1
|
Bassetti M, Cascio A, De Rosa FG, Meschiari M, Parrella R, Petrosillo N, Armuzzi A, Caprioli F, Dentali F, Pani M, Pilotto A, Restelli U, Sanguinetti M. Management of Clostridioides difficile infection: an Italian Delphi consensus. J Antimicrob Chemother 2024:dkae179. [PMID: 39008427 DOI: 10.1093/jac/dkae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Clostridioides difficile infection (CDI), a leading cause of nosocomial deaths, is a microbiota-mediated disease. As such, the use of broader spectrum antibiotics, such as vancomycin and metronidazole, can prime the gastrointestinal tract to become more prone to CDI recurrences. Fidaxomicin, a narrow-spectrum antibiotic, has been demonstrated to be superior in preventing recurrence and in preserving the intestinal microbiota; however, widespread employment worldwide has been hindered due to high acquisition costs. OBJECTIVES To integrate the currently available guidelines on the management of CDI and to shed light on the timeliest employment of fidaxomicin. METHODS An expert panel was gathered to obtain consensus using Delphi methodology on a series of statements regarding the management of CDI and on appropriate antibiotic use. RESULTS Consensus was reached on 21 of the 25 statements addressing the management of CDI. CONCLUSIONS Delphi methodology was used to achieve consensus on the management of CDI, on the identification of patients at risk of recurrences or severe infection, and on the most appropriate use of fidaxomicin, with the final aim of fostering clinical practice application of treatment algorithms proposed by previous guidelines, in absolute synergy. It could be an important tool to promote more appropriate and cost-effective CDI treatments in European settings with limited resources, like Italy.
Collapse
Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Antonio Cascio
- Department PROMISE-Infectious and Tropical Diseases Unit, AOU Policlinico "P. Giaccone", University of Palermo, 90127 Palermo, Italy
| | | | - Marianna Meschiari
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria di Modena, Policlinico di Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Roberto Parrella
- Unit of Respiratory Infectious Diseases, Cotugno Hospital, Azienda Ospedaliera dei Colli, 80131 Naples, Italy
| | - Nicola Petrosillo
- Infection Prevention and Control Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00127 Rome, Italy
| | - Alessandro Armuzzi
- IBD Unit, IRCCS Humanitas Research Hospital, Via A. Manzoni 56, Rozzano, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Flavio Caprioli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20133 Milan, Italy
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico di Milano, 20122 Milan, Italy
| | - Francesco Dentali
- Division of Internal Medicine, Medical Center, Ospedale di Circolo & Fondazione Macchi, ASST Sette Laghi, 21100 Varese, Italy
- Department of Medicine and Surgery, Insubria University, 21100 Varese, Italy
| | - Marcello Pani
- Hospital Pharmacy, Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Alberto Pilotto
- Department of Interdisciplinary Medicine, 'Aldo Moro' University of Bari, 70121 Bari, Italy
- Geriatrics Unit, Department of Geriatric Care, Neurology and Rehabilitation, Galliera Hospitals, 16128 Genova, Italy
| | | | - Maurizio Sanguinetti
- Department of Laboratory and Infectious Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| |
Collapse
|
2
|
Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
Collapse
Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
| |
Collapse
|
3
|
Bosnjak M, Karpe AV, Van TTH, Kotsanas D, Jenkin GA, Costello SP, Johanesen P, Moore RJ, Beale DJ, Srikhanta YN, Palombo EA, Larcombe S, Lyras D. Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection. Nat Commun 2023; 14:7737. [PMID: 38007555 PMCID: PMC10676382 DOI: 10.1038/s41467-023-43671-8] [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: 06/04/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023] Open
Abstract
Hospital-acquired diarrhoea (HAD) is common, and often associated with gut microbiota and metabolome dysbiosis following antibiotic administration. Clostridioides difficile is the most significant antibiotic-associated diarrhoeal (AAD) pathogen, but less is known about the microbiota and metabolome associated with AAD and C. difficile infection (CDI) with contrasting antibiotic treatment. We characterised faecal microbiota and metabolome for 169 HAD patients (33 with CDI and 133 non-CDI) to determine dysbiosis biomarkers and gain insights into metabolic strategies C. difficile might use for gut colonisation. The specimen microbial community was analysed using 16 S rRNA gene amplicon sequencing, coupled with untargeted metabolite profiling using gas chromatography-mass spectrometry (GC-MS), and short-chain fatty acid (SCFA) profiling using GC-MS. AAD and CDI patients were associated with a spectrum of dysbiosis reflecting non-antibiotic, short-term, and extended-antibiotic treatment. Notably, extended antibiotic treatment was associated with enterococcal proliferation (mostly vancomycin-resistant Enterococcus faecium) coupled with putative biomarkers of enterococcal tyrosine decarboxylation. We also uncovered unrecognised metabolome dynamics associated with concomitant enterococcal proliferation and CDI, including biomarkers of Stickland fermentation and amino acid competition that could distinguish CDI from non-CDI patients. Here we show, candidate metabolic biomarkers for diagnostic development with possible implications for CDI and vancomycin-resistant enterococci (VRE) treatment.
Collapse
Affiliation(s)
- Marijana Bosnjak
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Avinash V Karpe
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Queensland, Australia
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Despina Kotsanas
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Grant A Jenkin
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Samuel P Costello
- Department of Gastroenterology, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - Priscilla Johanesen
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Yogitha N Srikhanta
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Sarah Larcombe
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
4
|
Ke S, Xiao Y, Weiss ST, Chen X, Kelly CP, Liu YY. A computational method to dissect colonization resistance of the gut microbiota against pathogens. CELL REPORTS METHODS 2023; 3:100576. [PMID: 37751698 PMCID: PMC10545914 DOI: 10.1016/j.crmeth.2023.100576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/09/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023]
Abstract
The mammalian gut microbiome protects the host through colonization resistance (CR) against the incursion of exogenous and often harmful microorganisms, but identifying the exact microbes responsible for the gut microbiota-mediated CR against a particular pathogen remains a challenge. To address this limitation, we developed a computational method: generalized microbe-phenotype triangulation (GMPT). We first systematically validated GMPT using a classical population dynamics model in community ecology and demonstrated its superiority over baseline methods. We then tested GMPT on simulated data generated from the ecological network inferred from a real community (GnotoComplex microflora) and real microbiome data on two mouse studies on Clostridioides difficile infection. We demonstrated GMPT's ability to streamline the discovery of microbes that are potentially responsible for microbiota-mediated CR against pathogens. GMPT holds promise to advance our understanding of CR mechanisms and facilitate the rational design of microbiome-based therapies for preventing and treating enteric infections.
