1
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Osbelt L, Almási ÉDH, Wende M, Kienesberger S, Voltz A, Lesker TR, Muthukumarasamy U, Knischewski N, Nordmann E, Bielecka AA, Giralt-Zúñiga M, Kaganovitch E, Kühne C, Baier C, Pietsch M, Müsken M, Greweling-Pils MC, Breinbauer R, Flieger A, Schlüter D, Müller R, Erhardt M, Zechner EL, Strowig T. Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms. Nat Microbiol 2024; 9:1792-1811. [PMID: 38862602 PMCID: PMC11222139 DOI: 10.1038/s41564-024-01710-0] [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: 06/06/2023] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
The Klebsiella oxytoca species complex is part of the human microbiome, especially during infancy and childhood. K. oxytoca species complex strains can produce enterotoxins, namely, tilimycin and tilivalline, while also contributing to colonization resistance (CR). The relationship between these seemingly contradictory roles is not well understood. Here, by coupling ex vivo assays with CRISPR-mutagenesis and various mouse models, we show that K. oxytoca provides CR against Salmonella Typhimurium. In vitro, the antimicrobial activity against various Salmonella strains depended on tilimycin production and was induced by various simple carbohydrates. In vivo, CR against Salmonella depended on toxin production in germ-free mice, while it was largely toxin-independent in mice with residual microbiota. This was linked to the relative levels of toxin-inducing carbohydrates in vivo. Finally, dulcitol utilization was essential for toxin-independent CR in gnotobiotic mice. Together, this demonstrates that nutrient availability is key to both toxin-dependent and substrate-driven competition between K. oxytoca and Salmonella.
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Affiliation(s)
- Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Éva D H Almási
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Alexander Voltz
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Nele Knischewski
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Elke Nordmann
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Agata A Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - María Giralt-Zúñiga
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eugen Kaganovitch
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Kühne
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claas Baier
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Pietsch
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Rolf Breinbauer
- BioTechMed-Graz, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Schlüter
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Marc Erhardt
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany.
- Center for Individualized Infection Medicine, Hannover, Germany.
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2
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Dabernig-Heinz J, Wagner GE, Prior K, Lipp M, Kienesberger S, Ruppitsch W, Rønning TG, Harmsen D, Steinmetz I, Leitner E. Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex. J Clin Microbiol 2024; 62:e0172523. [PMID: 38780286 PMCID: PMC11237601 DOI: 10.1128/jcm.01725-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.
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Affiliation(s)
- Johanna Dabernig-Heinz
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gabriel E Wagner
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Karola Prior
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Michaela Lipp
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Torunn G Rønning
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dag Harmsen
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Ivo Steinmetz
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
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3
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Almási ÉDH, Knischewski N, Osbelt L, Muthukumarasamy U, El Mouali Y, Vialetto E, Beisel CL, Strowig T. An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between Klebsiella species. J Bacteriol 2024; 206:e0031723. [PMID: 38353529 PMCID: PMC10955844 DOI: 10.1128/jb.00317-23] [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: 09/27/2023] [Accepted: 01/26/2024] [Indexed: 03/22/2024] Open
Abstract
Cas9-based gene editing tools have revolutionized genetics, enabling the fast and precise manipulation of diverse bacterial species. However, widely applicable genetic tools for non-model gut bacteria are unavailable. Here, we present a two-plasmid Cas9-based system designed for gene deletion and knock-in complementation in three members of the Klebsiella oxytoca species complex (KoSC), which we applied to study the genetic factors underlying the role of these bacteria in competition against Klebsiella pneumoniae. Firstly, the system allowed efficient and precise full-length gene deletion via enhanced lambda Red expression. Furthermore, we tested the efficiency of two independent, functionally validated complementation strategies. Ultimately, the insertion of universal "bookmark" targets during gene deletion subsequently allows the most optimal genetic complementation in K. oxytoca, Klebsiella michiganensis, and Klebsiella grimontii. This approach offers a significant advantage by enabling the use of a single high-efficiency "bookmark" for complementing other loci or strains, eliminating the need for site-specific design. We revealed that the carbohydrate permease CasA is critical in ex vivo assays for K. pneumoniae inhibition by K. oxytoca but is neither sufficient nor required for K. michiganensis and K. grimontii. Thus, the adaptation of state-of-the-art genetic tools to KoSC allows the identification of species-specific functions in microbial competition. IMPORTANCE Cas9-based gene editing tools have revolutionized bacterial genetics, yet, their application to non-model gut bacteria is frequently hampered by various limitations. We utilized a two-plasmid Cas9-based system designed for gene deletion in Klebsiella pneumoniae and demonstrate after optimization its utility for gene editing in three members of the Klebsiella oxytoca species complex (KoSC) namely K. oxytoca, Klebsiella michiganensis, and Klebsiella grimontii. We then adapted a recently developed protocol for functional complementation based on universal "bookmark" targets applicable to all tested species. In summary, species-specific adaptation of state-of-the-art genetic tools allows efficient gene deletion and complementation in type strains as well as natural isolates of KoSC members to study microbial interactions.
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Affiliation(s)
- Éva d. H. Almási
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Nele Knischewski
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Lisa Osbelt
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | - Youssef El Mouali
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L. Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Center for Individualized Infection Medicine, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
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4
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Elmassry MM, Sugihara K, Chankhamjon P, Camacho FR, Wang S, Sugimoto Y, Chatterjee S, Chen LA, Kamada N, Donia MS. A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579278. [PMID: 38370680 PMCID: PMC10871352 DOI: 10.1101/2024.02.07.579278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.
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Affiliation(s)
- Moamen M Elmassry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | | | - Francine R Camacho
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA
| | - Shuo Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
| | - Yuki Sugimoto
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Seema Chatterjee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Lea Ann Chen
- Department of Medicine, Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, 08901, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
- Lead Contact
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5
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Granger MF, Kelly M, Fortier LC, Fournier E, Côté-Gravel J, Malouin F, Valiquette L, Lévesque S. Chronic Diarrhea Caused by a Klebsiella oxytoca Toxin Producer Strain Following Antibiotic-Associated Hemorrhagic Colitis: Successful Treatment by Fecal Microbiota Transplant. Clin Infect Dis 2023; 77:1700-1703. [PMID: 37477511 DOI: 10.1093/cid/ciad436] [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: 05/03/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023] Open
Abstract
Klebsiella oxytoca is a gram-negative bacterium found in fecal microbiota and known to cause several infections in humans, including antibiotic-associated hemorrhagic colitis. We present here a case of colitis caused by K. oxytoca toxin-producing strains that evolved in chronic diarrhea successfully treated by fecal microbiota transplant.
