile infection in high fat diet-induced obese mice. Mucosal Immunol 2021; 14:500-510. [PMID: 32811993 PMCID: PMC7889747 DOI: 10.1038/s41385-020-00338-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Severe Clostridiodes difficile infection (CDI) is life-threatening and responds poorly to treatment. Obesity is associated with development of severe CDI. Therefore, to define the mechanisms that exacerbate disease severity, we examined CDI pathogenesis in high-fat diet (HFD)-fed obese mice. Compared to control mice, HFD-fed mice failed to clear C. difficile bacteria which resulted in protracted diarrhea, weight loss and colonic damage. After infection, HFD-induced obese mice had an intestinal bile acid (BA) pool that was dominated by primary BAs which are known promoters of C. difficile spore germination, and lacked secondary BAs that inhibit C. difficile growth. Concurrently, synthesis of primary BAs from liver was significantly increased in C. difficile-infected HFD-fed mice. A key pathway that regulates hepatic BA synthesis is via feedback inhibition from intestinal Farnesoid X receptors (FXRs). Our data reveal that the proportion of FXR agonist BAs to FXR antagonist BAs in the intestinal lumen was significantly reduced in HFD-fed mice after CDI. Treatment of HFD-fed mice with an FXR agonist Obeticholic acid, resulted in decreased primary BA synthesis, fewer C. difficile bacteria and better CDI outcomes. Thus, OCA treatment holds promise as a therapy for severe CDI.
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Affiliation(s)
- Shinsmon Jose
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Anindita Mukherjee
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Olivia Horrigan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Kenneth D R Setchell
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Wujuan Zhang
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Maria E Moreno-Fernandez
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Heidi Andersen
- Department of Pediatric Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Divya Sharma
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - David B Haslam
- Department of Pediatric Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Senad Divanovic
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Rajat Madan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA.
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Veterans Affairs Medical Center, Cincinnati, OH, 45220, USA.
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87
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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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88
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Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium. Microorganisms 2021; 9:microorganisms9020371. [PMID: 33673352 PMCID: PMC7918557 DOI: 10.3390/microorganisms9020371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a key role in colonization resistance. They are able to modify bile acids which alter the C. difficile life cycle. Commensal Clostridium also produce other inhibitory metabolites including antimicrobials and short chain fatty acids. They also compete with C. difficile for vital nutrients such as proline. Understanding the mechanistic effects that these metabolites have on C. difficile and other gut pathogens is important for the development of new therapeutics against C. difficile infection (CDI), which are urgently needed.
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89
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Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection. Nat Commun 2021; 12:755. [PMID: 33531483 PMCID: PMC7854624 DOI: 10.1038/s41467-020-20793-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a successful therapeutic strategy for treating recurrent Clostridioides difficile infection. Despite remarkable efficacy, implementation of FMT therapy is limited and the mechanism of action remains poorly understood. Here, we demonstrate a critical role for the immune system in supporting FMT using a murine C. difficile infection system. Following FMT, Rag1 heterozygote mice resolve C. difficile while littermate Rag1-/- mice fail to clear the infection. Targeted ablation of adaptive immune cell subsets reveal a necessary role for CD4+ Foxp3+ T-regulatory cells, but not B cells or CD8+ T cells, in FMT-mediated resolution of C. difficile infection. FMT non-responsive mice exhibit exacerbated inflammation, impaired engraftment of the FMT bacterial community and failed restoration of commensal bacteria-derived secondary bile acid metabolites in the large intestine. These data demonstrate that the host's inflammatory immune status can limit the efficacy of microbiota-based therapeutics to treat C. difficile infection.
