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Midani FS, Danhof HA, Mathew N, Ardis CK, Garey KW, Spinler JK, Britton RA. Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608124. [PMID: 39185189 PMCID: PMC11343193 DOI: 10.1101/2024.08.15.608124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Clostridioides difficile is a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. Although C. difficile is a genetically diverse species, certain ribotypes are overrepresented in human infections. It is unknown if metabolic adaptations are essential for the emergence of these epidemic ribotypes. Here, we tested carbon substrate utilization by 88 C. difficile isolates and looked for differences in growth between 22 ribotypes. By profiling clinical isolates, we assert that C. difficile is a generalist species capable of growing on a variety of carbon substrates. Further, C. difficile strains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, although C. difficile Clade 5 is the most evolutionary distant clade and often detected in animals, it displayed more robust growth on simple dietary sugars than Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy of C. difficile and demonstrate lineage-specific metabolic capabilities. In addition, our approach can be adapted to the study of additional pathogens to ascertain their metabolic niches in the gut. IMPORTANCE The gut pathogen Clostridioides difficile utilizes a wide range of carbon sources. Microbial communities can be rationally designed to combat C. difficile by depleting its preferred nutrients in the gut. However, C. difficile is genetically diverse with hundreds of identified ribotypes and most of its metabolic studies were performed with lab-adapted strains. Here, we profiled carbon metabolism by a myriad of C. difficile clinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that the most genetically distant clade grew robustly on simple dietary sugars, posing intriguing questions about the adaptation of C. difficile to the human gut. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.
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Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, Vivas EI, Simcox J, Venturelli O. Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603560. [PMID: 39071283 PMCID: PMC11275832 DOI: 10.1101/2024.07.15.603560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Clostridioides difficile can transiently or persistently colonize the human gut, posing a risk factor for infections. This colonization is influenced by complex molecular and ecological interactions with human gut microbiota. By investigating C. difficile dynamics in human gut communities over hundreds of generations, we show patterns of stable coexistence, instability, or competitive exclusion. Lowering carbohydrate concentration shifted a community containing C. difficile and the prevalent human gut symbiont Phocaeicola vulgatus from competitive exclusion to coexistence, facilitated by increased cross-feeding. In this environment, C. difficile adapted via single-point mutations in key metabolic genes, altering its metabolic niche from proline to glucose utilization. These metabolic changes substantially impacted inter-species interactions and reduced disease severity in the mammalian gut. In sum, human gut microbiota interactions are crucial in shaping the long-term growth dynamics and evolutionary adaptations of C. difficile, offering key insights for developing anti-C. difficile strategies.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jaron Thompson
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jericha Mill
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Isabella James
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Simcox
- Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
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3
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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a One Health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 PMCID: PMC11180571 DOI: 10.1016/j.anaerobe.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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4
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Pensinger DA, Dobrila HA, Stevenson DM, Hryckowian ND, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile. mBio 2024; 15:e0253523. [PMID: 38289141 PMCID: PMC10936429 DOI: 10.1128/mbio.02535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/20/2023] [Indexed: 02/13/2024] Open
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short-chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of a butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile-inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.IMPORTANCEThe gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions for C. difficile infection (CDI). We investigated how C. difficile responds to butyrate, an end-product of gut microbiome community metabolism which inhibits C. difficile growth. We show that exogenously produced butyrate is internalized into C. difficile, which inhibits C. difficile growth by interfering with its own butyrate production. This growth inhibition coincides with increased toxin release from C. difficile cells and the production of environmentally resistant spores necessary for transmission between hosts. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrict C. difficile growth in the gut and minimize its pathogenesis during CDI.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicole D. Hryckowian
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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5
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Cersosimo LM, Worley JN, Bry L. Approaching pathogenic Clostridia from a One Health perspective. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574718. [PMID: 38260382 PMCID: PMC10802438 DOI: 10.1101/2024.01.08.574718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M. Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
| | - Jay N. Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- National Center for Biotechnology Information, NIH, Bethesda, MD
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- Clinical Microbiology Laboratory, Dept. Pathology, Brigham & Women's Hospital, Boston, MA
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6
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Pensinger DA, Dobrila HA, Stevenson DM, Davis NM, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters expression of virulence genes in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548018. [PMID: 37461482 PMCID: PMC10350080 DOI: 10.1101/2023.07.06.548018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells, is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) in C. difficile coincides with alterations in toxin production and sporulation. Together, this work highlights butyrate as a signal of a C. difficile inhospitable environment to which C. difficile responds by producing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate serves as a signal to alter C. difficile virulence in the face of a highly competitive and dynamic gut environment.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicole M. Davis
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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7
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Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates. Infect Immun 2023; 91:e0057022. [PMID: 36692308 PMCID: PMC9933713 DOI: 10.1128/iai.00570-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A disrupted "dysbiotic" gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota-accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C. difficile and for developing alternative approaches for coping with this pathogen. One prominent class of metabolites produced by the gut microbiome is short-chain fatty acids (SCFAs), the major metabolic end products of MAC metabolism. SCFAs are known to decrease the fitness of C. difficile in vitro, and high intestinal SCFA concentrations are associated with reduced fitness of C. difficile in animal models of C. difficile infection (CDI). Here, we use controlled dietary conditions (8 diets that differ only by MAC composition) to show that C. difficile fitness is most consistently impacted by butyrate, rather than the other two prominent SCFAs (acetate and propionate), during murine model CDI. We similarly show that butyrate concentrations are lower in fecal samples from humans with CDI than in those from healthy controls. Finally, we demonstrate that butyrate impacts growth in diverse C. difficile isolates. These findings provide a foundation for future work which will dissect how butyrate directly impacts C. difficile fitness and will lead to the development of diverse approaches distinct from antibiotics or fecal transplant, such as dietary interventions, for mitigating CDI in at-risk human populations. IMPORTANCE Clostridioides difficile is a leading cause of infectious diarrhea in humans, and it imposes a tremendous burden on the health care system. Current treatments for C. difficile infection (CDI) include antibiotics and fecal microbiota transplant, which contribute to recurrent CDIs and face major regulatory hurdles, respectively. Therefore, there is an ongoing need to develop new ways to cope with CDI. Notably, a disrupted "dysbiotic" gut microbiota is the primary risk factor for CDI, but we incompletely understand how a healthy microbiota resists CDI. Here, we show that a specific molecule produced by the gut microbiota, butyrate, is negatively associated with C. difficile burdens in humans and in a mouse model of CDI and that butyrate impedes the growth of diverse C. difficile strains in pure culture. These findings help to build a foundation for designing alternative, possibly diet-based, strategies for mitigating CDI in humans.