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Affiliation(s)
- Marie-Félixe Granger
- Service de Microbiologie, CIUSSS de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mirabelle Kelly
- Service de Microbiologie, CIUSSS de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Louis-Charles Fortier
- Département de Microbiologie et Infectiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Julie Côté-Gravel
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - François Malouin
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Louis Valiquette
- Service de Microbiologie, CIUSSS de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Microbiologie et Infectiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Simon Lévesque
- Service de Microbiologie, CIUSSS de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Microbiologie et Infectiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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6
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Shu LZ, Ding YD, Xue QM, Cai W, Deng H. Direct and indirect effects of pathogenic bacteria on the integrity of intestinal barrier. Therap Adv Gastroenterol 2023; 16:17562848231176427. [PMID: 37274298 PMCID: PMC10233627 DOI: 10.1177/17562848231176427] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/01/2023] [Indexed: 06/06/2023] Open
Abstract
Bacterial translocation is a pathological process involving migration of pathogenic bacteria across the intestinal barrier to enter the systemic circulation and gain access to distant organs. This phenomenon has been linked to a diverse range of diseases including inflammatory bowel disease, pancreatitis, and cancer. The intestinal barrier is an innate structure that maintains intestinal homeostasis. Pathogenic infections and dysbiosis can disrupt the integrity of the intestinal barrier, increasing its permeability, and thereby facilitating pathogen translocation. As translocation represents an essential step in pathogenesis, a clear understanding of how barrier integrity is disrupted and how this disruption facilitates bacterial translocation could identify new routes to effective prophylaxis and therapy. In this comprehensive review, we provide an in-depth analysis of bacterial translocation and intestinal barrier function. We discuss currently understood mechanisms of bacterial-enterocyte interactions, with a focus on tight junctions and endocytosis. We also discuss the emerging concept of bidirectional communication between the intestinal microbiota and other body systems. The intestinal tract has established 'axes' with various organs. Among our regulatory systems, the nervous, immune, and endocrine systems have been shown to play pivotal roles in barrier regulation. A mechanistic understanding of intestinal barrier regulation is crucial for the development of personalized management strategies for patients with bacterial translocation-related disorders. Advancing our knowledge of barrier regulation will pave the way for future research in this field and novel clinical intervention strategies.
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Affiliation(s)
- Lin-Zhen Shu
- Medical College, Nanchang University, Nanchang,
Jiangxi Province, China
| | - Yi-Dan Ding
- Medical College, Nanchang University, Nanchang,
Jiangxi Province, China
| | - Qing-Ming Xue
- Medical College, Nanchang University, Nanchang,
Jiangxi Province, China
| | - Wei Cai
- Medical College, Nanchang University, Nanchang,
Jiangxi Province, China
- Department of Pathology, the Fourth Affiliated
Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Huan Deng
- Department of Pathology, The Fourth Affiliated
Hospital of Nanchang University, No. 133 South Guangchang Road, Nanchang
330003, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang
University, Nanchang, China
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7
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Coleman S, Unterhauser K, Rezaul K, Ledala N, Lesmes S, Caimano MJ, Zhou Y, Jackson E, Gratalo D, Driscoll MD, Matson AP. High-resolution microbiome analysis reveals exclusionary Klebsiella species competition in preterm infants at risk for necrotizing enterocolitis. Sci Rep 2023; 13:7893. [PMID: 37193703 DOI: 10.1038/s41598-023-34735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023] Open
Abstract
Intestinal colonization with Klebsiella has been linked to necrotizing enterocolitis (NEC), but methods of analysis usually failed to discriminate Klebsiella species or strains. A novel ~ 2500-base amplicon (StrainID) that spans the 16S and 23S rRNA genes was used to generate amplicon sequence variant (ASV) fingerprints for Klebsiella oxytoca and Klebsiella pneumoniae species complexes (KoSC and KpSC, respectively) and co-occurring fecal bacterial strains from 10 preterm infants with NEC and 20 matched controls. Complementary approaches were used to identify cytotoxin-producing isolates of KoSC. Klebsiella species colonized most preterm infants, were more prevalent in NEC subjects versus controls, and replaced Escherichia in NEC subjects. Single KoSC or KpSC ASV fingerprinted strains dominated the gut microbiota, suggesting exclusionary Klebsiella competition for luminal resources. Enterococcus faecalis was co-dominant with KoSC but present infrequently with KpSC. Cytotoxin-producing KoSC members were identified in most NEC subjects and were less frequent in controls. Few Klebsiella strains were shared between subjects. We conclude that inter-species Klebsiella competition, within an environment of KoSC and E. faecalis cooperation, appears to be an important factor for the development of NEC. Preterm infants seem to acquire Klebsiella primarily through routes other than patient-to-patient transmission.
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Affiliation(s)
- Spencer Coleman
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | | | - Karim Rezaul
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | | | - Stephanie Lesmes
- Department of Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Melissa J Caimano
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- Department of Medicine, UConn Health, Farmington, CT, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Adam P Matson
- Department of Pediatrics, UConn Health, Farmington, CT, USA.
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.
- Department of Immunology, UConn Health, Farmington, CT, USA.
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8
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Pöltl L, Kitsera M, Raffl S, Schild S, Cosic A, Kienesberger S, Unterhauser K, Raber G, Lembacher-Fadum C, Breinbauer R, Gorkiewicz G, Sebastian C, Hoefler G, Zechner EL. Microbiota-derived genotoxin tilimycin generates colonic stem cell mutations. Cell Rep 2023; 42:112199. [PMID: 36870054 DOI: 10.1016/j.celrep.2023.112199] [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: 04/28/2022] [Revised: 12/19/2022] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
The DNA-alkylating metabolite tilimycin is a microbial genotoxin. Intestinal accumulation of tilimycin in individuals carrying til+ Klebsiella spp. causes apoptotic erosion of the epithelium and colitis. Renewal of the intestinal lining and response to injury requires the activities of stem cells located at the base of intestinal crypts. This study interrogates the consequences of tilimycin-induced DNA damage to cycling stem cells. We charted the spatial distribution and luminal quantities of til metabolites in Klebsiella-colonized mice in the context of a complex microbial community. Loss of marker gene G6pd function indicates genetic aberrations in colorectal stem cells that became stabilized in monoclonal mutant crypts. Mice colonized with tilimycin-producing Klebsiella displayed both higher frequencies of somatic mutation and more mutations per affected individual than animals carrying a non-producing mutant. Our findings imply that genotoxic til+ Klebsiella may drive somatic genetic change in the colon and increase disease susceptibility in human hosts.
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Affiliation(s)
- Lisa Pöltl
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Maksym Kitsera
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Stefan Schild
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Amar Cosic
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Katrin Unterhauser
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Georg Raber
- Institute of Chemistry, University of Graz, 8010 Graz, Austria
| | | | - Rolf Breinbauer
- BioTechMed-Graz, 8010 Graz, Austria; Institute of Organic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Gregor Gorkiewicz
- BioTechMed-Graz, 8010 Graz, Austria; Diagnostic and Research Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Carlos Sebastian
- Candiolo Cancer Institute-FPO, IRCCS, 10060 Candiolo, Italy; Departament de Biologia Cellular, Fisiologia i Immunologia, Facultad de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria.
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9
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Complete Genome Sequence of Klebsiella oxytoca Strain AHC-6, Isolated from a Patient during Acute Antibiotic-Associated Hemorrhagic Colitis. Microbiol Resour Announc 2023; 12:e0135022. [PMID: 36926996 PMCID: PMC10112055 DOI: 10.1128/mra.01350-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Klebsiella oxytoca is a ubiquitous bacterium that is increasingly associated with inflammatory diseases. Here, we report the hybrid assembled genome for cytotoxic K. oxytoca strain AHC-6. The genome comprises a total of 5.7 Mbp, with a GC content of 55.2% and 5,258 coding sequences after assembly and annotation.