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90
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Henson MA. Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection. PLoS Comput Biol 2021; 17:e1008782. [PMID: 33617526 PMCID: PMC7932513 DOI: 10.1371/journal.pcbi.1008782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 03/04/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Approximately 30% of patients who have Clostridioides difficile infection (CDI) will suffer at least one incident of reinfection. While the underlying causes of CDI recurrence are poorly understood, interactions between C. difficile and commensal gut bacteria are thought to play an important role. In this study, an in silico pipeline was used to process 16S rRNA gene amplicon sequence data of 225 stool samples from 93 CDI patients into sample-specific models of bacterial community metabolism. Clustered metabolite production rates generated from post-diagnosis samples generated a high Enterobacteriaceae abundance cluster containing disproportionately large numbers of recurrent samples and patients. This cluster was predicted to have significantly reduced capabilities for secondary bile acid synthesis but elevated capabilities for aromatic amino acid catabolism. When applied to 16S sequence data of 40 samples from fecal microbiota transplantation (FMT) patients suffering from recurrent CDI and their stool donors, the community modeling method generated a high Enterobacteriaceae abundance cluster with a disproportionate large number of pre-FMT samples. This cluster also was predicted to exhibit reduced secondary bile acid synthesis and elevated aromatic amino acid catabolism. Collectively, these in silico predictions suggest that Enterobacteriaceae may create a gut environment favorable for C. difficile spore germination and/or toxin synthesis.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
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91
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Pike CM, Theriot CM. Mechanisms of Colonization Resistance Against Clostridioides difficile. J Infect Dis 2020; 223:S194-S200. [PMID: 33326565 DOI: 10.1093/infdis/jiaa408] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile is an urgent antimicrobial-resistant bacterium, causing mild to moderate and sometimes life-threatening disease. Commensal gut microbes are critical for providing colonization resistance against C difficile and can be leveraged as non-antibiotic alternative therapeutics for the prevention and treatment of C difficile infection.
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Affiliation(s)
- Colleen M Pike
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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92
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Thanissery R, McLaren MR, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM. Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota. Anaerobe 2020; 66:102279. [PMID: 33022384 PMCID: PMC10760528 DOI: 10.1016/j.anaerobe.2020.102279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/31/2020] [Accepted: 09/27/2020] [Indexed: 02/08/2023]
Abstract
The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.
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Affiliation(s)
- R Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - M R McLaren
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - A Rivera
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - A D Reed
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - N S Betrapally
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - T Burdette
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - J A Winston
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - M Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - B J Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - C M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
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93
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Maslanka JR, Gu CH, Zarin I, Denny JE, Broadaway S, Fett B, Mattei LM, Walk ST, Abt MC. Detection and elimination of a novel non-toxigenic Clostridioides difficile strain from the microbiota of a mouse colony. Gut Microbes 2020; 12:1-15. [PMID: 33305657 PMCID: PMC7734020 DOI: 10.1080/19490976.2020.1851999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Clostridioides difficile is an enteric bacterial pathogen that can a cause nosocomial infection leading to debilitating colitis. The development of a murine model of C. difficile infection has led to fundamental discoveries in disease pathogenesis and the host immune response to infection. Recently, C. difficile endogenously present in the microbiota of mice has been reported and was found to complicate interpretation of mouse studies. Here, we report a novel C. difficile strain, named NTCD-035, isolated from the microbiota of our mouse colony. The presence of NTCD-035 in mice prior to challenge with a highly pathogenic C. difficile strain (VPI10463) led to significantly reduced disease severity. Phylogenetic characterization derived from whole genome sequencing and PCR ribotyping identified the isolate as a novel clade 1, ribotype 035 strain that lacks the pathogenicity locus required to produce toxins. Deficiency in toxin production along with sporulation capacity and secondary bile acid sensitivity was confirmed using in vitro assays. Inoculation of germ-free mice with NTCD-035 did not cause morbidity despite the strain readily colonizing the large intestine. Implementation of a culture-based screening procedure enabled the identification of mice harboring C. difficile in their microbiota, the establishment of a C. difficile-free mouse colony, and a monitoring system to prevent future contamination. Taken together, these data provide a framework for screening mice for endogenously harbored C. difficile and support clinical findings that demonstrate the therapeutic potential of non-toxigenic strains in preventing C. difficile associated disease. Abbreviations: PaLoc - Pathogenicity locus, CFUs - Colony forming units, TcdA - toxin-A, TcdB - toxin-B, CdtA - binary toxin A, CdtB - binary toxin B, CdtR - binary toxin R, NTCD - non-toxigenic C. difficile.