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8
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Marshall A, McGrath JW, Graham R, McMullan G. Food for thought-The link between Clostridioides difficile metabolism and pathogenesis. PLoS Pathog 2023; 19:e1011034. [PMID: 36602960 PMCID: PMC9815643 DOI: 10.1371/journal.ppat.1011034] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is an opportunistic pathogen that leads to antibiotic-associated diarrhoea and is a leading cause of morbidity and mortality worldwide. Antibiotic usage is the main risk factor leading to C. difficile infection (CDI), as a dysbiotic gut environment allows colonisation and eventual pathology manifested by toxin production. Although colonisation resistance is mediated by the action of secondary bile acids inhibiting vegetative outgrowth, nutrient competition also plays a role in preventing CDI as the gut microbiota compete for nutrient niches inhibiting C. difficile growth. C. difficile is able to metabolise carbon dioxide, the amino acids proline, hydroxyproline, and ornithine, the cell membrane constituent ethanolamine, and the carbohydrates trehalose, cellobiose, sorbitol, and mucin degradation products as carbon and energy sources through multiple pathways. Zinc sequestration by the host response mediates metabolic adaptation of C. difficile by perhaps signalling an inflamed gut allowing it to acquire abundant nutrients. Persistence within the gut environment is also mediated by the by-products of metabolism through the production of p-cresol, which inhibit gut commensal species growth promoting dysbiosis. This review aims to explore and describe the various metabolic pathways of C. difficile, which facilitate its survival and pathogenesis within the colonised host gut.
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Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Robert Graham
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
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Mitchell M, Nguyen SV, Macori G, Bolton D, McMullan G, Drudy D, Fanning S. Clostridioides difficile as a Potential Pathogen of Importance to One Health: A Review. Foodborne Pathog Dis 2022; 19:806-816. [PMID: 36516404 DOI: 10.1089/fpd.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile (basonym Clostridium) is a bacterial enteropathogen associated with cases of C. difficile infection that can result in pseudomembranous colitis, rapid fluid loss, and death. For decades following its isolation, C. difficile was thought to be a solely nosocomial pathogen, being isolated from individuals undergoing antimicrobial therapy and largely affecting elderly populations. More recently, C. difficile spores have been identified in the broader environment, including in food-producing animals, soil, and food matrices, in both ready-to-eat foods and meat products. Furthermore, evidence has emerged of hypervirulent ribotypes (RTs), such as RT078, similar to those cultured in asymptomatic carriers, also being identified in these environments. This finding may reflect on adaptations arising in these bacteria following selection pressures encountered in these niches, and which occurs due to an increase in antimicrobial usage in both clinical and veterinary settings. As C. difficile continues to adapt to new ecological niches, the taxonomy of this genus has also been evolving. To help understand the transmission and virulence potential of these bacteria of importance to veterinary public health, strategies applying multi-omics-based technologies may prove useful. These approaches may extend our current understanding of this recognized nosocomial pathogen, perhaps redefining it as a zoonotic bacterium. In this review, a brief background on the epidemiological presentation of C. difficile will be highlighted, followed by a review of C. difficile in food-producing animals and food products. The current state of C. difficile taxonomy will provide evidence of Clade 5 (ST11/RT078) delineation, as well as background on the genomic elements linked to C. difficile virulence and ongoing speciation. Recent studies applying second- and third-generation sequencing technologies will be highlighted, and which will further strengthen the argument made by many throughout the world regarding this pathogen and its consideration within a One Health dimension.
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Affiliation(s)
- Molly Mitchell
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland.,District of Columbia Department of Forensic Sciences, Public Health Laboratory, Washington, District of Columbia, USA
| | - Guerrino Macori
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland
| | | | - Geoff McMullan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
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10
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Bhute SS, Mefferd CC, Phan JR, Ahmed M, Fox-King AE, Alarcia S, Villarama JV, Abel-Santos E, Hedlund BP. A High-Carbohydrate Diet Prolongs Dysbiosis and Clostridioides difficile Carriage and Increases Delayed Mortality in a Hamster Model of Infection. Microbiol Spectr 2022; 10:e0180421. [PMID: 35708337 PMCID: PMC9431659 DOI: 10.1128/spectrum.01804-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/21/2022] [Indexed: 12/20/2022] Open
Abstract
Studies using mouse models of Clostridioides difficile infection (CDI) have demonstrated a variety of relationships between dietary macronutrients on antibiotic-associated CDI; however, few of these effects have been examined in more susceptible hamster models of CDI. In this study, we investigated the effect of a high-carbohydrate diet previously shown to protect mice from CDI on the progression and resolution of CDI in a hamster disease model, with 10 animals per group. Hamsters fed the high-carbohydrate diet developed distinct diet-specific microbiomes during antibiotic treatment and CDI, with lower diversity, persistent C. difficile carriage, and delayed microbiome restoration. In contrast to CDI protection in mice, most hamsters fed a high-carbohydrate diet developed fulminant CDI including several cases of late-onset CDI, that were not observed in hamsters fed a standard lab diet. We speculate that prolonged high-carbohydrate diet-specific dysbiosis in these animals allowed C. difficile to persist in the gut of the animals where they could proliferate postvancomycin treatment, leading to delayed CDI onset. This study, along with similar studies in mouse models of CDI, suggests some high-carbohydrate diets may promote antibiotic-associated dysbiosis and long-term C. difficile carriage, which may later convert to symptomatic CDI. IMPORTANCE The effects of diet on CDI are not completely known. Here, we used a high-carbohydrate diet previously shown to protect mice against CDI to assess its effect on a hamster model of CDI and paradoxically found that it promoted dysbiosis, C. difficile carriage, and higher mortality. A common thread in both mouse and hamster experimental models was that the high-carbohydrate diet promoted dysbiosis and long-term carriage of C. difficile, which may have converted to fulminant CDI only in the highly susceptible hamster model system. If diets high in carbohydrates also promote dysbiosis and C. difficile carriage in humans, then these diets might paradoxically increase chances of CDI relapse despite their protective effects against primary CDI.