Collapse
Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yandong Xiao
- College of System Engineering, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| |
Collapse
|
5
|
Wang R. Clostridioides difficile infection: microbe-microbe interactions and live biotherapeutics. Front Microbiol 2023; 14:1182612. [PMID: 37228365 PMCID: PMC10203151 DOI: 10.3389/fmicb.2023.1182612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023] Open
Abstract
Clostridioides difficile is a gram-positive, spore-forming, obligate anaerobe that infects the colon. C. difficile is estimated to cause nearly half a million cases in the United States annually, with about 29,000 associated deaths. Unfortunately, the current antibiotic treatment is not ideal. While antibiotics can treat the infections, they also disrupt the gut microbiota that mediates colonization resistance against enteric pathogens, including C. difficile; disrupted gut microbiota provides a window of opportunity for recurrent infections. Therefore, therapeutics that restore the gut microbiota and suppress C. difficile are being evaluated for safety and efficacy. This review will start with mechanisms by which gut bacteria affect C. difficile pathogenesis, followed by a discussion on biotherapeutics for recurrent C. difficile infections.
Collapse
|
6
|
Oliveira RA, Pamer EG. Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions. Cell Host Microbe 2023; 31:472-484. [PMID: 37054670 DOI: 10.1016/j.chom.2023.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Increasing experimental evidence suggests that administering live commensal bacterial species can optimize microbiome composition and lead to reduced disease severity and enhanced health. Our understanding of the intestinal microbiome and its functions has increased over the past two decades largely due to deep sequence analyses of fecal nucleic acids, metabolomic and proteomic assays to measure nutrient use and metabolite production, and extensive studies on the metabolism and ecological interactions of a wide range of commensal bacterial species inhabiting the intestine. Herein, we review new and important findings that have emerged from this work and provide thoughts and considerations on approaches to re-establish and optimize microbiome functions by assembling and administering commensal bacterial consortia.
Collapse
Affiliation(s)
- Rita A Oliveira
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA; Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, Chicago, IL, USA.
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA; Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, Chicago, IL, USA; Department of Microbiology, University of Chicago Medicine, Chicago, IL, USA; Department of Pathology, University of Chicago Medicine, Chicago, IL, USA
| |
Collapse
|
7
|
Caballano-Infantes E, Ho-Plágaro A, López-Gómez C, Martín-Reyes F, Rodríguez-Pacheco F, Taminiau B, Daube G, Garrido-Sánchez L, Alcaín-Martínez G, Andrade RJ, García-Cortés M, Lucena MI, García-Fuentes E, Rodríguez-Díaz C. Membrane Vesicles of Toxigenic Clostridioides difficile Affect the Metabolism of Liver HepG2 Cells. Antioxidants (Basel) 2023; 12:antiox12040818. [PMID: 37107193 PMCID: PMC10135135 DOI: 10.3390/antiox12040818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Clostridioides difficile infection (CDI) appears to be associated with different liver diseases. C. difficile secretes membrane vesicles (MVs), which may be involved in the development of nonalcoholic fatty liver disease (NALFD) and drug-induced liver injury (DILI). In this study, we investigated the presence of C. difficile-derived MVs in patients with and without CDI, and analyzed their effects on pathways related to NAFLD and DILI in HepG2 cells. Fecal extracellular vesicles from CDI patients showed an increase of Clostridioides MVs. C. difficile-derived MVs that were internalized by HepG2 cells. Toxigenic C. difficile-derived MVs decreased mitochondrial membrane potential and increased intracellular ROS compared to non-toxigenic C. difficile-derived MVs. In addition, toxigenic C. difficile-derived MVs upregulated the expression of genes related to mitochondrial fission (FIS1 and DRP1), antioxidant status (GPX1), apoptosis (CASP3), glycolysis (HK2, PDK1, LDHA and PKM2) and β-oxidation (CPT1A), as well as anti- and pro-inflammatory genes (IL-6 and IL-10). However, non-toxigenic C. difficile-derived MVs did not produce changes in the expression of these genes, except for CPT1A, which was also increased. In conclusion, the metabolic and mitochondrial changes produced by MVs obtained from toxigenic C. difficile present in CDI feces are common pathophysiological features observed in the NAFLD spectrum and DILI.
Collapse
Affiliation(s)
- Estefanía Caballano-Infantes
- Department of Regeneration and Cell Therapy Andalusian, Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Ailec Ho-Plágaro
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Carlos López-Gómez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Flores Martín-Reyes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Francisca Rodríguez-Pacheco
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Lourdes Garrido-Sánchez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Guillermo Alcaín-Martínez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Raúl J. Andrade
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
- CIBER de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miren García-Cortés
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
- CIBER de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - M. Isabel Lucena
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- CIBER de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Departamento de Farmacología, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
- UICEC IBIMA, Plataforma SCReN (Spanish Clinical Research Network), Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29010 Málaga, Spain
| | - Eduardo García-Fuentes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- CIBER de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence:
| | - Cristina Rodríguez-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina, IBIMA Plataforma BIONAND, 29010 Málaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| |
Collapse
|
8
|
Liu L, Li F, Shi H, Nahata MC. The Efficacy and Safety of Vonoprazan and Amoxicillin Dual Therapy for Helicobacter pylori Infection: A Systematic Review and Network Meta-Analysis. Antibiotics (Basel) 2023; 12:antibiotics12020346. [PMID: 36830257 PMCID: PMC9952735 DOI: 10.3390/antibiotics12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
The eradication of Helicobacter pylori (H. pylori) infection remains challenging due to increasing bacterial resistance. Resistance rates to clarithromycin, metronidazole, and levofloxacin were higher than 30% in the USA, making current therapies less effective. Vonoprazan triple therapy (VAC) has demonstrated similar efficacy and safety profiles compared to PPI-based triple therapy (PPI). However, the eradication rate of vonoprazan dual therapy (VA) for H. pylori infection in comparison to VAC, and PPI was poorly established. Electronic databases were searched up to 6 October 2022, to identify studies examining the safety and efficacy of VA compared to VAC and PPI. Six studies were included. For empiric therapies among treatment naïve patients, VA, VAC, and PPI did not achieve high cure rates (>90%). The comparative efficacy ranking showed VAC was the most effective therapy, followed by VA, and PPI. The results were similar for clarithromycin-resistant infections. The comparative safety ranking showed VA ranked first, whereas PPI triple therapy was the least safe regimen. These findings should guide the selection of the most effective and safe treatment and conduct additional studies to determine the place of vonoprazan dual versus triple therapies in patients with H. pylori from various countries across the world.