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10
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Sharma S, Hegde P, Panda S, Orimoloye MO, Aldrich CC. Drugging the microbiome: targeting small microbiome molecules. Curr Opin Microbiol 2023; 71:102234. [PMID: 36399893 DOI: 10.1016/j.mib.2022.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
The human microbiome represents a large and diverse collection of microbes that plays an integral role in human physiology and pathophysiology through interactions with the host and within the microbial community. While early work exploring links between microbiome signatures and diseases states has been associative, emerging evidence demonstrates the metabolic products of the human microbiome have more proximal causal effects on disease phenotypes. The therapeutic implications of this shift are profound as manipulation of the microbiome by the administration of live biotherapeutics, ongoing, can now be pursued alongside research efforts toward describing inhibitors of key microbiome enzymes involved in the biosynthesis of metabolites implicated in various disease states and processing of host-derived metabolites. With growing interest in 'drugging the microbiome', we review few notable microbial metabolites for which traditional drug-development campaigns have yielded compounds with therapeutic promise.
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Affiliation(s)
- Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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11
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Hussain A, Patwekar U, Mongad DS, Shouche YS. Strategizing the human microbiome for small molecules: Approaches and perspectives. Drug Discov Today 2023; 28:103459. [PMID: 36435302 DOI: 10.1016/j.drudis.2022.103459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/03/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022]
Abstract
Studies of the human microbiome are providing a deeper understanding of its significance to human health, and increasing evidence links the microbiota with several diseases. Nevertheless, the exact mechanisms involved in human-microbe interactions are mostly undefined. The genomic potential of the human microbiome to biosynthesize distinct molecules outmatches its known chemical space, and small-molecule discovery in this context remains in its infancy. The profiling of microbiome-derived small molecules and their contextualization through cause-effect mechanistic studies may provide a better understanding of host-microbe interactions, guide new therapeutic interventions, and modulate microbiome-based therapies. This review describes the advances, approaches, and allied challenges in mining new microbial scaffolds from the human microbiome using genomic, microbe cultivation, and chemical analytic platforms. In the future, the complete biological characterization of a single microbe-derived molecule that has a specific therapeutic application could resolve the current limitations of microbiota-modulating therapies.
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Affiliation(s)
- Aehtesham Hussain
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India.
| | - Umera Patwekar
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Dattatray S Mongad
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Yogesh S Shouche
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
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12
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Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice. Nat Microbiol 2022; 7:1834-1848. [PMID: 36289400 PMCID: PMC9613472 DOI: 10.1038/s41564-022-01260-3] [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: 03/27/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022]
Abstract
Klebsiella spp. that secrete the DNA-alkylating enterotoxin tilimycin colonize the human intestinal tract. Numbers of toxigenic bacteria increase during antibiotic use, and the resulting accumulation of tilimycin in the intestinal lumen damages the epithelium via genetic instability and apoptosis. Here we examine the impact of this genotoxin on the gut ecosystem. 16S rRNA sequencing of faecal samples from mice colonized with Klebsiella oxytoca strains and mechanistic analyses show that tilimycin is a pro-mutagenic antibiotic affecting multiple phyla. Transient synthesis of tilimycin in the murine gut antagonized niche competitors, reduced microbial richness and altered taxonomic composition of the microbiota both during and following exposure. Moreover, tilimycin secretion increased rates of mutagenesis in co-resident opportunistic pathogens such as Klebsiella pneumoniae and Escherichia coli, as shown by de novo acquisition of antibiotic resistance. We conclude that tilimycin is a bacterial mutagen, and flares of genotoxic Klebsiella have the potential to drive the emergence of resistance, destabilize the gut microbiota and shape its evolutionary trajectory. Production of the enterotoxin tilimycin by gut-resident Klebsiella species can alter gut microbiota composition, induce mutational evolution and drive the emergence of antibiotic resistance in mice.
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13
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Cao Y, Oh J, Xue M, Martin AL, Song D, Crawford JM, Herzon SB, Palm NW. Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites. Science 2022; 378:eabm3233. [PMID: 36302024 PMCID: PMC9993714 DOI: 10.1126/science.abm3233] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microbiota-derived metabolites that elicit DNA damage can contribute to colorectal cancer (CRC). However, the full spectrum of genotoxic chemicals produced by indigenous gut microbes remains to be defined. We established a pipeline to systematically evaluate the genotoxicity of an extensive collection of gut commensals from inflammatory bowel disease patients. We identified isolates from divergent phylogenies whose metabolites caused DNA damage and discovered a distinctive family of genotoxins-termed the indolimines-produced by the CRC-associated species Morganella morganii. A non-indolimine-producing M. morganii mutant lacked genotoxicity and failed to exacerbate colon tumorigenesis in mice. These studies reveal the existence of a previously unexplored universe of genotoxic small molecules from the microbiome that may affect host biology in homeostasis and disease.
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Affiliation(s)
- Yiyun Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Mengzhao Xue
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Anjelica L. Martin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
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14
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Sun H, Zhao F, Liu Y, Ma T, Jin H, Quan K, Leng B, Zhao J, Yuan X, Li Z, Li F, Kwok LY, Zhang S, Sun Z, Zhang J, Zhang H. Probiotics synergized with conventional regimen in managing Parkinson's disease. NPJ Parkinsons Dis 2022; 8:62. [PMID: 35610236 PMCID: PMC9130297 DOI: 10.1038/s41531-022-00327-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is mainly managed by pharmacological therapy (e.g., Benserazide and dopamine agonists). However, prolonged use of these drugs would gradually diminish their dopaminergic effect. Gut dysbiosis was observed in some patients with PD, suggesting close association between the gut microbiome and PD. Probiotics modulate the host's gut microbiota beneficially. A 3-month randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the beneficial effect of probiotic co-administration in patients with PD. Eighty-two PD patients were recruited and randomly divided into probiotic [n = 48; Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8), Benserazide, dopamine agonists] and placebo (n = 34; placebo, Benserazide, dopamine agonists) groups. Finally, 45 and 29 patients from Probio-M8 and placebo groups provided complete fecal and serum samples for further omics analysis, respectively. The results showed that Probio-M8 co-administration conferred added benefits by improving sleep quality, alleviating anxiety, and gastrointestinal symptoms. Metagenomic analysis showed that, after the intervention, there were significantly more species-level genome bins (SGBs) of Bifidobacterium animalis, Ruminococcaceae, and Lachnospira, while less Lactobacillus fermentum and Klebsiella oxytoca in Probio-M8 group (P < 0.05). Interestingly, Lactobacillus fermentum correlated positively with the scores of UPDRS-III, HAMA, HAMD-17, and negatively with MMSE. Klebsiella oxytoca correlated negatively with feces hardness. Moreover, co-administering Probio-M8 increased SGBs involved in tryptophan degradation, gamma-aminobutyric acid, short-chain fatty acids, and secondary bile acid biosynthesis, as well as serum acetic acid and dopamine levels (P < 0.05). Taken together, Probio-M8 synergized with the conventional regimen and strengthened the clinical efficacy in managing PD, accompanied by modifications of the host's gut microbiome, gut microbial metabolic potential, and serum metabolites.