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Affiliation(s)
- Shrikant S. Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Chrisabelle C. Mefferd
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- School of Public Health, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacqueline R. Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Muneeba Ahmed
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- College of Osteopathic Medicine, Touro University, Nevada, Henderson, Nevada, USA
| | - Amelia E. Fox-King
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- College of Osteopathic Medicine, Touro University, Nevada, Henderson, Nevada, USA
| | - Stephanie Alarcia
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacob V. Villarama
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Kirk Kerkorian School of Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
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11
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Santos MGDC, Trindade CNDR, Vommaro RC, Domingues RMCP, Ferreira EDO. Binding of the extracellular matrix laminin-1 to Clostridioides difficile strains. Mem Inst Oswaldo Cruz 2022; 117:e220035. [PMID: 35730804 PMCID: PMC9208321 DOI: 10.1590/0074-02760220035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/12/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Clostridioides difficile is the most common cause of nosocomial diarrhea associated with antibiotic use. The disease’s symptoms are caused by enterotoxins, but other surface adhesion factors also play a role in the pathogenesis. These adhesins will bind to components of extracellular matrix. OBJECTIVE There is a lack of knowledge on MSCRAMM, this work set-out to determine the adhesive properties of several C. difficile ribotypes (027, 133, 135, 014, 012) towards laminin-1 (LMN-1). METHODS A binding experiment revealed that different ribotypes have distinct adhesion capabilities. To identify this adhesin, an affinity chromatography column containing LMN-1 was prepared and total protein extracts were analysed using mass spectrometry. FINDINGS Strains from ribotypes 012 and 027 had the best adhesion when incubated with glucose supplementations (0.2%, 0.5%, and 1%), while RT135 had a poor adherence. The criteria were not met by RT014 and RT133. In the absence of glucose, there was no adhesion for any ribotype, implying that glucose is required and plays a significant role in adhesion. MAIN CONCLUSIONS These findings show that in the presence of glucose, each C. difficile ribotype interacts differently with LMN-1, and the adhesin responsible for recognition could be SlpA protein.
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Affiliation(s)
- Mayara Gil de Castro Santos
- Universidade Federal do Rio de Janeiro, Departamento de Microbiologia Médica, Laboratório de Biologia de Anaeróbios, Rio de Janeiro, RJ, Brasil
| | - Camilla Nunes Dos Reis Trindade
- Universidade Federal do Rio de Janeiro, Departamento de Microbiologia Médica, Laboratório de Biologia de Anaeróbios, Rio de Janeiro, RJ, Brasil
| | - Rossiane Cláudia Vommaro
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho e Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Laboratório de Ultraestrutura Celular Hertha Meyer, Rio de Janeiro, RJ, Brasil
| | | | - Eliane de Oliveira Ferreira
- Universidade Federal do Rio de Janeiro, Departamento de Microbiologia Médica, Laboratório de Biologia de Anaeróbios, Rio de Janeiro, RJ, Brasil
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12
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Ferreira WT, Hong HA, Adams JRG, Hess M, Kotowicz NK, Tan S, Ferrari E, Brisson A, Zentek J, Soloviev M, Cutting SM. Environmentally Acquired Bacillus and Their Role in C. difficile Colonization Resistance. Biomedicines 2022; 10:930. [PMID: 35625667 PMCID: PMC9138776 DOI: 10.3390/biomedicines10050930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 01/27/2023] Open
Abstract
Clostridioides difficile is an environmentally acquired, anaerobic, spore-forming bacterium which ordinarily causes disease following antibiotic-mediated dysbiosis of the intestinal microbiota. Although much is understood regarding the life cycle of C. difficile, the fate of C. difficile spores upon ingestion remains unclear, and the underlying factors that predispose an individual to colonization and subsequent development of C. difficile infection (CDI) are not fully understood. Here, we show that Bacillus, a ubiquitous and environmentally acquired, spore-forming bacterium is associated with colonization resistance to C. difficile. Using animal models, we first provide evidence that animals housed under conditions that mimic reduced environmental exposure have an increased susceptibility to CDI, correlating with a loss in Bacillus. Lipopeptide micelles (~10 nm) produced by some Bacilli isolated from the gastro-intestinal (GI)-tract and shown to have potent inhibitory activity to C. difficile have recently been reported. We show here that these micelles, that we refer to as heterogenous lipopeptide lytic micelles (HELMs), act synergistically with components present in the small intestine to augment inhibitory activity against C. difficile. Finally, we show that provision of HELM-producing Bacillus to microbiota-depleted animals suppresses C. difficile colonization thereby demonstrating the significant role played by Bacillus in colonization resistance. In the wider context, our study further demonstrates the importance of environmental microbes on susceptibility to pathogen colonization.
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Affiliation(s)
- William T. Ferreira
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Huynh A. Hong
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - James R. G. Adams
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Mateusz Hess
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Natalia K. Kotowicz
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK;
| | - Sisareuth Tan
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Enrico Ferrari
- School of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK;
| | - Alain Brisson
- Laboratoire d’Imagerie Moléculaire et Nano-Bio-Technologie, UMR-CBMN CNRS-Université de Bordeaux-IPB, 33607 Pessac, France; (S.T.); (A.B.)
| | - Jurgen Zentek
- Institute for Animal Health, Freie University of Berlin, Berlin 14195, Germany;
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
| | - Simon M. Cutting
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (W.T.F.); (H.A.H.); (J.R.G.A.); (M.H.)
- SporeGen Ltd., London Bioscience Innovation Centre, 2 Royal College Street, London NW1 0NH, UK;
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13
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Hazleton KZ, Martin CG, Orlicky DJ, Arnolds KL, Nusbacher NM, Moreno-Huizar N, Armstrong M, Reisdorph N, Lozupone CA. Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice. NPJ Biofilms Microbiomes 2022; 8:15. [PMID: 35365681 PMCID: PMC8975876 DOI: 10.1038/s41522-022-00276-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/21/2022] [Indexed: 11/15/2022] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea, and emerging evidence has linked dietary components with CDI pathogenesis, suggesting that dietary modulation may be an effective strategy for prevention. Here, we show that mice fed a high-fat/low-fiber “Western-type” diet (WD) had dramatically increased mortality in a murine model of antibiotic-induced CDI compared to a low-fat/low-fiber (LF/LF) diet and standard mouse chow controls. We found that the WD had a pro- C. difficile bile acid composition that was driven in part by higher levels of primary bile acids that are produced to digest fat, and a lower level of secondary bile acids that are produced by the gut microbiome. This lack of secondary bile acids was associated with a greater disturbance to the gut microbiome with antibiotics in both the WD and LF/LF diet compared to mouse chow. Mice fed the WD also had the highest level of toxin TcdA just prior to the onset of mortality, but not of TcdB or increased inflammation. These findings indicate that dietary intervention to decrease fat may complement previously proposed dietary intervention strategies to prevent CDI in high-risk individuals.
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Affiliation(s)
- Keith Z Hazleton
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition. University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA.,Digestive Health Institute, Children's Hospital Colorado, Aurora, CO, 80045, USA.,Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Arizona, Tucson, AZ, 85719, USA
| | - Casey G Martin
- Department of Immunology and Microbiology, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kathleen L Arnolds
- Department of Immunology and Microbiology, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nichole M Nusbacher
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nancy Moreno-Huizar
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michael Armstrong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Catherine A Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO, 80045, USA.
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14
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Ono T, Taniguchi I, Nakamura K, Nagano DS, Nishida R, Gotoh Y, Ogura Y, Sato MP, Iguchi A, Murase K, Yoshimura D, Itoh T, Shima A, Dubois D, Oswald E, Shiose A, Gotoh N, Hayashi T. Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex. Microb Genom 2022; 8:000793. [PMID: 35315751 PMCID: PMC9176281 DOI: 10.1099/mgen.0.000793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.