Collapse
Affiliation(s)
- Ligang Liu
- Institute of Therapeutic Innovations and Outcomes (ITIO), College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Fang Li
- Department of Pharmacy, Beijing You An Hospital, Capital Medical University, Beijing 100069, China
| | - Hekai Shi
- Department of General Surgery, Fudan University Affiliated Huadong Hospital, Shanghai 200040, China
| | - Milap C. Nahata
- Institute of Therapeutic Innovations and Outcomes (ITIO), College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Colleges of Pharmacy and Medicine, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +1-614-292-2472
| |
Collapse
|
9
|
Jaswal K, Todd OA, Behnsen J. Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens. Gut Microbes 2023; 15:2226916. [PMID: 37365731 DOI: 10.1080/19490976.2023.2226916] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
A diverse array of commensal microorganisms inhabits the human intestinal tract. The most abundant and most studied members of this microbial community are undoubtedly bacteria. Their important role in gut physiology, defense against pathogens, and immune system education has been well documented over the last decades. However, the gut microbiome is not restricted to bacteria. It encompasses the entire breadth of microbial life: viruses, archaea, fungi, protists, and parasitic worms can also be found in the gut. While less studied than bacteria, their divergent but important roles during health and disease have become increasingly more appreciated. This review focuses on these understudied members of the gut microbiome. We will detail the composition and development of these microbial communities and will specifically highlight their functional interactions with enteric pathogens, such as species of the family Enterobacteriaceae. The interactions can be direct through physical interactions, or indirect through secreted metabolites or modulation of the immune response. We will present general concepts and specific examples of how non-bacterial gut communities modulate bacterial pathogenesis and present an outlook for future gut microbiome research that includes these communities.
Collapse
Affiliation(s)
- Kanchan Jaswal
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Olivia A Todd
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| |
Collapse
|
10
|
Horvat S, Mahnic A, Makuc D, Pečnik K, Plavec J, Rupnik M. Children gut microbiota exhibits a different composition and metabolic profile after in vitro exposure to Clostridioides difficile and increases its sporulation. Front Microbiol 2022; 13:1042526. [PMID: 36569098 PMCID: PMC9780542 DOI: 10.3389/fmicb.2022.1042526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (Clostridium difficile) infection (CDI) is one of the main public health concerns in adults, while children under 2 years of age are often colonized asymptomatically. In both adults and children, CDI is strongly associated with disturbances in gut microbiota. In this study, an in-vitro model of children gut microbiota was challenged with vegetative cells or a conditioned media of six different toxigenic C. difficile strains belonging to the ribotypes 027, 078, and 176. In the presence of C. difficile or conditioned medium the children gut microbiota diversity decreased and all main phyla (Bacteroidetes, Firmicutes, and Proteobacteria) were affected. The NMR metabolic spectra divided C. difficile exposed children gut microbiota into three clusters. The grouping correlated with nine metabolites (short chain fatty acids, ethanol, phenolic acids and tyramine). All strains were able to grow in the presence of children gut microbiota and showed a high sporulation rate of up to 57%. This high sporulation rate in combination with high asymptomatic carriage in children could contribute to the understanding of the reported role of children in C. difficile transmissions.
Collapse
Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Aleksander Mahnic
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia,Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Damjan Makuc
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Klemen Pečnik
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia,Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia,*Correspondence: Maja Rupnik,
| |
Collapse
|
11
|
Dawkins JJ, Allegretti JR, Gibson TE, McClure E, Delaney M, Bry L, Gerber GK. Gut metabolites predict Clostridioides difficile recurrence. MICROBIOME 2022; 10:87. [PMID: 35681218 PMCID: PMC9178838 DOI: 10.1186/s40168-022-01284-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/02/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is the most common hospital acquired infection in the USA, with recurrence rates > 15%. Although primary CDI has been extensively linked to gut microbial dysbiosis, less is known about the factors that promote or mitigate recurrence. Moreover, previous studies have not shown that microbial abundances in the gut measured by 16S rRNA amplicon sequencing alone can accurately predict CDI recurrence. RESULTS We conducted a prospective, longitudinal study of 53 non-immunocompromised participants with primary CDI. Stool sample collection began pre-CDI antibiotic treatment at the time of diagnosis, and continued up to 8 weeks post-antibiotic treatment, with weekly or twice weekly collections. Samples were analyzed using (1) 16S rRNA amplicon sequencing, (2) liquid chromatography/mass-spectrometry metabolomics measuring 1387 annotated metabolites, and (3) short-chain fatty acid profiling. The amplicon sequencing data showed significantly delayed recovery of microbial diversity in recurrent participants, and depletion of key anaerobic taxa at multiple time-points, including Clostridium cluster XIVa and IV taxa. The metabolomic data also showed delayed recovery in recurrent participants, and moreover mapped to pathways suggesting distinct functional abnormalities in the microbiome or host, such as decreased microbial deconjugation activity, lowered levels of endocannabinoids, and elevated markers of host cell damage. Further, using predictive statistical/machine learning models, we demonstrated that the metabolomic data, but not the other data sources, can accurately predict future recurrence at 1 week (AUC 0.77 [0.71, 0.86; 95% interval]) and 2 weeks (AUC 0.77 [0.69, 0.85; 95% interval]) post-treatment for primary CDI. CONCLUSIONS The prospective, longitudinal, and multi-omic nature of our CDI recurrence study allowed us to uncover previously unrecognized dynamics in the microbiome and host presaging recurrence, and, in particular, to elucidate changes in the understudied gut metabolome. Moreover, we demonstrated that a small set of metabolites can accurately predict future recurrence. Our findings have implications for development of diagnostic tests and treatments that could ultimately short-circuit the cycle of CDI recurrence, by providing candidate metabolic biomarkers for diagnostics development, as well as offering insights into the complex microbial and metabolic alterations that are protective or permissive for recurrence. Video Abstract.