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Affiliation(s)
- Hairong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
- Department of neurology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China
| | - Feiyan Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yuanyuan Liu
- Department of neurology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China
| | - Teng Ma
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Keyu Quan
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Bing Leng
- Department of neurology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China
| | - Junwu Zhao
- Department of neurology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China
| | - Xiaoling Yuan
- Department of Neurology, Liaocheng People's Hospital and Liaocheng Clinical School of Taishan Medical University, Liaocheng, Shandong, 264200, China
| | - Zhenguang Li
- Department of neurology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China
| | - Fang Li
- Department of Neurology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, 121000, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Shukun Zhang
- Department of Pathology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Jinbiao Zhang
- Department of neurology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, 264200, China.
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
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15
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Leitner E, Bozic M, Kienesberger S, Cosic A, Landt O, Högenauer C, Kessler HH. Improved diagnosis of antibiotic-associated haemorrhagic colitis (AAHC) in faecal specimens by a new qualitative real-time PCR assay detecting relevant toxin genes of Klebsiella oxytoca sensu lato. Clin Microbiol Infect 2022; 28:690-694. [PMID: 34582979 DOI: 10.1016/j.cmi.2021.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/27/2021] [Accepted: 09/15/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for the detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated. METHODS DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. In total, 130 residual faecal specimens collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method. RESULTS With the new kit, the limit of detection was 15 CFU/mL for all targets. For the pehX target specific to K. oxytoca s.l., 65 of 130 clinical specimens were positive, while toxin-specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95%CI 80.5-100%) and a specificity of 73.5% (95%CI 64.3-81.3%) with a positive predictive value of 16.5% (95%CI 12.7-21.2%) and a negative predictive value of 100%. CONCLUSION Compared with culture, additional clinical specimens positive for K. oxytoca s.l. were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve the diagnosis of AAHC.
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Affiliation(s)
- Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria.
| | - Michael Bozic
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria; Field of Excellence BioHealth, University of Graz, Austria
| | - Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | - Christoph Högenauer
- BioTechMed-Graz, Austria; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Harald H Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
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16
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Synthesis of polycyclic 3,3′-spirooxindoles and some new 2-arylquinoxalines from (E/Z)- 1-(2-oxo-2-arylethylidene)-5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-2(1H)-ones. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Abstract
Gastrointestinal microbes respond to biochemical metabolites that coordinate their behaviors. Here, we demonstrate that bacterial indole functions as a multifactorial mitigator of Klebsiella grimontii and Klebsiella oxytoca pathogenicity. These closely related microbes produce the enterotoxins tilimycin and tilivalline; cytotoxin-producing strains are the causative agent of antibiotic-associated hemorrhagic colitis and have been associated with necrotizing enterocolitis of premature infants. We demonstrate that carbohydrates induce cytotoxin synthesis while concurrently repressing indole biosynthesis. Conversely, indole represses cytotoxin production. In both cases, the alterations stemmed from differential transcription of npsA and npsB, key genes involved in tilimycin biosynthesis. Indole also enhances conversion of tilimycin to tilivalline, an indole analog with reduced cytotoxicity. In this context, we established that tilivalline, but not tilimycin, is a strong agonist of pregnane X receptor (PXR), a master regulator of xenobiotic detoxification and intestinal inflammation. Tilivalline binding upregulated PXR-responsive detoxifying genes and inhibited tubulin-directed toxicity. Bacterial indole, therefore, acts in a multifunctional manner to mitigate cytotoxicity by Klebsiella spp.: suppression of toxin production, enhanced conversion of tilimycin to tilivalline, and activation of PXR. IMPORTANCE The human gut harbors a complex community of microbes, including several species and strains that could be commensals or pathogens depending on context. The specific environmental conditions under which a resident microbe changes its relationship with a host and adopts pathogenic behaviors, in many cases, remain poorly understood. Here, we describe a novel communication network involving the regulation of K. grimontii and K. oxytoca enterotoxicity. Bacterial indole was identified as a central modulator of these colitogenic microbes by suppressing bacterial toxin (tilimycin) synthesis and converting tilimycin to tilivalline while simultaneously activating a host receptor, PXR, as a means of mitigating tissue cytotoxicity. On the other hand, fermentable carbohydrates were found to inhibit indole biosynthesis and enhance toxin production. This integrated network involving microbial, host, and metabolic factors provides a contextual framework to better understand K. oxytoca complex pathogenicity.
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18
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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19
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Chandra H, Sharma KK, Tuovinen OH, Sun X, Shukla P. Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile. Gut Microbes 2022; 13:1979882. [PMID: 34724858 PMCID: PMC8565823 DOI: 10.1080/19490976.2021.1979882] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion. Their proliferations can aggravate inflammatory manifestations, trigger autoimmune diseases, and lead to severe life-threatening conditions. Current surge in microbiome research is unwinding these complex interplays between disease development and protection against pathobionts. This review summarizes the current knowledge of pathobiont emergence with a focus on Clostridioides difficile and the recent findings on the roles of immune cells such as iTreg cells, Th17 cells, innate lymphoid cells, and cytokines in protection against pathobionts. The review calls for adoption of innovative tools and cutting-edge technologies in clinical diagnostics and therapeutics to provide insights in identification and quantification of pathobionts.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India,Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA,Xingmin Sun Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India,CONTACT Pratyoosh Shukla School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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20
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Greimel TM, Stampfer L, Leitner E, Kienesberger S, Zechner EL, Bozic M, Wagner GE, Unterhauser K, Kitsera M, Hauer AC, Gorkiewicz G, Wurm P, Valitutti F, Högenauer C, Hoffmann KM. Toxin-Producing Klebsiella oxytoca in Healthy Infants: Commensal or Pathobiont? J Pediatr Gastroenterol Nutr 2022; 74:e1-e7. [PMID: 34520403 DOI: 10.1097/mpg.0000000000003299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Klebsiella oxytoca is a gastrointestinal pathobiont with the potential to produce the toxins tilivalline and tilimycin, which cause antibiotic-associated hemorrhagic colitis. Overgrowth of toxigenic K oxytoca has recently been implicated in necrotizing enterocolitis. K oxytoca colonizes 2-9% of healthy adults, however, there is no systematic data on colonization in healthy children. We investigated K oxytoca colonization and its toxigenic properties in healthy infants. METHODS We sampled stool of healthy infants and determined K oxytoca colonization using stool culture and PCR (pehX). Toxin in stool was measured with HPLC/high-resolution mass spectrometry. K oxytoca isolates were typed using multi-locus sequence typing (MLST) and K oxytoca toxin PCR (npsA/B). Cytotoxin production of isolates was analyzed by MTT assay. RESULTS K oxytoca was detected in 30 of 61 infants (49%) using stool culture and in 45 of 61 (73%) using PCR (pehX). Toxin marker PCR (npsA/B) was positive in 66% of stool samples positive for K oxytoca PCR. Stool toxin levels were too low for quantitation but traces of tilivalline were detected. Contrarily, 49% of K oxytoca isolates demonstrated toxicity in the MTT assay. MLST revealed 36 distinct sequence types affiliated with all known K oxytoca sequence type clusters (A, B1 and B2). CONCLUSIONS More than 70% of healthy infants were colonized with K oxytoca. Toxin quantities in stool of colonized healthy infants were below detection level, yet half of the isolates produced toxin in vitro demonstrating their pathobiont potential. The high occurrence of toxigenic K oxytoca in healthy infants has to be considered for future disease association studies.