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Affiliation(s)
- Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Mitsuhiko P. Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Present address: Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Iguchi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, 889-8192, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Sakyou-ku, Kyoto, 6060-8501, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ayaka Shima
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- Present address: Anicon Insurance, Inc., 8-17-1 Nishi-shinjuku, Shinjuku, Tokyo, 160-0023, Japan
| | - Damien Dubois
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Eric Oswald
- IRSD, INSERM, ENVT, INRAE, Université de Toulouse, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Akira Shiose
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Naomasa Gotoh
- Kyoto Pharmaceutical University, Yamashiro, Kyoto, 607-8414, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- *Correspondence: Tetsuya Hayashi,
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15
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Fishbein SR, Robinson JI, Hink T, Reske KA, Newcomer EP, Burnham CAD, Henderson JP, Dubberke ER, Dantas G. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. eLife 2022; 11:72801. [PMID: 35083969 PMCID: PMC8794467 DOI: 10.7554/elife.72801] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile infection (CDI) imposes a substantial burden on the health care system in the United States. Understanding the biological basis for the spectrum of C. difficile-related disease manifestations is imperative to improving treatment and prevention of CDI. Here, we investigate the correlates of asymptomatic C. difficile colonization using a multi-omics approach. We compared the fecal microbiome and metabolome profiles of patients with CDI versus asymptomatically colonized patients, integrating clinical and pathogen factors into our analysis. We found that CDI patients were more likely to be colonized by strains with the binary toxin (CDT) locus or strains of ribotype 027, which are often hypervirulent. We find that microbiomes of asymptomatically colonized patients are significantly enriched for species in the class Clostridia relative to those of symptomatic patients. Relative to CDI microbiomes, asymptomatically colonized patient microbiomes were enriched with sucrose degradation pathways encoded by commensal Clostridia, in addition to glycoside hydrolases putatively involved in starch and sucrose degradation. Fecal metabolomics corroborates the carbohydrate degradation signature: we identify carbohydrate compounds enriched in asymptomatically colonized patients relative to CDI patients. Further, we reveal that across C. difficile isolates, the carbohydrates sucrose, rhamnose, and lactulose do not serve as robust growth substrates in vitro, consistent with their enriched detection in our metagenomic and metabolite profiling of asymptomatically colonized individuals. We conclude that pathogen genetic variation may be strongly related to disease outcome. More interestingly, we hypothesize that in asymptomatically colonized individuals, carbohydrate metabolism by other commensal Clostridia may prevent CDI by inhibiting C. difficile proliferation. These insights into C. difficile colonization and putative commensal competition suggest novel avenues to develop probiotic or prebiotic therapeutics against CDI.
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Affiliation(s)
- Skye Rs Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, United States
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Kimberly A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Erin P Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, United States
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, United States.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States
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16
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Monaghan TM, Biswas R, Satav A, Ambalkar S, Kashyap RS. Mini-review: Clostridioides difficile epidemiology in India. Anaerobe 2022; 74:102517. [DOI: 10.1016/j.anaerobe.2022.102517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/20/2021] [Accepted: 01/14/2022] [Indexed: 02/08/2023]
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17
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Weiss A, Lopez CA, Beavers WN, Rodriguez J, Skaar EP. Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment. Microb Genom 2021; 7:000738. [PMID: 34908523 PMCID: PMC8767335 DOI: 10.1099/mgen.0.000738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) colonizes the gastrointestinal tract following disruption of the microbiota and can initiate a spectrum of clinical manifestations ranging from asymptomatic to life-threatening colitis. Following antibiotic treatment, luminal oxygen concentrations increase, exposing gut microbes to potentially toxic reactive oxygen species. Though typically regarded as a strict anaerobe, C. difficile can grow at low oxygen concentrations. How this bacterium adapts to a microaerobic environment and whether those responses to oxygen are conserved amongst strains is not entirely understood. Here, two C. difficile strains (630 and CD196) were cultured in 1.5% oxygen and the transcriptional response to long-term oxygen exposure was evaluated via RNA-sequencing. During growth in a microaerobic environment, several genes predicted to protect against oxidative stress were upregulated, including those for rubrerythrins and rubredoxins. Transcription of genes involved in metal homeostasis was also positively correlated with increased oxygen levels and these genes were amongst the most differentially transcribed. To directly compare the transcriptional landscape between C. difficile strains, a 'consensus-genome' was generated. On the basis of the identified conserved genes, basal transcriptional differences as well as variations in the response to oxygen were evaluated. While several responses were similar between the strains, there were significant differences in the abundance of transcripts involved in amino acid and carbohydrate metabolism. Furthermore, intracellular metal concentrations significantly varied both in an oxygen-dependent and oxygen-independent manner. Overall, these results indicate that C. difficile adapts to grow in a low oxygen environment through transcriptional changes, though the specific strategy employed varies between strains.
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Affiliation(s)
- Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher A. Lopez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, USA
| | - William N. Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jhoana Rodriguez
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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18
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Midani FS, Collins J, Britton RA. AMiGA: Software for Automated Analysis of Microbial Growth Assays. mSystems 2021; 6:e0050821. [PMID: 34254821 PMCID: PMC8409736 DOI: 10.1128/msystems.00508-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
The analysis of microbial growth is one of the central methods in the field of microbiology. Microbial growth dynamics can be characterized by meaningful parameters, including carrying capacity, exponential growth rate, and growth lag. However, microbial assays with clinical isolates, fastidious organisms, or microbes under stress often produce atypical growth shapes that do not follow the classical microbial growth pattern. Here, we introduce the analysis of microbial growth assays (AMiGA) software, which streamlines the analysis of growth curves without any assumptions about their shapes. AMiGA can pool replicates of growth curves and infer summary statistics for biologically meaningful growth parameters. In addition, AMiGA can quantify death phases and characterize diauxic shifts. It can also statistically test for differential growth under distinct experimental conditions. Altogether, AMiGA streamlines the organization, analysis, and visualization of microbial growth assays. IMPORTANCE Our current understanding of microbial physiology relies on the simple method of measuring microbial populations' sizes over time and under different conditions. Many advances have increased the throughput of those assays and enabled the study of nonlab-adapted microbes under diverse conditions that widely affect their growth dynamics. Our software provides an all-in-one tool for estimating the growth parameters of microbial cultures and testing for differential growth in a high-throughput and user-friendly fashion without any underlying assumptions about how microbes respond to their growth conditions.