Collapse
Affiliation(s)
- Jennifer J. Dawkins
- Department of Pathology, Brigham & Woman’s Hospital, Harvard Medical School, Boston, MA USA
- Harvard-MIT Health Sciences & Technology, Harvard Medical School, MIT, Cambridge, MA USA
| | - Jessica R. Allegretti
- Massachusetts Host-Microbiome Center, Boston, MA USA
- Division of Gastroenterology, Brigham & Woman’s Hospital, Harvard Medical School, Boston, MA USA
| | - Travis E. Gibson
- Department of Pathology, Brigham & Woman’s Hospital, Harvard Medical School, Boston, MA USA
| | - Emma McClure
- Division of Gastroenterology, Brigham & Woman’s Hospital, Harvard Medical School, Boston, MA USA
| | - Mary Delaney
- Massachusetts Host-Microbiome Center, Boston, MA USA
| | - Lynn Bry
- Department of Pathology, Brigham & Woman’s Hospital, Harvard Medical School, Boston, MA USA
- Massachusetts Host-Microbiome Center, Boston, MA USA
| | - Georg K. Gerber
- Department of Pathology, Brigham & Woman’s Hospital, Harvard Medical School, Boston, MA USA
- Harvard-MIT Health Sciences & Technology, Harvard Medical School, MIT, Cambridge, MA USA
- Massachusetts Host-Microbiome Center, Boston, MA USA
| |
Collapse
|
12
|
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers. Cell Host Microbe 2022; 30:583-598.e8. [PMID: 35421353 DOI: 10.1016/j.chom.2022.03.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/22/2021] [Accepted: 03/10/2022] [Indexed: 11/20/2022]
Abstract
Manipulation of the gut microbiota via fecal microbiota transplantation (FMT) has shown clinical promise in diseases such as recurrent Clostridioides difficile infection (rCDI). However, the variable nature of this approach makes it challenging to describe the relationship between fecal strain colonization, corresponding microbiota changes, and clinical efficacy. Live biotherapeutic products (LBPs) consisting of defined consortia of clonal bacterial isolates have been proposed as an alternative therapeutic class because of their promising preclinical results and safety profile. We describe VE303, an LBP comprising 8 commensal Clostridia strains under development for rCDI, and its early clinical development in healthy volunteers (HVs). In a phase 1a/b study in HVs, VE303 is determined to be safe and well-tolerated at all doses tested. VE303 strains optimally colonize HVs if dosed over multiple days after vancomycin pretreatment. VE303 promotes the establishment of a microbiota community known to provide colonization resistance.
Collapse
|
13
|
Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature 2022; 604:541-545. [PMID: 35388215 PMCID: PMC9635844 DOI: 10.1038/s41586-022-04545-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023]
Abstract
Fidaxomicin (Fdx) is widely used to treat Clostridioides difficile (Cdiff) infections, but the molecular basis of its narrow-spectrum activity in the human gut microbiome remains unknown. Cdiff infections are a leading cause of nosocomial deaths1. Fidaxomicin, which inhibits RNA polymerase, targets Cdiff with minimal effects on gut commensals, reducing recurrence of Cdiff infection2,3. Here we present the cryo-electron microscopy structure of Cdiff RNA polymerase in complex with fidaxomicin and identify a crucial fidaxomicin-binding determinant of Cdiff RNA polymerase that is absent in most gut microbiota such as Proteobacteria and Bacteroidetes. By combining structural, biochemical, genetic and bioinformatic analyses, we establish that a single residue in Cdiff RNA polymerase is a sensitizing element for fidaxomicin narrow-spectrum activity. Our results provide a blueprint for targeted drug design against an important human pathogen.
Collapse
Affiliation(s)
- Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Hande Boyaci
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States
| | - Yu Bao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States.
| |
Collapse
|
14
|
Yang L, Bajinka O, Jarju PO, Tan Y, Taal AM, Ozdemir G. The varying effects of antibiotics on gut microbiota. AMB Express 2021; 11:116. [PMID: 34398323 PMCID: PMC8368853 DOI: 10.1186/s13568-021-01274-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 12/21/2022] Open
Abstract
Antibiotics are lifesaving therapeutic drugs that have been used by human for decades. They are used both in the fight against bacterial pathogens for both human and for animal feeding. However, of recent, their effects on the gut microbial compositions and diversities have attracted much attention. Existing literature have established the dysbiosis (reduced diversity) in the gut microbiota in association with antibiotic and antibiotic drug doses. In the light of spelling out the varying effects of antibiotic use on gut microbiota, this review aimed at given an account on the degree of gut microbial alteration caused by common antibiotics. While some common antibiotics are found to destroy the common phyla, other debilitating effects were observed. The effects can be attributed to the mode of mechanism, the class of antibiotic, the degree of resistance of the antibiotic used, the dosage used during the treatment, the route of administration, the pharmacokinetic and pharmacodynamics properties and the spectrum of the antibiotic agent. Health status, stress or the type of diet an individual feeds on could be a great proportion as confounding factors. While it is understood that only the bacterial communities are explored in the quest to establishing the role of gut in health, other gut microbial species are somehow contributing to the dysbiosis status of the gut microbiota. Until now, long term natural fluctuations like diseases outbreaks and mutations of the strain might as well rendered alteration to the gut independent of antibiotic treatments.
Collapse
|
15
|
Li J, Chen J, Yang G, Tao L. Sublancin protects against methicillin-resistant Staphylococcus aureus infection by the combined modulation of innate immune response and microbiota. Peptides 2021; 141:170533. [PMID: 33775803 DOI: 10.1016/j.peptides.2021.170533] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/25/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen responsible for community and hospital bacterial infections. In the present study, the protective role of sublancin, an antimicrobial peptides, was explored in MRSA infection model. We report that sublancin directly induce macrophage migration through the chemotactic receptors. We further show that sublancin exhibits protection in a mouse MRSA infection model. This protection involved an immunomodulatory activity, but was blocked by depletion of monocyte/macrophages or neutrophils. Sublancin selectively up-regulates the levels of chemokines (C-X-C motif chemokine ligand 1, CXCL1 and monocyte chemoattractant protein-1, MCP-1) while reducing the production of pro-inflammatory cytokine (tumor necrosis factor-α, TNF-α). Meanwhile, sublancin regulated the microbiota composition disrupted by MRSA injection, increasing the abundance of Lactobacillus and decreasing that of Staphylococcus and Pseudomonas. Also, sublancin restored to normal levels of metabolic functional pathways, especially amino acid biosynthesis (e.g., branched amino acid, histidine and tryptophan), disrupted after injection, and this restoration was significantly correlated with neutrophils. These results demonstrates that sublancin stimulates the innate response and modulates the microbiota community to protect against MRSA infection.