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Affiliation(s)
- Jeffrey R. Maslanka
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher H. Gu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Isma Zarin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua E. Denny
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan Broadaway
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Bryton Fett
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Seth T. Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Michael C. Abt
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,CONTACT Michael C Abt Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Blake AB, Cigarroa A, Klein HL, Khattab MR, Keating T, Van De Coevering P, Lidbury JA, Steiner JM, Suchodolski JS. Developmental stages in microbiota, bile acids, and clostridial species in healthy puppies. J Vet Intern Med 2020; 34:2345-2356. [PMID: 33047396 PMCID: PMC7694855 DOI: 10.1111/jvim.15928] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Background The fecal microbiota, fecal bile acid concentrations, and abundance of Clostridium perfringens and Clostridium difficile are altered in acute and chronic gastrointestinal disease in adult dogs. However, less is known in young puppies. Hypothesis/Objectives To determine composition of the fecal microbiota, assess development of fecal bile acid profiles, and determine the abundance of Clostridial species in puppies, young adult dogs, and adult dogs. Animals Healthy puppies from a whelping kennel (n = 53) and healthy client‐owned dogs <1 year old (n = 20) were separated into 6 age groups, then compared to client‐owned dogs over 1 year of age (n = 13). Methods Prospective observational study. Naturally voided fecal samples were analyzed by quantitative polymerase chain reaction to measure bacterial abundances. Fecal bile acids were quantified using gas chromatography‐mass spectrometry. Results Puppies up to 5 to 6 weeks of age had increased Dysbiosis Index (median [min‐max]: 5.39 [1.32‐8.6], P < .001), increased abundance of C. difficile (4.1 [0.01‐4.85] log DNA, P < .001), decreased secondary bile acid concentrations (0.61 [0.28‐5.06] μg/mg, P = .006), and decreased abundance of C. hiranonis (0.84 [0.01‐6.71], P = .005) compared to adult dogs (−4.62 [−8.36 to −0.61], 0.01 [0.01‐0.01], 4.12 [0.32‐8.94], and 6.02 [5.06‐7.00], respectively). Secondary bile acid concentration positively correlated with C. hiranonis abundance (ρ = 0.77; P < .001). Conclusions and Clinical Importance The increase in secondary bile acids and simultaneous decrease of C. difficile and C. perfringens after 5 to 6 weeks of age warrants further investigation into regulatory impacts that secondary bile acids could have on clostridial species in dogs.
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Affiliation(s)
- Amanda B Blake
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
| | - Annalis Cigarroa
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
| | - Hannah L Klein
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
| | - Mohammad R Khattab
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
| | | | | | - Jonathan A Lidbury
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
| | - Jörg M Steiner
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
| | - Jan S Suchodolski
- Gastrointestinal Laboratory - Texas A&M University, College Station, Texas, USA
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95
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Orozco-Aguilar J, Alfaro-Alarcón A, Acuña-Amador L, Chaves-Olarte E, Rodríguez C, Quesada-Gómez C. In vivo animal models confirm an increased virulence potential and pathogenicity of the NAP1/RT027/ST01 genotype within the Clostridium difficile MLST Clade 2. Gut Pathog 2020; 12:45. [PMID: 32983262 PMCID: PMC7510272 DOI: 10.1186/s13099-020-00383-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023] Open
Abstract