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Affiliation(s)
- Firas S. Midani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - James Collins
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
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19
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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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20
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Xu X, Luo Y, Chen H, Song X, Bian Q, Wang X, Liang Q, Zhao J, Li C, Song G, Yang J, Sun L, Jiang J, Wang H, Zhu B, Ye G, Chen L, Tang YW, Jin D. Genomic evolution and virulence association of Clostridioides difficile sequence type 37 (ribotype 017) in China. Emerg Microbes Infect 2021; 10:1331-1345. [PMID: 34125660 PMCID: PMC8253194 DOI: 10.1080/22221751.2021.1943538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Clostridioides difficile sequence type (ST) 37 (ribotype 017) is one of the most prevalent genotypes circulating in China. However, its genomic evolution and virulence determinants were rarely explored. Whole-genome sequencing, phylogeographic and phylogenetic analyses were conducted for C. difficile ST37 isolates. The 325 ST37 genomes from six continents, including North America (n = 66), South America (n = 4), Oceania (n = 7), Africa (n = 9), Europe (n = 138) and Asia (n = 101), were clustered into six major lineages, with region-dependent distributions, harbouring an array of antibiotic-resistance genes. The ST37 strains from China were divided into four distinct sublineages, showing five importation times and international sources. Isolates associated with severe infections exhibited significantly higher toxin productions, tcdB mRNA levels, and sporulation capacities (P < 0.001). Kyoto Encyclopedia of Genes and Genomes analysis showed 10 metabolic pathways were significantly enriched in the mutations among isolates associated with severe CDI (P < 0.05). Gene mutations in glycometabolism, amino acid metabolism and biosynthesis virtually causing instability in protein activity were correlated positively to the transcription of tcdR and negatively to the expression of toxin repressor genes, ccpA and codY. In summary, our study firstly presented genomic insights into genetic characteristics and virulence association of C. difficile ST37 in China. Gene mutations in certain important metabolic pathways are associated with severe symptoms and correlated with higher virulence in C. difficile ST37 isolates.
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Affiliation(s)
- Xingxing Xu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yuo Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Huan Chen
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Qiao Bian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, People's Republic of China
| | - Qian Liang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianhong Zhao
- Department of Clinical Microbiology, Second Hospital of Hebei Medical University, Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, People's Republic of China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Guangzhong Song
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Jun Yang
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Lingli Sun
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Huanying Wang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Guangyong Ye
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, People's Republic of China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China.,Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
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21
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Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021; 10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
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Affiliation(s)
- Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Brian Kullin
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enzo Guerrero-Araya
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.,Department of Biology, Texas A&M University, College Station, United States
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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22
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Pruss KM, Sonnenburg JL. C. difficile exploits a host metabolite produced during toxin-mediated disease. Nature 2021; 593:261-265. [PMID: 33911281 PMCID: PMC9067157 DOI: 10.1038/s41586-021-03502-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/26/2021] [Indexed: 02/02/2023]
Abstract
Several enteric pathogens can gain specific metabolic advantages over other members of the microbiota by inducing host pathology and inflammation. The pathogen Clostridium difficile is responsible for a toxin-mediated colitis that causes 450,000 infections and 15,000 deaths in the United States each year1; however, the molecular mechanisms by which C. difficile benefits from this pathology remain unclear. To understand how the metabolism of C. difficile adapts to the inflammatory conditions that its toxins induce, here we use RNA sequencing to define, in a mouse model, the metabolic states of wild-type C. difficile and of an isogenic mutant that lacks toxins. By combining bacterial and mouse genetics, we demonstrate that C. difficile uses sorbitol derived from both diet and host. Host-derived sorbitol is produced by the enzyme aldose reductase, which is expressed by diverse immune cells and is upregulated during inflammation-including during toxin-mediated disease induced by C. difficile. This work highlights a mechanism by which C. difficile can use a host-derived nutrient that is generated during toxin-induced disease by an enzyme that has not previously been associated with infection.
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23
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Li J, Zhang Y, Jilg AL, Wolk DM, Khara HS, Kolinovsky A, Rolston DDK, Hontecillas R, Bassaganya-Riera J, Williams MS, Abedi V, Lee MTM. Variants at the MHC Region Associate With Susceptibility to Clostridioides difficile Infection: A Genome-Wide Association Study Using Comprehensive Electronic Health Records. Front Immunol 2021; 12:638913. [PMID: 33841421 PMCID: PMC8026859 DOI: 10.3389/fimmu.2021.638913] [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: 12/07/2020] [Accepted: 03/09/2021] [Indexed: 01/13/2023] Open
Abstract
Background Clostridioides difficile is a major cause of healthcare-associated and community-acquired diarrhea. Host genetic susceptibility to Clostridioides difficile infection has not been studied on a large-scale. Methods A total of 1,160 Clostridioides difficile infection cases and 15,304 controls were identified by applying the eMERGE Clostridioides difficile infection algorithm to electronic health record data. A genome-wide association study was performed using a linear mixed model, adjusted for significant covariates in the full dataset and the antibiotic subgroup. Colocalization and MetaXcan were performed to identify potential target genes in Clostridioides difficile infection - relevant tissue types. Results No significant genome-wide association was found in the meta-analyses of the full Clostridioides difficile infection dataset. One genome-wide significant variant, rs114751021, was identified (OR = 2.42; 95%CI = 1.84-3.11; p=4.50 x 10-8) at the major histocompatibility complex region associated with Clostridioides difficile infection in the antibiotic group. Colocalization and MetaXcan identified MICA, C4A/C4B, and NOTCH4 as potential target genes. Down-regulation of MICA, upregulation of C4A and NOTCH4 was associated with a higher risk for Clostridioides difficile infection. Conclusions Leveraging the EHR and genetic data, genome-wide association, and fine-mapping techniques, this study identified variants and genes associated with Clostridioides difficile infection, provided insights into host immune mechanisms, and described the potential for novel treatment strategies for Clostridioides difficile infection. Future replication and functional validation are needed.