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Affiliation(s)
- Theresa M Greimel
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Laura Stampfer
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz
- BioTechMed-Graz
- Field of Excellence BioHealth - University of Graz, Graz
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz
- BioTechMed-Graz
- Field of Excellence BioHealth - University of Graz, Graz
| | - Michael Bozic
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | - Gabriel E Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | | | | | - Almuthe C Hauer
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, Austria
- BioTechMed-Graz
| | - Philipp Wurm
- Institute of Pathology, Medical University of Graz, Austria
| | | | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz
- BioTechMed-Graz
| | - Karl Martin Hoffmann
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
- Kinderärzte Zentrum Graz-Raaba, Raaba-Grambach, Austria
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21
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Next-generation microbial drugs developed from microbiome's natural products. ADVANCES IN GENETICS 2021; 108:341-382. [PMID: 34844715 DOI: 10.1016/bs.adgen.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Scientists working in natural products chemistry have been enticed by the current advancements being made in the discovery of novel "magic bullets" from microbes homed to all conceivable environments. Even though researchers continue to face challenges funneling the novel bioactive compounds in the global therapeutic industries, it seems most likely that the discovery of some "hit molecules" with significant biomedical applications is not that far. We applaud novel natural products for their ability to combat the spread of superbugs and aid in the prevention of currently observed antibiotic resistance. This in-depth investigation covers a wide range of microbiomes with a proclivity for synthesizing novel compounds to combat the spread of superbugs. Furthermore, we use this opportunity to explore various groups of secondary metabolites and their biosynthetic pathways in various microbiota found in mammals, insects, and humans. This systematic study, when taken as a whole, offers detail understanding on the biomedical fate of various groups of compounds originated from diverse microbiomes. For gathering all information that has been uncovered and released so far, we have also presented the huge diversity of microbes that are associated with humans and their metabolic products. To conclude, this concrete review suggests novel ideas that will prove immensely helpful in reducing the danger posed by superbugs while also improving the efficacy of antibiotics.
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22
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Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence. Clin Microbiol Rev 2021; 35:e0000621. [PMID: 34851134 DOI: 10.1128/cmr.00006-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic blaOXY, many genes encoding β-lactamases with varying spectra of hydrolysis, including extended-spectrum β-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. blaKPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.
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Rodríguez-Valverde D, León-Montes N, Soria-Bustos J, Martínez-Cruz J, González-Ugalde R, Rivera-Gutiérrez S, González-y-Merchand JA, Rosales-Reyes R, García-Morales L, Hirakawa H, Fox JG, Girón JA, De la Cruz MA, Ares MA. cAMP Receptor Protein Positively Regulates the Expression of Genes Involved in the Biosynthesis of Klebsiella oxytoca Tilivalline Cytotoxin. Front Microbiol 2021; 12:743594. [PMID: 34659176 PMCID: PMC8515920 DOI: 10.3389/fmicb.2021.743594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 01/09/2023] Open
Abstract
Klebsiella oxytoca is a resident of the human gut. However, certain K. oxytoca toxigenic strains exist that secrete the nonribosomal peptide tilivalline (TV) cytotoxin. TV is a pyrrolobenzodiazepine that causes antibiotic-associated hemorrhagic colitis (AAHC). The biosynthesis of TV is driven by enzymes encoded by the aroX and NRPS operons. In this study, we determined the effect of environmental signals such as carbon sources, osmolarity, and divalent cations on the transcription of both TV biosynthetic operons. Gene expression was enhanced when bacteria were cultivated in tryptone lactose broth. Glucose, high osmolarity, and depletion of calcium and magnesium diminished gene expression, whereas glycerol increased transcription of both TV biosynthetic operons. The cAMP receptor protein (CRP) is a major transcriptional regulator in bacteria that plays a key role in metabolic regulation. To investigate the role of CRP on the cytotoxicity of K. oxytoca, we compared levels of expression of TV biosynthetic operons and synthesis of TV in wild-type strain MIT 09-7231 and a Δcrp isogenic mutant. In summary, we found that CRP directly activates the transcription of the aroX and NRPS operons and that the absence of CRP reduced cytotoxicity of K. oxytoca on HeLa cells, due to a significant reduction in TV production. This study highlights the importance of the CRP protein in the regulation of virulence genes in enteric bacteria and broadens our knowledge on the regulatory mechanisms of the TV cytotoxin.
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Affiliation(s)
- Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Nancy León-Montes
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jessica Martínez-Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ricardo González-Ugalde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A. González-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lázaro García-Morales
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jorge A. Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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24
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Bianco C, Andreozzi A, Romano S, Fagorzi C, Cangioli L, Prieto P, Cisse F, Niangado O, Sidibé A, Pianezze S, Perini M, Mengoni A, Defez R. Endophytes from African Rice ( Oryza glaberrima L.) Efficiently Colonize Asian Rice ( Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll. Microorganisms 2021; 9:microorganisms9081714. [PMID: 34442793 PMCID: PMC8398951 DOI: 10.3390/microorganisms9081714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Bacterial endophytes support the adaptation of host plants to harsh environments. In this study, culturable bacterial endophytes were isolated from the African rice Oryza glaberrima L., which is well-adapted to grow with poor external inputs in the tropical region of Mali. Among these, six N-fixer strains were used to inoculate O. glaberrima RAM133 and the Asian rice O. sativa L. cv. Baldo, selected for growth in temperate climates. The colonization efficiency and the N-fixing activity were evaluated and compared for the two rice varieties. Oryza sativa-inoculated plants showed a fairly good colonization efficiency and nitrogenase activity. The inoculation of Oryza sativa with the strains Klebsiella pasteurii BDA134-6 and Phytobacter diazotrophicus BDA59-3 led to the highest nitrogenase activity. In addition, the inoculation of ‘Baldo’ plants with the strain P. diazotrophicus BDA59-3 led to a significant increase in nitrogen, carbon and chlorophyll content. Finally, ‘Baldo’ plants inoculated with Kl. pasteurii BDA134-6 showed the induction of antioxidant enzymes activity and the maintenance of nitrogen-fixation under salt stress as compared to the unstressed controls. As these endophytes efficiently colonize high-yielding crop varieties grown in cold temperate climates, they become good candidates to promote their growth under unfavorable conditions.
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Affiliation(s)
- Carmen Bianco
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
- Correspondence: ; Tel.: +39-081-613-2610
| | - Anna Andreozzi
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
| | - Silvia Romano
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Lisa Cangioli
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Pilar Prieto
- Departamento de Mejora Genética, Campus ‘Alamedadel Obispo’, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain;
| | - Fousseyni Cisse
- Institut d’Economie Rurale, Rue Mohamed V Bamako, Bamako B.P. 258, Mali; (F.C.); (A.S.)
| | - Oumar Niangado
- Syngenta Foundation for Sustainable Agriculture, Bamako B.P.E. 1449, Mali;
| | - Amadou Sidibé
- Institut d’Economie Rurale, Rue Mohamed V Bamako, Bamako B.P. 258, Mali; (F.C.); (A.S.)
| | - Silvia Pianezze
- Fondazione Edmund Mach, Via Mach 1, 38098 San Michele All’Adige, Italy; (S.P.); (M.P.)