Collapse
Affiliation(s)
- Jiantao Li
- College of Animal Husbandry and Veterinary, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China.
| | - Jing Chen
- College of Animal Husbandry and Veterinary, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China
| | - Guiqin Yang
- College of Animal Husbandry and Veterinary, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China
| | - Lijuan Tao
- College of Animal Husbandry and Veterinary, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China
| |
Collapse
|
16
|
Shah T, Baloch Z, Shah Z, Cui X, Xia X. The Intestinal Microbiota: Impacts of Antibiotics Therapy, Colonization Resistance, and Diseases. Int J Mol Sci 2021; 22:ijms22126597. [PMID: 34202945 PMCID: PMC8235228 DOI: 10.3390/ijms22126597] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
Trillions of microbes exist in the human body, particularly the gastrointestinal tract, coevolved with the host in a mutually beneficial relationship. The main role of the intestinal microbiome is the fermentation of non-digestible substrates and increased growth of beneficial microbes that produce key antimicrobial metabolites such as short-chain fatty acids, etc., to inhibit the growth of pathogenic microbes besides other functions. Intestinal microbiota can prevent pathogen colonization through the mechanism of colonization resistance. A wide range of resistomes are present in both beneficial and pathogenic microbes. Giving antibiotic exposure to the intestinal microbiome (both beneficial and hostile) can trigger a resistome response, affecting colonization resistance. The following review provides a mechanistic overview of the intestinal microbiome and the impacts of antibiotic therapy on pathogen colonization and diseases. Further, we also discuss the epidemiology of immunocompromised patients who are at high risk for nosocomial infections, colonization and decolonization of multi-drug resistant organisms in the intestine, and the direct and indirect mechanisms that govern colonization resistance to the pathogens.
Collapse
Affiliation(s)
- Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Yunnan Key Laboratory of Sustainable Utilization of Panax Notoginseng, Kunming 650500, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Correspondence: (Z.B.); (X.C.); (X.X.)
| | - Zahir Shah
- Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar 25120, Pakistan;
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Yunnan Key Laboratory of Sustainable Utilization of Panax Notoginseng, Kunming 650500, China
- Correspondence: (Z.B.); (X.C.); (X.X.)
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Correspondence: (Z.B.); (X.C.); (X.X.)
| |
Collapse
|
17
|
Ghasemi A, Mohabati Mobarez A, Mostafavi E. Investigation of Clostridium difficile in elderly people: A preliminary study in Iran. Trop Doct 2021; 51:319-322. [PMID: 33847546 DOI: 10.1177/0049475521999221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Elderly people are at increased risk for infections such as with Clostridium difficile. This can colonize their gut and cause various gastro-intestinal manifestations. Our survey investigated its prevalence in a nursing home in Iran. Faecal samples were collected and tested by polymerase chain reaction for identification of A, B and binary toxin genes. From 289 samples, 42(14.5%) isolates were found. Toxin genes were positive in 19 isolates (17 AþBþ and 2 isolates ABþ). The elderly are especially at risk and great attention should be paid to contamination within their nursing homes. This is not an isolated regional problem.
Collapse
Affiliation(s)
- Ahmad Ghasemi
- PhD student of Bacteriology, Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ashraf Mohabati Mobarez
- Professor, Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Mostafavi
- Professor, Department of Epidemiology and Biostatics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
18
|
Henson MA. Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection. PLoS Comput Biol 2021; 17:e1008782. [PMID: 33617526 PMCID: PMC7932513 DOI: 10.1371/journal.pcbi.1008782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 03/04/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Approximately 30% of patients who have Clostridioides difficile infection (CDI) will suffer at least one incident of reinfection. While the underlying causes of CDI recurrence are poorly understood, interactions between C. difficile and commensal gut bacteria are thought to play an important role. In this study, an in silico pipeline was used to process 16S rRNA gene amplicon sequence data of 225 stool samples from 93 CDI patients into sample-specific models of bacterial community metabolism. Clustered metabolite production rates generated from post-diagnosis samples generated a high Enterobacteriaceae abundance cluster containing disproportionately large numbers of recurrent samples and patients. This cluster was predicted to have significantly reduced capabilities for secondary bile acid synthesis but elevated capabilities for aromatic amino acid catabolism. When applied to 16S sequence data of 40 samples from fecal microbiota transplantation (FMT) patients suffering from recurrent CDI and their stool donors, the community modeling method generated a high Enterobacteriaceae abundance cluster with a disproportionate large number of pre-FMT samples. This cluster also was predicted to exhibit reduced secondary bile acid synthesis and elevated aromatic amino acid catabolism. Collectively, these in silico predictions suggest that Enterobacteriaceae may create a gut environment favorable for C. difficile spore germination and/or toxin synthesis.
Collapse
Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| |
Collapse
|
19
|
Gazzola A, Panelli S, Corbella M, Merla C, Comandatore F, De Silvestri A, Piralla A, Zuccaro V, Bandi C, Marone P, Cambieri P. Microbiota in Clostridioides difficile-Associated Diarrhea: Comparison in Recurrent and Non-Recurrent Infections. Biomedicines 2020; 8:biomedicines8090335. [PMID: 32911854 PMCID: PMC7554755 DOI: 10.3390/biomedicines8090335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/07/2020] [Indexed: 01/20/2023] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea, especially in hospitalized elderly patients, representing a global public health concern. Clinical presentations vary from mild diarrhea to severe pseudomembranous colitis that may progress to toxic megacolon or intestinal perforation. Antibiotic therapy is recognized as a risk factor and exacerbates dysbiosis of the intestinal microbiota, whose role in CDI is increasingly acknowledged. A clinically challenging complication is the development of recurrent disease (rCDI). In this study, using amplicon metagenomics, we compared the fecal microbiota of CDI and rCDI patients (sampled at initial and recurrent episode) and of non-infected controls. We also investigated whether CDI severity relates to specific microbiota compositions. rCDI patients showed a significantly decreased bacterial diversity as compared to controls (p < 0.01). The taxonomic composition presented significant shifts: both CDI and rCDI patients displayed significantly increased frequencies of Firmicutes, Peptostreptococcaceae, Clostridium XI, Clostridium XVIII, and Enterococcaceae. Porphyromonadaceae and, within it, Parabacteroides displayed opposite behaviors in CDI and rCDI, appearing discriminant between the two. Finally, the second episode of rCDI was characterized by significant shifts of unclassified Clostridiales, Escherichia/Shigella and Veillonella. No peculiar taxa composition correlated with the severity of infection, likely reflecting the role of host-related factors in determining severity.
Collapse
Affiliation(s)
- Alessandra Gazzola
- Infectious Diseases Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (A.G.); (V.Z.)
- Department of Veterinary Medicine, University of Milano, 20133 Milan, Italy
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences “L. Sacco” and Pediatric Clinical Research Center “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milan, Italy;
- Correspondence:
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (M.C.); (C.M.); (A.P.); (P.M.); (P.C.)
| | - Cristina Merla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (M.C.); (C.M.); (A.P.); (P.M.); (P.C.)