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Affiliation(s)
- Jiang Li
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, United States
| | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger, Danville, PA, United States
| | - Alexandria L Jilg
- Department of Internal Medicine, Geisinger, Danville, PA, United States
| | - Donna M Wolk
- Diagnostic Medicine Institute, Department of Laboratory Medicine, Geisinger, Danville, PA, United States
| | - Harshit S Khara
- Department of Gastroenterology and Hepatology, Geisinger, Danville, PA, United States
| | | | - David D K Rolston
- Department of Internal Medicine, Geisinger, Danville, PA, United States
| | | | | | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA, United States
| | - Vida Abedi
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, United States
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24
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Global Landscape of Clostridioides Difficile Phylogeography, Antibiotic Susceptibility, and Toxin Polymorphisms by Post-Hoc Whole-Genome Sequencing from the MODIFY I/II Studies. Infect Dis Ther 2021; 10:853-870. [PMID: 33751421 PMCID: PMC8116447 DOI: 10.1007/s40121-021-00426-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/26/2021] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Clostridioides (Clostridium) difficile infection, the leading cause of healthcare-associated diarrhea, represents a significant burden on global healthcare systems. Despite being a global issue, information on C. difficile from a global perspective is lacking. The aim of this study is to model the global phylogeography of clinical C. difficile. METHODS Using samples collected from the MODIFY I and II studies (NCT01241552, NCT01513239), we performed whole-genome sequencing of 1501 clinical isolates including 37 novel sequence types (STs), representing the largest worldwide collection to date. RESULTS Our data showed ribotypes, multi-locus sequence typing clades, and whole-genome phylogeny were in good accordance. The clinical C. difficile genome was found to be more conserved than previously reported (61% core genes), and modest recombination rates of 1.4-5.0 were observed across clades. We observed a significant continent distribution preference among five C. difficile clades (Benjamini-Hochberg corrected Fisher's exact test P < 0.01); moreover, weak association between geographic and genetic distance among ribotypes suggested sources beyond healthcare-related transmission. Markedly different trends of antibiotic susceptibility among lineages and regions were identified, and three novel mutations (in pyridoxamine 5'-phosphate oxidase family protein: Tyr130Ser, Tyr130Cys, and a promoter SNP) associated with metronidazole-reduced susceptibility were discovered on a nim-related gene and its promotor by genome-wide association study. Toxin gene polymorphisms were shown to vary within and between prevalent ribotypes, and novel severe mutations were found on the tcdC toxin regulator protein. CONCLUSION Our systematic characterization of a global set of clinical trial C. difficile isolates from infected individuals demonstrated the complexity of the genetic makeup of this pathogenic organism. The geographic variability of clades, variability in toxin genes, and mutations associated with antibiotic susceptibility indicate a highly complex interaction of C. difficile between host and environment. This dataset will provide a useful resource for validation of findings and future research of C. difficile.
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25
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Kulecka M, Waker E, Ambrozkiewicz F, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. BMC Microbiol 2021; 21:36. [PMID: 33509087 PMCID: PMC7842062 DOI: 10.1186/s12866-021-02090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward. METHODS C. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper. RESULTS We have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates - they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence. CONCLUSIONS Our findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates' virulence.
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Affiliation(s)
- Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Edyta Waker
- Department of Clinical Microbiology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland.
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26
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Engevik MA, Danhof HA, Shrestha R, Chang-Graham AL, Hyser JM, Haag AM, Mohammad MA, Britton RA, Versalovic J, Sorg JA, Spinler JK. Reuterin disrupts Clostridioides difficile metabolism and pathogenicity through reactive oxygen species generation. Gut Microbes 2020; 12:1788898. [PMID: 32804011 PMCID: PMC7524292 DOI: 10.1080/19490976.2020.1795388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 02/03/2023] Open
Abstract
Antibiotic resistance is one of the world's greatest public health challenges and adjunct probiotic therapies are strategies that could lessen this burden. Clostridioides difficile infection (CDI) is a prime example where adjunct probiotic therapies could decrease disease incidence through prevention. Human-derived Lactobacillus reuteri is a probiotic that produces the antimicrobial compound reuterin known to prevent C. difficile colonization of antibiotic-treated fecal microbial communities. However, the mechanism of inhibition is unclear. We show that reuterin inhibits C. difficile outgrowth from spores and vegetative cell growth, however, no effect on C. difficile germination or sporulation was observed. Consistent with published studies, we found that exposure to reuterin stimulated reactive oxygen species (ROS) in C. difficile, resulting in a concentration-dependent reduction in cell viability that was rescued by the antioxidant glutathione. Sublethal concentrations of reuterin enhanced the susceptibility of vegetative C. difficile to vancomycin and metronidazole treatment and reduced toxin synthesis by C. difficile. We also demonstrate that reuterin is protective against C. difficile toxin-mediated cellular damage in the human intestinal enteroid model. Overall, our results indicate that ROS are essential mediators of reuterin activity and show that reuterin production by L. reuteri is compatible as a therapeutic in a clinically relevant model.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Heather A. Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ritu Shrestha
- Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M. Haag
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Mahmoud A. Mohammad
- Department of Pediatrics, Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
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Norsigian CJ, Danhof HA, Brand CK, Oezguen N, Midani FS, Palsson BO, Savidge TC, Britton RA, Spinler JK, Monk JM. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. NPJ Syst Biol Appl 2020; 6:31. [PMID: 33082337 PMCID: PMC7576604 DOI: 10.1038/s41540-020-00151-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Hospital acquired Clostridioides (Clostridium) difficile infection is exacerbated by the continued evolution of C. difficile strains, a phenomenon studied by multiple laboratories using stock cultures specific to each laboratory. Intralaboratory evolution of strains contributes to interlaboratory variation in experimental results adding to the challenges of scientific rigor and reproducibility. To explore how microevolution of C. difficile within laboratories influences the metabolic capacity of an organism, three different laboratory stock isolates of the C. difficile 630 reference strain were whole-genome sequenced and profiled in over 180 nutrient environments using phenotypic microarrays. The results identified differences in growth dynamics for 32 carbon sources including trehalose, fructose, and mannose. An updated genome-scale model for C. difficile 630 was constructed and used to contextualize the 28 unique mutations observed between the stock cultures. The integration of phenotypic screens with model predictions identified pathways enabling catabolism of ethanolamine, salicin, arbutin, and N-acetyl-galactosamine that differentiated individual C. difficile 630 laboratory isolates. The reconstruction was used as a framework to analyze the core-genome of 415 publicly available C. difficile genomes and identify areas of metabolism prone to evolution within the species. Genes encoding enzymes and transporters involved in starch metabolism and iron acquisition were more variable while C. difficile distinct metabolic functions like Stickland fermentation were more consistent. A substitution in the trehalose PTS system was identified with potential implications in strain virulence. Thus, pairing genome-scale models with large-scale physiological and genomic data enables a mechanistic framework for studying the evolution of pathogens within microenvironments and will lead to predictive modeling to combat pathogen emergence.