- Environmental and Animal Sciences DI4A, Università degli Studi di Udine, Via Sondrio 2/A, 33100 Udine, Italy
| | - Matteo Perini
- Fondazione Edmund Mach, Via Mach 1, 38098 San Michele All’Adige, Italy; (S.P.); (M.P.)
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy; (C.F.); (L.C.); (A.M.)
| | - Roberto Defez
- Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.R.); (R.D.)
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25
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The Role of DNA Damage Response in Dysbiosis-Induced Colorectal Cancer. Cells 2021; 10:cells10081934. [PMID: 34440703 PMCID: PMC8391204 DOI: 10.3390/cells10081934] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/16/2022] Open
Abstract
The high incidence of colorectal cancer (CRC) in developed countries indicates a predominant role of the environment as a causative factor. Natural gut microbiota provides multiple benefits to humans. Dysbiosis is characterized by an unbalanced microbiota and causes intestinal damage and inflammation. The latter is a common denominator in many cancers including CRC. Indeed, in an inflammation scenario, cellular growth is promoted and immune cells release Reactive Oxygen Species (ROS) and Reactive Nitrogen Species (RNS), which cause DNA damage. Apart from that, many metabolites from the diet are converted into DNA damaging agents by microbiota and some bacteria deliver DNA damaging toxins in dysbiosis conditions as well. The interactions between diet, microbiota, inflammation, and CRC are not the result of a straightforward relationship, but rather a network of multifactorial interactions that deserve deep consideration, as their consequences are not yet fully elucidated. In this paper, we will review the influence of dysbiosis in the induction of DNA damage and CRC.
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26
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Shibu P, McCuaig F, McCartney AL, Kujawska M, Hall LJ, Hoyles L. Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster. Microb Genom 2021; 7. [PMID: 34142942 PMCID: PMC8461473 DOI: 10.1099/mgen.0.000592] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
As part of the ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. blaOXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis. Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to distinguish members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii. The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four (K. oxytoca, K. pasteurii, K. grimontii, K. michiganensis) of the six species of complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.
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Affiliation(s)
- Preetha Shibu
- Life Sciences, University of Westminster, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Frazer McCuaig
- Department of Biosciences, Nottingham Trent University, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, UK
| | - Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,Chair of Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, UK.,Department of Surgery and Cancer, Imperial College London, UK
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27
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Healthcare associated diarrhea, not Clostridioides difficile. Curr Opin Infect Dis 2021; 33:319-326. [PMID: 32657969 DOI: 10.1097/qco.0000000000000653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE OF REVIEW The aim of this article is to review the epidemiology, cause, diagnostic evaluation, and management of healthcare-associated diarrhea (HCAD) with particular attention to current epidemiology and recent developments in diagnostics. RECENT FINDINGS Multiplex polymerase chain reaction gastrointestinal panels allow rapid detection of a wide array of potential enteropathogens but the role, yield, and utility of these tests have not been systematically assessed in patients with HCAD. Recent epidemiologic studies reaffirm that HCAD is predominantly a noninfectious condition most often caused by medications or underlying medical conditions, sometimes Clostridioides difficile, and occasionally viruses. Other infections are rare. SUMMARY Clinical assessment remains fundamental to the evaluation of HCAD and targeted testing for C. difficile is sufficient in most patients. Multiplex gastrointestinal panels may have a role in immunocompromised patients but more study is needed. Medication-induced diarrhea is common and underappreciated and not limited to antibiotics, laxatives, and enemas.
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28
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Zhu HC, Jia XK, Fan Y, Xu SH, Li XY, Huang MQ, Lan ML, Xu W, Wu SS. Alisol B 23-Acetate Ameliorates Azoxymethane/Dextran Sodium Sulfate-Induced Male Murine Colitis-Associated Colorectal Cancer via Modulating the Composition of Gut Microbiota and Improving Intestinal Barrier. Front Cell Infect Microbiol 2021; 11:640225. [PMID: 33996624 PMCID: PMC8117151 DOI: 10.3389/fcimb.2021.640225] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
Hunting for natural compounds that can modulate the structure of the intestinal flora is a new hotspot for colitis‐associated cancer (CAC) prevention or treatment. Alisol B 23-acetate (AB23A) is a natural tetracyclic triterpenoid found in Alismatis rhizoma which is well known for dietary herb. Alismatis rhizoma is often used clinically to treat gastrointestinal diseases in China. In this study, we investigated the potential prevention of AB23A in male mouse models of azoxymethane (AOM) and dextran sulfate sodium (DSS)-induced CAC. AB23A intervention alleviated the body weight loss, disease activity index, colon tumor load, tissue injury, and inflammatory cytokine changes in CAC mice. AB23A intervention leads to remarkable reductions in the activation of TLR, NF-κB and MAPK. AB23A significantly decreased the phosphorylation of p38, ERK, and JNK and up-regulated mucin-2 and the expression of tight junction proteins. The gut microbiota of AB23A-interfered mice was characterized with high microbial diversity, the reduced expansion of pathogenic bacteria, such as Klebsiella, Citrobacter, and Akkermansia, and the increased growth of bacteria including Bacteroides, Lactobacillus, and Alloprevotella. These data reveal that AB23A has the potential to be used to treat CAC in the future.
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Affiliation(s)
- Huai-Chang Zhu
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiao-Kang Jia
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yong Fan
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Shao-Hua Xu
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiao-Yan Li
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Ming-Qing Huang
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Meng-Liu Lan
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Wen Xu
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Shui-Sheng Wu
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Centre of Biomedical Research & Development, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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29
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Yuan S, Yue YL, Zhang DQ, Zhang JY, Yu B, Liu HM. Synthesis of new tetracyclic benzodiazepine-fused isoindolinones using recyclable mesoporous silica nanoparticles. Chem Commun (Camb) 2021; 56:11461-11464. [PMID: 32853306 DOI: 10.1039/d0cc04875e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pseudo natural products (NPs) feature structural novelty and diversity and thus are a new source of lead compounds for drug discovery. We first report the mesoporous silica nanoparticles (MSNs)-catalyzed de novo combination of benzodiazepine and isoindolinone, giving tetracyclic benzodiazepine-fused isoindolinone pseudo natural products (21 examples, 55-91% yields). The work also demonstrates that MSNs are efficient acidic catalysts for multi-component reactions.
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Affiliation(s)
- Shuo Yuan
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou 450001, China.