Background Based on MLST analyses the global population of C. difficile is distributed in eight clades, of which Clade 2 includes the “hypervirulent” NAP1/RT027/ST01 strain along with various unexplored sequence types (STs). Methods To clarify whether this clinically relevant phenotype is a widespread feature of C. difficile Clade 2, we used the murine ileal loop model to compare the in vivo pro-inflammatory (TNF-α, IL-1β, IL-6) and oxidative stress activities (MPO) of five Clade 2 clinical C. difficile isolates from sequence types (STs) 01, 41, 67, and 252. Besides, we infected Golden Syrian hamsters with spores from these strains to determine their lethality, and obtain a histological evaluation of tissue damage, WBC counts, and serum injury biomarkers (LDH, ALT, AST, albumin, BUN, creatinine, Na+, and Cl−). Genomic distances were calculated using Mash and FastANI to explore whether the responses were dictated by phylogeny. Results The ST01 isolate tested ranked first in all assays, as it induced the highest overall levels of pro-inflammatory cytokines, MPO activity, epithelial damage, biochemical markers, and mortality measured in both animal models. Statistically indistinguishable or rather similar outputs were obtained for a ST67 isolate in tests such as tissue damage, neutrophils count, and lethal activity. The results recorded for the two ST41 isolates tested were of intermediate magnitude and the ST252 isolate displayed the lowest pathogenic potential in all animal experiments. This ordering matched the genomic distance of the ST01 isolate to the non-ST01 isolates. Conclusions Despite their close phylogenic relatedness, our results demonstrate differences in pathogenicity and virulence levels in Clade 2 C. difficile strains, confirm the high severity of infections caused by the NAP1/RT027/ST01 strain, and highlight the importance of C. difficile typing.
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Affiliation(s)
- Josué Orozco-Aguilar
- Laboratorio de Ensayos Biológicos (LEBi), Universidad de Costa Rica, San José, Costa Rica.,Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica.,Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica
| | - Alejandro Alfaro-Alarcón
- Departamento de Patología, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Luis Acuña-Amador
- Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Quesada-Gómez
- Laboratorio de Ensayos Biológicos (LEBi), Universidad de Costa Rica, San José, Costa Rica.,Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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96
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The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens. Infect Immun 2020; 88:IAI.00865-19. [PMID: 32661122 DOI: 10.1128/iai.00865-19] [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] [Indexed: 12/14/2022] Open
Abstract
Throughout the course of infection, many pathogens encounter bactericidal conditions that threaten the viability of the bacteria and impede the establishment of infection. Bile is one of the most innately bactericidal compounds present in humans, functioning to reduce the bacterial burden in the gastrointestinal tract while also aiding in digestion. It is becoming increasingly apparent that pathogens successfully resist the bactericidal conditions of bile, including bacteria that do not normally cause gastrointestinal infections. This review highlights the ability of Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter (ESKAPE), and other enteric pathogens to resist bile and how these interactions can impact the sensitivity of bacteria to various antimicrobial agents. Given that pathogen exposure to bile is an essential component to gastrointestinal transit that cannot be avoided, understanding how bile resistance mechanisms align with antimicrobial resistance is vital to our ability to develop new, successful therapeutics in an age of widespread and increasing antimicrobial resistance.
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97
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Kreuzer M, Hardt WD. How Food Affects Colonization Resistance Against Enteropathogenic Bacteria. Annu Rev Microbiol 2020; 74:787-813. [DOI: 10.1146/annurev-micro-020420-013457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.