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Affiliation(s)
- Charles J Norsigian
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Heather A Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Colleen K Brand
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Firas S Midani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer K Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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28
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Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway. J Bacteriol 2020; 202:JB.00233-20. [PMID: 32967909 DOI: 10.1128/jb.00233-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
Clostridium difficile is the leading cause of hospital-acquired antibiotic-associated diarrhea and is the only widespread human pathogen that contains a complete set of genes encoding the Wood-Ljungdahl pathway (WLP). In acetogenic bacteria, synthesis of acetate from 2 CO2 molecules by the WLP functions as a terminal electron accepting pathway; however, C. difficile contains various other reductive pathways, including a heavy reliance on Stickland reactions, which questions the role of the WLP in this bacterium. In rich medium containing high levels of electron acceptor substrates, only trace levels of key WLP enzymes were found; therefore, conditions were developed to adapt C. difficile to grow in the absence of amino acid Stickland acceptors. Growth conditions were identified that produce the highest levels of WLP activity, determined by Western blot analyses of the central component acetyl coenzyme A synthase (AcsB) and assays of other WLP enzymes. Fermentation substrate and product analyses, enzyme assays of cell extracts, and characterization of a ΔacsB mutant demonstrated that the WLP functions to dispose of metabolically generated reducing equivalents. While WLP activity in C. difficile does not reach the levels seen in classical acetogens, coupling of the WLP to butyrate formation provides a highly efficient system for regeneration of NAD+ "acetobutyrogenesis," requiring only low flux through the pathways to support efficient ATP production from glucose oxidation. Additional insights redefine the amino acid requirements in C. difficile, explore the relationship of the WLP to toxin production, and provide a rationale for colocalization of genes involved in glycine synthesis and cleavage within the WLP operon.IMPORTANCE Clostridium difficile is an anaerobic, multidrug-resistant, toxin-producing pathogen with major health impacts worldwide. It is the only widespread pathogen harboring a complete set of Wood-Ljungdahl pathway (WLP) genes; however, the role of the WLP in C. difficile is poorly understood. In other anaerobic bacteria and archaea, the WLP can operate in one direction to convert CO2 to acetic acid for biosynthesis or in either direction for energy conservation. Here, conditions are defined in which WLP levels in C. difficile increase markedly, functioning to support metabolism of carbohydrates. Amino acid nutritional requirements were better defined, with new insight into how the WLP and butyrate pathways act in concert, contributing significantly to energy metabolism by a mechanism that may have broad physiological significance within the group of nonclassical acetogens.
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29
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Shen E, Zhu K, Li D, Pan Z, Luo Y, Bian Q, He L, Song X, Zhen Y, Jin D, Tao L. Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin B. Commun Biol 2020; 3:347. [PMID: 32620855 PMCID: PMC7335066 DOI: 10.1038/s42003-020-1078-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile toxins (TcdA and TcdB) are major exotoxins responsible for C. difficile infection (CDI) associated diseases. The previously reported TcdB variants showed distinct biological features, immunoactivities, and potential pathogenicity in disease progression. Here, we performed global comparisons of amino acid sequences of both TcdA and TcdB from 3,269 C. difficile genomes and clustered them according to the evolutionary relatedness. We found that TcdB was much diverse and could be divided into eight subtypes, of which four were first described. Further analysis indicates that the tcdB gene undergoes accelerated evolution to maximize diversity. By tracing TcdB subtypes back to their original isolates, we found that the distribution of TcdB subtypes was not completely aligned with the phylogeny of C. difficile. These findings suggest that the tcdB genes not only frequently mutate, but also continuously transfer and exchange among C. difficile strains. Shen et al. compare the amino acid sequences of bacterial toxins TcdA and TcdB from 3,269 Clostridioides difficile genomes to identify four new TcdB subtypes. They find that TcdB was more diverse in amino acid sequence than TcdA. This study suggests that the tcdB genes not only frequently mutate, but they also continuously transfer and exchange among C. difficile strains.
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Affiliation(s)
- Enhui Shen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Kangli Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Danyang Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Zhenrui Pan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Yun Luo
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, China.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Qiao Bian
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Liuqing He
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Ying Zhen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Dazhi Jin
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China
| | - Liang Tao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. .,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
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30
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Li Z, Lee K, Rajyaguru U, Jones CH, Janezic S, Rupnik M, Anderson AS, Liberator P. Ribotype Classification of Clostridioides difficile Isolates Is Not Predictive of the Amino Acid Sequence Diversity of the Toxin Virulence Factors TcdA and TcdB. Front Microbiol 2020; 11:1310. [PMID: 32636819 PMCID: PMC7318873 DOI: 10.3389/fmicb.2020.01310] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides (Clostridium) difficile is the most commonly recognized cause of infectious diarrhea in healthcare settings. Currently there is no vaccine to prevent initial or recurrent C. difficile infection (CDI). Two large clostridial toxins, TcdA and TcdB, are the primary virulence factors for CDI. Immunological approaches to prevent CDI include antibody-mediated neutralization of the cytotoxicity of these toxins. An understanding of the sequence diversity of the two toxins expressed by disease causing isolates is critical for the interpretation of the immune response to the toxins. In this study, we determined the whole genome sequence (WGS) of 478 C. difficile isolates collected in 12 countries between 2004 and 2018 to probe toxin variant diversity. A total of 44 unique TcdA variants and 37 unique TcdB variants were identified. The amino acid sequence conservation among the TcdA variants (≥98%) is considerably greater than among the TcdB variants (as low as 86.1%), suggesting that different selection pressures may have contributed to the evolution of the two toxins. Phylogenomic analysis of the WGS data demonstrate that isolates grouped together based on ribotype or MLST code for multiple different toxin variants. These findings illustrate the importance of determining not only the ribotype but also the toxin sequence when evaluating strain coverage using vaccine strategies that target these virulence factors. We recommend that toxin variant type and sequence type (ST), be used together with ribotype data to provide a more comprehensive strain classification scheme for C. difficile surveillance during vaccine development objectives.
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Affiliation(s)
- Zhenghui Li
- Vaccine Research and Development, Pfizer Inc., Pearl River, NY, United States
| | - Kwok Lee
- Vaccine Research and Development, Pfizer Inc., Pearl River, NY, United States
| | - Urvi Rajyaguru
- Vaccine Research and Development, Pfizer Inc., Pearl River, NY, United States
| | - C Hal Jones
- Vaccine Research and Development, Pfizer Inc., Pearl River, NY, United States
| | - Sandra Janezic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - Paul Liberator
- Vaccine Research and Development, Pfizer Inc., Pearl River, NY, United States
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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32
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Shaw HA, Preston MD, Vendrik KEW, Cairns MD, Browne HP, Stabler RA, Crobach MJT, Corver J, Pituch H, Ingebretsen A, Pirmohamed M, Faulds-Pain A, Valiente E, Lawley TD, Fairweather NF, Kuijper EJ, Wren BW. The recent emergence of a highly related virulent Clostridium difficile clade with unique characteristics. Clin Microbiol Infect 2020; 26:492-498. [PMID: 31525517 PMCID: PMC7167513 DOI: 10.1016/j.cmi.2019.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Clostridium difficile is a major global human pathogen divided into five clades, of which clade 3 is the least characterized and consists predominantly of PCR ribotype (RT) 023 strains. Our aim was to analyse and characterize this clade. METHODS In this cohort study the clinical presentation of C. difficile RT023 infections was analysed in comparison with known 'hypervirulent' and non-hypervirulent strains, using data from the Netherlands national C. difficile surveillance programme. European RT023 strains of diverse origin were collected and whole-genome sequenced to determine the genetic similarity between isolates. Distinctive features were investigated and characterized. RESULTS Clinical presentation of C. difficile RT023 infections show severe infections akin to those seen with 'hypervirulent' strains from clades 2 (RT027) and 5 (RT078) (35%, 29% and 27% severe CDI, respectively), particularly with significantly more bloody diarrhoea than RT078 and non-hypervirulent strains (RT023 8%, other RTs 4%, p 0.036). The full genome sequence of strain CD305 is presented as a robust reference. Phylogenetic comparison of CD305 and a further 79 previously uncharacterized European RT023 strains of diverse origin revealed minor genetic divergence with >99.8% pairwise identity between strains. Analyses revealed distinctive features among clade 3 strains, including conserved pathogenicity locus, binary toxin and phage insertion toxin genotypes, glycosylation of S-layer proteins, presence of the RT078 four-gene trehalose cluster and an esculinase-negative genotype. CONCLUSIONS Given their recent emergence, virulence and genomic characteristics, the surveillance of clade 3 strains should be more highly prioritized.