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences “L. Sacco” and Pediatric Clinical Research Center “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milan, Italy;
| | - Annalisa De Silvestri
- Clinical Epidemiology and Biometry Unit, Fondazione IRCCS Policlinico san Matteo, 27100 Pavia, Italy;
| | - Antonio Piralla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (M.C.); (C.M.); (A.P.); (P.M.); (P.C.)
| | - Valentina Zuccaro
- Infectious Diseases Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (A.G.); (V.Z.)
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center “Romeo ed Enrica Invernizzi”, University of Milano, 20157 Milan, Italy;
| | - Piero Marone
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (M.C.); (C.M.); (A.P.); (P.M.); (P.C.)
| | - Patrizia Cambieri
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (M.C.); (C.M.); (A.P.); (P.M.); (P.C.)
| |
Collapse
|
20
|
Kokai-Kun JF, Le C, Trout K, Cope JL, Ajami NJ, Degar AJ, Connelly S. Ribaxamase, an Orally Administered β-Lactamase, Diminishes Changes to Acquired Antimicrobial Resistance of the Gut Resistome in Patients Treated with Ceftriaxone. Infect Drug Resist 2020; 13:2521-2535. [PMID: 32801790 PMCID: PMC7383106 DOI: 10.2147/idr.s260258] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
Abstract
Introduction Intravenous (IV) β-lactam antibiotics, excreted through bile into the gastrointestinal (GI) tract, may disrupt the gut microbiome by eliminating the colonization resistance from beneficial bacteria. This increases the risk for Clostridium difficile infection (CDI) and can promote antimicrobial resistance by selecting resistant organisms and eliminating competition by non-resistant organisms. Ribaxamase is an orally administered β-lactamase for use with IV β-lactam antibiotics (penicillins and cephalosporins) and is intended to degrade excess antibiotics in the upper GI before they can disrupt the gut microbiome and alter the resistome. Methods Longitudinal fecal samples (349) were collected from patients who participated in a previous Phase 2b clinical study with ribaxamase for prevention of CDI. In that previous study, patients were treated with ceftriaxone for a lower respiratory tract infection and received concurrent ribaxamase or placebo. Extracted fecal DNA from the samples was subjected to whole-genome shotgun sequencing and analyzed for the presence of antimicrobial resistance (AMR) genes by alignment of sequences against the Comprehensive Antibiotic Resistance Database. A qPCR assay was also used to confirm some of the results. Results Database alignment identified ~1300 acquired AMR genes and gene variants, including those encoding β-lactamases and vancomycin resistance which were significantly increased in placebo vs ribaxamase-treated patients following antibiotic exposure. qPCR corroborated the presence of these genes and supported both new acquisition and expansion of existing gene pools based on no detectable copy number or a low copy number in pre-antibiotic samples which increased post-antibiotics. Additional statistical analyses demonstrated significant correlations between changes in the gut resistome and clinical study parameters including study drug assignment and β-lactamase and vancomycin resistance gene frequency. Discussion These findings demonstrated that ribaxamase reduced changes to the gut resistome subsequent to ceftriaxone administration and may help limit the emergence of AMR.
Collapse
|
21
|
Pickens C, Wunderink RG, Qi C, Mopuru H, Donnelly H, Powell K, Sims MD. A multiplex polymerase chain reaction assay for antibiotic stewardship in suspected pneumonia. Diagn Microbiol Infect Dis 2020; 98:115179. [PMID: 32927409 PMCID: PMC7428672 DOI: 10.1016/j.diagmicrobio.2020.115179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Background Multiplexed molecular rapid diagnostic tests (RDTs) may allow for rapid and accurate diagnosis of the microbial etiology of pneumonia. However, little data are available on multiplexed RDTs in pneumonia and their impact on clinical practice. Methods This retrospective study analyzed 659 hospitalized patients for microbiological diagnosis of suspected pneumonia. Results The overall sensitivity of the Unyvero LRT Panel was 85.7% (95% CI 82.3–88.7) and the overall specificity was 98.4% (95% CI 98.2–98.7) with a negative predictive value of 97.9% (95% CI 97.6–98.1). The LRT Panel result predicted no change in antibiotics in 12.4% of cases but antibiotic de-escalation in 65.9% (405/615) of patients, of whom 278/405 (69%) had unnecessary MRSA coverage and 259/405 (64%) had unnecessary P. aeruginosa coverage. Interpretation In hospitalized adults with suspected pneumonia, use of an RDT on respiratory samples can allow for early adjustment of initial antibiotics, most commonly de-escalation.
Collapse
Affiliation(s)
- Chiagozie Pickens
- Northwestern University Feinberg School of Medicine, Department of Medicine, Pulmonary and Critical Care Division, Chicago, IL.
| | - Richard G Wunderink
- Northwestern University Feinberg School of Medicine, Department of Medicine, Pulmonary and Critical Care Division, Chicago, IL
| | - Chao Qi
- Northwestern University Feinberg School of Medicine, Department of Pathology, Chicago, IL
| | - Haritha Mopuru
- Beaumont Hospital, Royal Oak, Section of Infectious Diseases and International Medicine, Royal Oak, MI
| | - Helen Donnelly
- Northwestern University Feinberg School of Medicine, Department of Medicine, Pulmonary and Critical Care Division, Chicago, IL
| | - Kimberly Powell
- Beaumont Hospital, Royal Oak, Section of Infectious Diseases and International Medicine, Royal Oak, MI
| | - Matthew D Sims
- Beaumont Hospital, Royal Oak, Section of Infectious Diseases and International Medicine, Royal Oak, MI; Oakland University William Beaumont School of Medicine, Department of Internal Medicine, Rochester, MI
| |
Collapse
|
22
|
Insights into the Role of Human Gut Microbiota in Clostridioides difficile Infection. Microorganisms 2020; 8:microorganisms8020200. [PMID: 32023967 PMCID: PMC7074861 DOI: 10.3390/microorganisms8020200] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile infection (CDI) has emerged as a major health problem worldwide. A major risk factor for disease development is prior antibiotic use, which disrupts the normal gut microbiota by altering its composition and the gut’s metabolic functions, leading to the loss of colonization resistance and subsequent CDI. Data from human studies have shown that the presence of C. difficile, either as a colonizer or as a pathogen, is associated with a decreased level of gut microbiota diversity. The investigation of the gut’s microbial communities, in both healthy subjects and patients with CDI, elucidate the role of microbiota and improve the current biotherapeutics for patients with CDI. Fecal microbiota transplantation has a major role in managing CDI, aiming at re-establishing colonization resistance in the host gastrointestinal tract by replenishing the gut microbiota. New techniques, such as post-genomics, proteomics and metabolomics analyses, can possibly determine in the future the way in which C. difficile eradicates colonization resistance, paving the way for the development of new, more successful treatments and prevention. The aim of the present review is to present recent data concerning the human gut microbiota with a focus on its important role in health and disease.