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30
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Sakaine G, Ture A, Pedroni J, Smits G. Isolation, chemistry, and biology of pyrrolo[1,4]benzodiazepine natural products. Med Res Rev 2021; 42:5-55. [PMID: 33846985 DOI: 10.1002/med.21803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 02/11/2021] [Accepted: 03/23/2021] [Indexed: 11/06/2022]
Abstract
The isolation of the antitumor antibiotic anthramycin in the 1960s prompted extensive research into pyrrolo[1,4]benzodiazepines (PBD) as potential therapeutics for the treatment of cancers. Since then, nearly 60 PBD natural products have been isolated and evaluated with regard to their biological activity. Synthetic studies and total syntheses have enabled access to PBD analogues, culminating in the development of highly potent anticancer agents. This review provides a summary of the occurrence and biological activity of PBD natural products and covers the strategies employed for their total syntheses.
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Affiliation(s)
- Guna Sakaine
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Julia Pedroni
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gints Smits
- Latvian Institute of Organic Synthesis, Riga, Latvia
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31
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Abstract
The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.
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Affiliation(s)
- Emilee E Shine
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Current affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason M Crawford
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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32
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Neog N, Phukan U, Puzari M, Sharma M, Chetia P. Klebsiella oxytoca and Emerging Nosocomial Infections. Curr Microbiol 2021; 78:1115-1123. [PMID: 33656584 DOI: 10.1007/s00284-021-02402-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 02/10/2021] [Indexed: 12/12/2022]
Abstract
Klebsiella oxytoca is rising as a significant opportunistic pathogen causing nosocomial infections in neonates as well as adults. This pathogen's prevalence varies from 2 to 24%, but outbreaks of infections due to multidrug-resistant strains can be fatal in immunocompromised individuals with comorbidities. Klebsiella oxytoca is responsible for a wide range of ailments from colitis to infective endocarditis, other than the common urinary and respiratory tract infections. The microbe's pathogenicity has been attributed to cytotoxins' production- Tilivalline and Tilimycin, in some intestinal disorders. Klebsiella oxytoca is reported to be resistant to a wide range of antibiotics. Here, we have tried to showcase a brief overview of the emergence of Klebsiella oxytoca in healthcare facilities and the nature of resistance in this species of Klebsiella.
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Affiliation(s)
- Nakul Neog
- Department of Life Sciences, Dibrugarh Univerity, Dibrugarh, Assam, 786004, India
| | - Upasana Phukan
- Department of Life Sciences, Dibrugarh Univerity, Dibrugarh, Assam, 786004, India
| | - Minakshi Puzari
- Department of Life Sciences, Dibrugarh Univerity, Dibrugarh, Assam, 786004, India
| | - Mohan Sharma
- Department of Life Sciences, Dibrugarh Univerity, Dibrugarh, Assam, 786004, India
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh Univerity, Dibrugarh, Assam, 786004, India.
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33
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Paveglio S, Ledala N, Rezaul K, Lin Q, Zhou Y, Provatas AA, Bennett E, Lindberg T, Caimano M, Matson AP. Cytotoxin-producing Klebsiella oxytoca in the preterm gut and its association with necrotizing enterocolitis. Emerg Microbes Infect 2021; 9:1321-1329. [PMID: 32525754 PMCID: PMC7473113 DOI: 10.1080/22221751.2020.1773743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Necrotizing enterocolitis (NEC) is a devastating intestinal inflammatory disease of premature infants associated with gut bacterial dysbiosis. Using 16S rRNA-based methods, our laboratory identified an unclassified Enterobacteriaceae sequence (NEC_unk_OTU) with high abundance in NEC fecal samples. We aimed to identify this bacterium and determine its potential role in the disease. NCBI database searches for the 16S sequence, selective culture systems, biotyping and polymerase chain reaction were employed to refine classification of NEC_unk_OTU and identify toxin-encoding genes from the index NEC case. Bacterial cytotoxin production was confirmed by mass spectrometry and apoptosis assays. Additional fecal samples from 9 NEC and 5 non-NEC controls were analyzed using similar methods and multi-locus sequence typing (MLST) was performed to investigate clonal relationships and define sequence types of the isolates. NEC_unk_OTU was identified as Klebsiella oxytoca, a pathobiont known to cause antibiotic-associated hemorrhagic colitis, but not previously linked to NEC. Including the index case, cytotoxin-producing strains of K. oxytoca were isolated from 6 of 10 subjects with NEC; in these, the K. oxytoca 16S sequence predominated the fecal microbiota. Cytotoxin-producing strains of K. oxytoca also were isolated from 4 of 5 controls; in these, however, the abundance of the corresponding 16S sequence was very low. MLST analysis of the toxin-positive isolates demonstrated no clonal relationships and similar genetic clustering between cases and controls. These results suggest cytotoxin-producing strains of K. oxytoca colonize a substantial proportion of premature infants. Some, perhaps many, cases of NEC may be precipitated by outgrowth of this opportunistic pathogen.
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Affiliation(s)
- Sara Paveglio
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.,Department of Pediatrics, UConn Health, Farmington, CT, USA
| | | | - Karim Rezaul
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | - Qingqi Lin
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, CT, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Anthony A Provatas
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, CT, USA
| | - Erin Bennett
- Department of Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Tristan Lindberg
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Melissa Caimano
- Department of Pediatrics, UConn Health, Farmington, CT, USA.,Department of Medicine, UConn Health, Farmington, CT, USA.,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Adam P Matson
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.,Department of Pediatrics, UConn Health, Farmington, CT, USA.,Department of Immunology, UConn Health, Farmington, CT, USA
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34
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Simultaneous quantification of enterotoxins tilimycin and tilivalline in biological matrices using HPLC high resolution ESMS 2 based on isotopically 15N-labeled internal standards. Talanta 2021; 222:121677. [PMID: 33167283 DOI: 10.1016/j.talanta.2020.121677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
Non-ribosomal peptides are one class of bacterial metabolites formed by gut microbiota. Intestinal resident Klebsiella oxytoca produces two pyrrolobenzodiazepines, tilivalline and tilimycin, via the same nonribosomal biosynthesis platform. These molecules cause human disease by genotoxic and tubulin inhibitory activities resulting in apoptosis of the intestinal epithelium, loss of barrier integrity and ultimately colitis. Here we report a fast, reliable, HPLC-HR-ESMS2 method for quantifying simultaneously the bacterial enterotoxins tilimycin and tilivalline in complex biological matrices. We synthesized and applied stable isotopically labeled internal standards for precise quantification of the metabolites. Sample preparation was optimized using clinical and laboratory specimens including serum, colonic fluid and stool. The developed method overcame the disadvantage of low selectivity by applying high resolution mass spectrometry in MS2 mode. High sensitivity and low interference from matrices were achieved and validated. We show that the approach is suitable for detection and quantification of the enterotoxic metabolites produced in vivo, in infected human or animal hosts, and in bacterial culture in vitro.
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35
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Cosic A, Leitner E, Petternel C, Galler H, Reinthaler FF, Herzog-Obereder KA, Tatscher E, Raffl S, Feierl G, Högenauer C, Zechner EL, Kienesberger S. Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping. Front Microbiol 2021; 12:692453. [PMID: 34276625 PMCID: PMC8283571 DOI: 10.3389/fmicb.2021.692453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/28/2021] [Indexed: 02/03/2023] Open
Abstract
Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (bla OXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting bla OXY and accessory genes defined here.