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Affiliation(s)
- H A Shaw
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK; Division of Bacteriology, National Institute for Biological Standards and Controls, South Mimms, Potters Bar, UK
| | - M D Preston
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK; Analytical Biological Service Division, National Institute for Biological Standards and Controls, Potters Bar, UK
| | - K E W Vendrik
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - M D Cairns
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK; Public Health Laboratory London, Division of Infection, The Royal London Hospital, London, UK
| | - H P Browne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - R A Stabler
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - M J T Crobach
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - J Corver
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - H Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - A Ingebretsen
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Department of Infection Prevention, Oslo University Hospital, Oslo, Norway
| | - M Pirmohamed
- Department of Molecular and Clinical Pharmacology, The University of Liverpool, Liverpool, UK
| | - A Faulds-Pain
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - E Valiente
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - T D Lawley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - E J Kuijper
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - B W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.
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33
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Reduced Clostridioides difficile infection in a pragmatic stepped-wedge initiative using admission surveillance to detect colonization. PLoS One 2020; 15:e0230475. [PMID: 32191763 PMCID: PMC7082001 DOI: 10.1371/journal.pone.0230475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/29/2020] [Indexed: 12/12/2022] Open
Abstract
Background Clostridioides difficile Infection (CDI) is a persistent healthcare issue. In the US, CDI is the most common infectious cause of hospital-onset (HO) diarrhea. Objective Assess the impact of admission testing for toxigenic C. difficile colonization on the incidence of HO-CDI. Design Pragmatic stepped-wedge Infection Control initiative. Setting NorthShore University HealthSystem is a four-hospital system near Chicago, IL. Patients All patients admitted to the four hospitals during the initiative. Interventions From September 2017 through August 2018 we conducted a quality improvement program where admitted patients had a peri-rectal swab tested for toxigenic C. difficile. All colonized patients were placed into contact precautions. Measurements We tested admissions who: i) had been hospitalized within two months, ii) had a past C. difficile positive test, and/or iii) were in a long-term care facility within six months. We measured compliance with all other practices to reduce the incidence of HO-CDI. Results 30% of admissions were tested and 8.3% were positive. In the year prior to the initiative (Period 1) there were 63,057 admitted patients when HO-CDI incidence was 5.96 cases/10,000 patient days. During the 12-month initiative (Period 2) there were 62,760 admissions and the HO-CDI incidence was 4.23 cases/10,000 patient days (p = 0.02). There were no other practice or antibiotic use changes. Continuing admission surveillance provided a HO-CDI incidence of 2.9 cases/10,000 patient days during the final 9 months of 2018 (p<0.0001 compared to Period 1), equaling <1 case/1,000 admissions. Limitations This was not a randomized controlled trial, and multiple prevention practices were in place at the time of the admission surveillance initiative. Conclusion Admission C. difficile surveillance testing is an important tool for preventing hospital-onset C. difficile infection. Registration This quality improvement initiative is registered at ClinicalTrials.gov. The unique registration identifier number is NCT04014608.
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34
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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35
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Mefferd CC, Bhute SS, Phan JR, Villarama JV, Do DM, Alarcia S, Abel-Santos E, Hedlund BP. A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides ( Clostridium) difficile Infection in Mice, whereas a High-Carbohydrate Diet Protects. mSystems 2020; 5:e00765-19. [PMID: 32047064 PMCID: PMC7018531 DOI: 10.1128/msystems.00765-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection (CDI) can result from the disruption of the resident gut microbiota. Western diets and popular weight-loss diets drive large changes in the gut microbiome; however, the literature is conflicted with regard to the effect of diet on CDI. Using the hypervirulent strain C. difficile R20291 (RT027) in a mouse model of antibiotic-induced CDI, we assessed disease outcome and microbial community dynamics in mice fed two high-fat diets in comparison with a high-carbohydrate diet and a standard rodent diet. The two high-fat diets exacerbated CDI, with a high-fat/high-protein, Atkins-like diet leading to severe CDI and 100% mortality and a high-fat/low-protein, medium-chain-triglyceride (MCT)-like diet inducing highly variable CDI outcomes. In contrast, mice fed a high-carbohydrate diet were protected from CDI, despite the high levels of refined carbohydrate and low levels of fiber in the diet. A total of 28 members of the Lachnospiraceae and Ruminococcaceae decreased in abundance due to diet and/or antibiotic treatment; these organisms may compete with C. difficile for amino acids and protect healthy animals from CDI in the absence of antibiotics. Together, these data suggest that antibiotic treatment might lead to loss of C. difficile competitors and create a favorable environment for C. difficile proliferation and virulence with effects that are intensified by high-fat/high-protein diets; in contrast, high-carbohydrate diets might be protective regardless of the source of carbohydrate or of antibiotic-driven loss of C. difficile competitors.IMPORTANCE The role of Western and weight-loss diets with extreme macronutrient composition in the risk and progression of CDI is poorly understood. In a longitudinal study, we showed that a high-fat/high-protein, Atkins-type diet greatly exacerbated antibiotic-induced CDI, whereas a high-carbohydrate diet protected, despite the high monosaccharide and starch content. Our study results, therefore, suggest that popular high-fat/high-protein weight-loss diets may enhance CDI risk during antibiotic treatment, possibly due to the synergistic effects of a loss of the microorganisms that normally inhibit C. difficile overgrowth and an abundance of amino acids that promote C. difficile overgrowth. In contrast, a high-carbohydrate diet might be protective, despite reports on the recent evolution of enhanced carbohydrate metabolism in C. difficile.
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Affiliation(s)
| | - Shrikant S Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacqueline R Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacob V Villarama
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Dung M Do
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Stephanie Alarcia
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
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