Collapse
|
23
|
Kachlíková M, Sabaka P, Koščálová A, Bendžala M, Dovalová Z, Stankovič I. Comorbid status and the faecal microbial transplantation failure in treatment of recurrent Clostridioides difficile infection - pilot prospective observational cohort study. BMC Infect Dis 2020; 20:52. [PMID: 31948404 PMCID: PMC6966799 DOI: 10.1186/s12879-020-4773-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Faecal microbial transplantation (FMT) is currently the most effective treatment of recurrent Clostridioides difficile infection (CDI). However, up to 20% of patients experience further recurrences after single FMT. The mechanisms that lead to FMT failure and its risk factors are poorly understood. Comorbidity is one of the risk factors of the failure of standard antibiotic therapy of recurrent CDI. It is not known if comorbidity is also associated with the risk of FMT failure. METHODS We conducted a prospective observational cohort study in order to elucidate if comorbid status is associated with FMT failure. Patients with microbiologically proven recurrent CDI were recruited and underwent FMT via retention enema. Patients were followed up for 12 weeks after FMT for signs and symptoms of CDI recurrence. Single FMT failure was defined as recurrence of diarrhoea and a positive stool test for the presence of C. difficile antigen or toxin at any time point during the 12 weeks of follow-up. We assessed the association of single FMT failure with possible manageable and unmanageable risk factors. As a surrogate of comorbid status, we used Charlson Comorbidity Index (CCI) ≥ 7. RESULTS A total of 60 patients that underwent single FMT (34 women, 26 men) were included in the study. Overall, 15 patients (25%) experienced single FMT failure. 24 patients (40%) had CCI ≥ 7, and 45.0% patients with CCI ≥ 7 experienced failure of single FMT. Patients who experienced single FMT failure had a significantly higher CCI and significantly lower albumin concentration as compared to patients who experienced single FMT success. There was no difference in age, C-reactive protein concentration, leukocyte count and time from FMT to first defecation. In multivariate analysis, CCI ≥ 7 was positively associated with the failure of single FMT. Analysis was controlled for sex, age, time from FMT to first defecation, concomitant PPI therapy, severe CDI, hospital-acquired infection and albumin concentration. CONCLUSIONS Comorbid status surrogated by CCI is positively associated with the failure of single FMT in the treatment of recurrent CDI.
Collapse
Affiliation(s)
- M. Kachlíková
- 0000000109409708grid.7634.6Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - P. Sabaka
- 0000000109409708grid.7634.6Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - A. Koščálová
- 0000000095755967grid.9982.aDepartment of Infectology and Geographical Medicine, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - M. Bendžala
- 0000000109409708grid.7634.6Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Z. Dovalová
- 0000000109409708grid.7634.6Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - I. Stankovič
- 0000000109409708grid.7634.6Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovak Republic
| |
Collapse
|
24
|
Rohde JM, Jones K, Padron N, Olmsted RN, Chopra V, Dubberke ER. A Tiered Approach for Preventing Clostridioides difficile Infection. Ann Intern Med 2019; 171:S45-S51. [PMID: 31569223 DOI: 10.7326/m18-3444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Jeffrey M Rohde
- University of Michigan Medical School, Ann Arbor, Michigan (J.M.R., K.J.)
| | - Karen Jones
- University of Michigan Medical School, Ann Arbor, Michigan (J.M.R., K.J.)
| | - Norma Padron
- Health Research & Educational Trust, American Hospital Association, Chicago, Illinois (N.P.)
| | - Russell N Olmsted
- Integrated Clinical Services, Trinity Health, Livonia, Michigan (R.N.O.)
| | - Vineet Chopra
- University of Michigan Medical School and Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan (V.C.)
| | - Erik R Dubberke
- Washington University School of Medicine, St. Louis, Missouri (E.R.D.)
| |
Collapse
|
25
|
Griffin DW, Benzel WM, Fisher SC, Focazio MJ, Iwanowicz LR, Loftin KA, Reilly TJ, Jones DK. The presence of antibiotic resistance genes in coastal soil and sediment samples from the eastern seaboard of the USA. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:300. [PMID: 31254080 DOI: 10.1007/s10661-019-7426-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Infections from antibiotic resistant microorganisms are considered to be one of the greatest global public health challenges that result in huge annual economic losses. While genes that impart resistance to antibiotics (AbR) existed long before the discovery and use of antibiotics, anthropogenic uses of antibiotics in agriculture, domesticated animals, and humans are known to influence the prevalence of these genes in pathogenic microorganisms. It is critical to understand the role that natural and anthropogenic processes have on the occurrence and distribution of antibiotic resistance in microbial populations to minimize health risks associated with exposures. As part of this research, 15 antibiotic resistance genes were analyzed in coastal sediments and soils along the eastern seaboard of the USA using presence/absence quantitative and digital polymerase chain reaction assays. Samples (53 soil and 192 sediment samples including 54 replicates) were collected from a variety of coastal settings where human and wildlife exposure is likely. At least one of the antibiotic resistance genes was detected in 76.4% of the samples. Samples that contained at least five or more antibiotic resistance genes (5.7%) where typically hydrologically down gradient of watersheds influenced by combined sewer outfalls (CSO). The most frequently detected antibiotic resistance target genes were found in 33.2%, 34.4%, and 42.2% of samples (target genes blaSHV, tetO, and aadA2, respectively). These data provide unique insight into potential exposure of AbR genes over a large geographical region of the eastern seaboard of the USA.