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Affiliation(s)
- Markus Kreuzer
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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98
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Lawler AJ, Lambert PA, Worthington T. A Revised Understanding of Clostridioides difficile Spore Germination. Trends Microbiol 2020; 28:744-752. [DOI: 10.1016/j.tim.2020.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022]
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99
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Bushman FD, Conrad M, Ren Y, Zhao C, Gu C, Petucci C, Kim MS, Abbas A, Downes KJ, Devas N, Mattei LM, Breton J, Kelsen J, Marakos S, Galgano A, Kachelries K, Erlichman J, Hart JL, Moraskie M, Kim D, Zhang H, Hofstaedter CE, Wu GD, Lewis JD, Zackular JP, Li H, Bittinger K, Baldassano R. Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease. Cell Host Microbe 2020; 28:422-433.e7. [PMID: 32822584 DOI: 10.1016/j.chom.2020.07.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 06/09/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
Abstract
Children with inflammatory bowel diseases (IBD) are particularly vulnerable to infection with Clostridioides difficile (CDI). IBD and IBD + CDI have overlapping symptoms but respond to distinctive treatments, highlighting the need for diagnostic biomarkers. Here, we studied pediatric patients with IBD and IBD + CDI, comparing longitudinal data on the gut microbiome, metabolome, and other measures. The microbiome is dysbiotic and heterogeneous in both disease states, but the metabolome reveals disease-specific patterns. The IBD group shows increased concentrations of markers of inflammation and tissue damage compared with healthy controls, and metabolic changes associate with susceptibility to CDI. In IBD + CDI, we detect both metabolites associated with inflammation/tissue damage and fermentation products produced by C. difficile. The most discriminating metabolite found is isocaproyltaurine, a covalent conjugate of a distinctive C. difficile fermentation product (isocaproate) and an amino acid associated with tissue damage (taurine), which may be useful as a joint marker of the two disease processes.
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Affiliation(s)
- Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Maire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yue Ren
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher Gu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Petucci
- Metabolomics Core, Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Min-Soo Kim
- Metabolomics Core, Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arwa Abbas
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kevin J Downes
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nina Devas
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessica Breton
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Marakos
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alissa Galgano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessi Erlichman
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessica L Hart
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Moraskie
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Casey E Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James D Lewis
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph P Zackular
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongzhe Li
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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100
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Qian X, Yanagi K, Kane AV, Alden N, Lei M, Snydman DR, Vickers RJ, Lee K, Thorpe CM. Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids. Am J Physiol Gastrointest Liver Physiol 2020; 319:G227-G237. [PMID: 32597706 PMCID: PMC7500266 DOI: 10.1152/ajpgi.00046.2020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
Antibiotic treatment is a standard therapy for Clostridioides difficile infection, but dysbiosis of the gut microbiota due to antibiotic exposure is also a major risk factor for the disease. Following an initial episode of C. difficile infection, a relentless cycle of recurrence can occur, where persistent treatment-related dysbiosis predisposes the patient to subsequent relapse. This study uses a longitudinal study design to compare the effects of a narrow-spectrum (ridinilazole) or broad-spectrum antibiotic (vancomycin) on intestinal bile acid profiles and their associations with gut bacteria over the course of C. difficile infection treatment. At the end of treatment (day 10), subjects receiving vancomycin showed a nearly 100-fold increase in the ratio of conjugated to secondary bile acids in their stool compared with baseline, whereas subjects receiving ridinilazole maintained this ratio near baseline levels. Correlation analysis detected significant positive associations between secondary bile acids and several Bacteroidales and Clostridiales families. These families were depleted in the vancomycin group but preserved at near-baseline abundance in the ridinilazole group. Enterobacteriaceae, which expanded to a greater extent in the vancomycin group, correlated negatively and positively with secondary and conjugated primary bile acids, respectively. Bile acid ratios at the end of treatment were significantly different between those who recurred and those who did not. These results indicate that a narrow-spectrum antibiotic maintains an intestinal bile acid profile associated with a lowered risk of recurrence.NEW & NOTEWORTHY This is the first study to demonstrate in humans the relationships between Clostridioides difficile antibiotic treatment choice and bile acid metabolism both during therapy and after treatment cessation. The results show a microbiota- and metabolome-preserving property of a novel narrow-spectrum agent that correlates with the agent's favorable sustained clinical response rates compared with broad-spectrum antibiotic treatment.
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Affiliation(s)
- Xi Qian
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
| | - Karin Yanagi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | | | - Nicholas Alden
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - Ming Lei
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - David R Snydman
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
- Tufts Medical Center, Boston, Massachusetts
- Tufts University School of Medicine, Boston, Massachusetts
| | | | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - Cheleste M Thorpe
- Tufts Medical Center, Boston, Massachusetts
- Tufts University School of Medicine, Boston, Massachusetts
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