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Affiliation(s)
- Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christian Petternel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Herbert Galler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Franz F. Reinthaler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Kathrin A. Herzog-Obereder
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Elisabeth Tatscher
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Gebhard Feierl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- BioTechMed-Graz, Graz, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ellen L. Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- *Correspondence: Sabine Kienesberger,
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36
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Li J, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jhe‐Hao Li
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Joonseok Oh
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | | | - Nam Yoon Kim
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - David J. Clarke
- School of Microbiology and APC Microbiome Ireland University College Cork Cork Ireland
| | - Ellen L. Zechner
- Institute of Molecular Biosciences University of Graz 8010 Graz Austria
- BioTechMed-Graz 8010 Graz Austria
| | - Jason M. Crawford
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
- Department of Microbial Pathogenesis Yale University School of Medicine New Haven CT 06536 USA
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37
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Li JH, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl 2020; 59:17872-17880. [PMID: 32609431 DOI: 10.1002/anie.202005506] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/29/2020] [Indexed: 12/12/2022]
Abstract
Leupeptin is a bacterial small molecule that is used worldwide as a protease inhibitor. However, its biosynthesis and genetic distribution remain unknown. We identified a family of leupeptins in gammaproteobacterial pathogens, including Photorhabdus, Xenorhabdus, and Klebsiella species, amongst others. Through genetic, metabolomic, and heterologous expression analyses, we established their construction by discretely expressed ligases and accessory enzymes. In Photorhabdus species, a hypothetical protein required for colonizing nematode hosts was established as a new class of proteases. This enzyme cleaved the tripeptide aldehyde protease inhibitors, leading to the formation of "pro-pyrazinones" featuring a hetero-tricyclic architecture. In Klebsiella oxytoca, the pathway was enriched in clinical isolates associated with respiratory tract infections. Thus, the bacterial production and proteolytic degradation of leupeptins can be associated with animal colonization phenotypes.
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Affiliation(s)
- Jhe-Hao Li
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | | | - Nam Yoon Kim
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,BioTechMed-Graz, 8010, Graz, Austria
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
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38
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Alexander EM, Kreitler DF, Guidolin V, Hurben AK, Drake E, Villalta PW, Balbo S, Gulick AM, Aldrich CC. Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic Pathogen Klebsiella oxytoca. ACS Infect Dis 2020; 6:1976-1997. [PMID: 32485104 PMCID: PMC7354218 DOI: 10.1021/acsinfecdis.0c00326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tilimycin is an enterotoxin produced by the opportunistic pathogen Klebsiella oxytoca that causes antibiotic-associated hemorrhagic colitis (AAHC). This pyrrolobenzodiazepine (PBD) natural product is synthesized by a bimodular nonribosomal peptide synthetase (NRPS) pathway composed of three proteins: NpsA, ThdA, and NpsB. We describe the functional and structural characterization of the fully reconstituted NRPS system and report the steady-state kinetic analysis of all natural substrates and cofactors as well as the structural characterization of both NpsA and ThdA. The mechanism of action of tilimycin was confirmed using DNA adductomics techniques through the detection of putative N-2 guanine alkylation after tilimycin exposure to eukaryotic cells, providing the first structural characterization of a PBD-DNA adduct formed in cells. Finally, we report the rational design of small-molecule inhibitors that block tilimycin biosynthesis in whole cell K. oxytoca (IC50 = 29 ± 4 μM) through the inhibition of NpsA (KD = 29 ± 4 nM).
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Affiliation(s)
- Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Dale F. Kreitler
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Valeria Guidolin
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Eric Drake
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Peter W. Villalta
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, New York 14203, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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39
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Abstract
Natural products from microorganisms are important small molecules that play roles in various biological processes like cellular growth, motility, nutrient acquisition, stress response, biofilm formation, and defense. It is hypothesized that pathogens exploit these molecules to regulate virulence and persistence during infections. Here, we present selected examples of signaling natural products from human pathogenic bacteria that use these metabolites to gain a competitive advantage. Targeting these signaling systems provides novel strategies to antimicrobial treatments.
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Affiliation(s)
- Zhijuan Hu
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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40
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Hering NA, Fromm A, Bücker R, Gorkiewicz G, Zechner E, Högenauer C, Fromm M, Schulzke JD, Troeger H. Tilivalline- and Tilimycin-Independent Effects of Klebsiella oxytoca on Tight Junction-Mediated Intestinal Barrier Impairment. Int J Mol Sci 2019; 20:E5595. [PMID: 31717457 PMCID: PMC6888351 DOI: 10.3390/ijms20225595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Klebsiella oxytoca causes antibiotic-associated hemorrhagic colitis and diarrhea. This was attributed largely to its secreted cytotoxins tilivalline and tilimycin, inductors of epithelial apoptosis. To study whether Klebsiella oxytoca exerts further barrier effects, T84 monolayers were challenged with bacterial supernatants derived from tilivalline/tilimycin-producing AHC6 or its isogeneic tilivalline/tilimycin-deficient strain Mut-89. Both preparations decreased transepithelial resistance, enhanced fluorescein and FITC-dextran-4kDa permeabilities, and reduced expression of barrier-forming tight junction proteins claudin-5 and -8. Laser scanning microscopy indicated redistribution of both claudins off the tight junction region in T84 monolayers as well as in colon crypts of mice infected with AHC6 or Mut-89, indicating that these effects are tilivalline/tilimycin-independent. Furthermore, claudin-1 was affected, but only in a tilivalline/tilimycin-dependent manner. In conclusion, Klebsiella oxytoca induced intestinal barrier impairment by two mechanisms: the tilivalline/tilimycin-dependent one, acting by increasing cellular apoptosis and a tilivalline/tilimycin-independent one, acting by weakening the paracellular pathway through the tight junction proteins claudin-5 and -8.
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Affiliation(s)
- Nina A. Hering
- Medical Department of General, Visceral and Vascular Surgery, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Anja Fromm
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Roland Bücker
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria;
| | - Ellen Zechner
- BioTechMed-Graz, Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria;
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Medical University of Graz, A-8036 Graz, Austria;
| | - Michael Fromm
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Jörg-Dieter Schulzke
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Hanno Troeger
- Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany;
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41
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Chua MD, Bogdan AC, Guttman JA. Klebsiella pneumoniae Redistributes Katanin Severing Proteins and Alters Astral Microtubules during Mitosis. Anat Rec (Hoboken) 2019; 303:1859-1864. [PMID: 31595676 DOI: 10.1002/ar.24286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/31/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Klebsiella pneumoniae has become a growing concern within hospitals due to multidrug resistant strains and increasing mortality rates. Recently, we showed that at the subcellular level, K. pneumoniae compromises the integrity of the epithelia by disassembling the microtubule networks of cells through the actions of katanin microtubule severing proteins. In this study, we report on the observation that mitotic cells are targeted by K. pneumoniae and that during infections, the katanin proteins are excluded from the microtubule organizing centers of dividing cells, resulting in the alteration of the microtubule cytoskeleton. Anat Rec, 2019. © 2019 American Association for Anatomy Anat Rec, 303:1859-1864, 2020. © 2019 American Association for Anatomy.
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Affiliation(s)
- Michael D Chua
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alexander C Bogdan
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Julian A Guttman
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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