Collapse
Affiliation(s)
- Dale W Griffin
- USGS, 600 4th Street South, St. Petersburg, FL, 33701, USA.
| | - W M Benzel
- USGS, Box 25046, MS-973, Denver Federal Center, Denver, CO, 80225, USA
| | - S C Fisher
- USGS, 2045 Route 112, Coram, NY, 11727, USA
| | - M J Focazio
- USGS, 12201 Sunrise Valley Drive, Reston, VA, 20192, USA
| | - L R Iwanowicz
- USGS, 11649 Leetown Road, Kearneysville, WV, 25430, USA
| | - K A Loftin
- USGS, 1217 Biltmore Drive, Lawrence, KS, 66049, USA
| | - T J Reilly
- USGS, 12201 Sunrise Valley Drive, Reston, VA, 20192, USA
| | - D K Jones
- USGS, 2329 West Orton Circle, West Valley City, UT, 84119, USA
| |
Collapse
|
26
|
Brukner I, Eintracht S, Forgetta V, Papadakis AI, Spatz A, Oughton M. Laboratory-developed test for detection of acute Clostridium difficile infections with the capacity for quantitative sample normalization. Diagn Microbiol Infect Dis 2019; 95:113-118. [PMID: 31176521 DOI: 10.1016/j.diagmicrobio.2019.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022]
Abstract
We describe a laboratory-developed test intended for the detection of acute Clostridium difficile infections (CDI) with the capacity for quantitative sample normalization. The test is based on the detection of the tcdB gene. However, this biomarker is also present among people without symptoms, implying that individuals with diarrhea, not caused by C. difficile may nonetheless test positive. Therefore, clinical diagnosis based on this format of testing can be challenging. In order to improve diagnostic assays capability, tcdB-based quantification methods were suggested as a potential solution, however they did not increase clinical specificity. We report methodology for a dual biomarker monitoring (total bacterial load and tcdB assay), allowing for the calculation of the relative presence of tcdB in the total bacterial population in the tested samples. We believe that this approach is clinically relevant to current assays and can improve CDI testing algorithms.
Collapse
Affiliation(s)
- Ivan Brukner
- Department of Medical Microbiology, Jewish General Hospital, Quebec, Canada; Lady Davis Institute for Medical Research, Quebec, Canada; McGill University, Faculty of Medicine, Montreal, Quebec, Canada.
| | - Shaun Eintracht
- Department of Medicine, Jewish General Hospital, Quebec, Canada; McGill University, Faculty of Medicine, Montreal, Quebec, Canada
| | | | | | - Alan Spatz
- Lady Davis Institute for Medical Research, Quebec, Canada; McGill University, Department of Pathology, Quebec, Canada
| | - Matthew Oughton
- Department of Medical Microbiology, Jewish General Hospital, Quebec, Canada; McGill University, Faculty of Medicine, Montreal, Quebec, Canada.
| |
Collapse
|
27
|
Stone NE, Nunnally AE, Jimenez V, Cope EK, Sahl JW, Sheridan K, Hornstra HM, Vinocur J, Settles EW, Headley KC, Williamson CHD, Rideout JR, Bolyen E, Caporaso JG, Terriquez J, Monroy FP, Busch JD, Keim P, Wagner DM. Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins. Anaerobe 2019; 58:53-72. [PMID: 30946985 DOI: 10.1016/j.anaerobe.2019.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/11/2019] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
Clostridioides difficile infection (CDI) is an emerging public health threat and C. difficile is the most common cause of antimicrobial-associated diarrhea worldwide and the leading cause of hospital-associated infections in the US, yet the burden of community-acquired infections (CAI) is poorly understood. Characterizing C. difficile isolated from canines is important for understanding the role that canines may play in CAI. In addition, several studies have suggested that canines carry toxigenic C. difficile asymptomatically, which may imply that there are mechanisms responsible for resistance to CDI in canines that could be exploited to help combat human CDI. To assess the virulence potential of canine-derived C. difficile, we tested whether toxins TcdA and TcdB (hereafter toxins) derived from a canine isolate were capable of causing tight junction disruptions to colonic epithelial cells. Additionally, we addressed whether major differences exist between human and canine cells regarding C. difficile pathogenicity by exposing them to identical toxins. We then examined the canine gut microbiome associated with C. difficile carriage using 16S rRNA gene sequencing and searched for deviations from homeostasis as an indicator of CDI. Finally, we queried 16S rRNA gene sequences for bacterial taxa that may be associated with resistance to CDI in canines. Clostridioides difficile isolated from a canine produced toxins that reduced tight junction integrity in both human and canine cells in vitro. However, canine guts were not dysbiotic in the presence of C. difficile. These findings support asymptomatic carriage in canines and, furthermore, suggest that there are features of the gut microbiome and/or a canine-specific immune response that may protect canines against CDI. We identified two biologically relevant bacteria that may aid in CDI resistance in canines: 1) Clostridium hiranonis, which synthesizes secondary bile acids that have been shown to provide resistance to CDI in mice; and 2) Sphingobacterium faecium, which produces sphingophospholipids that may be associated with regulating homeostasis in the canine gut. Our findings suggest that canines may be cryptic reservoirs for C. difficile and, furthermore, that mechanisms of CDI resistance in the canine gut could provide insights into targeted therapeutics for human CDI.
Collapse
Affiliation(s)
- Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Amalee E Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Victor Jimenez
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Emily K Cope
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Krystal Sheridan
- Translational Genomics Research Institute, Flagstaff, AZ, 86001, USA.
| | - Heidie M Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jacob Vinocur
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ, 86001, USA.
| | - Erik W Settles
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Kyle C Headley
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Charles H D Williamson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jai Ram Rideout
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Evan Bolyen
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Joel Terriquez
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ, 86001, USA.
| | - Fernando P Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Joseph D Busch
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA; Translational Genomics Research Institute, Flagstaff, AZ, 86001, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| |
Collapse
|
28
|
Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota. Processes (Basel) 2019. [DOI: 10.3390/pr7020097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota and reduce competition for available nutrients, resulting in imbalance among commensal species and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of C. difficile with commensal species from the three dominant phyla in the human gut, we developed a multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile, Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance. We tuned the model to produce species abundances and short-chain fatty acid levels consistent with available data for healthy individuals. The model predicted that experimentally-observed host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels and/or increased primary bile acid levels would induce large increases in C. difficile abundance and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation of increased host nitrate secretion, the model also was able to predict increased E. coli abundance associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient levels and disease progression, the model generated hypotheses for future testing and has the capability to support the development of new treatment strategies for C. difficile gut infections.
Collapse
|
29
|
A reliable method for colorectal cancer prediction based on feature selection and support vector machine. Med Biol Eng Comput 2018; 57:901-912. [PMID: 30478811 DOI: 10.1007/s11517-018-1930-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 11/17/2018] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is a common cancer responsible for approximately 600,000 deaths per year worldwide. Thus, it is very important to find the related factors and detect the cancer accurately. However, timely and accurate prediction of the disease is challenging. In this study, we build an integrated model based on logistic regression (LR) and support vector machine (SVM) to classify the CRC into cancer and normal samples. From various factors, human location, age, gender, BMI, and cancer tumor type, tumor grade, and DNA, of the cancer, we select the most significant factors (p < 0.05) using logistic regression as main features, and with these features, a grid-search SVM model is designed using different kernel types (Linear, radial basis function (RBF), Sigmoid, and Polynomial). The result of the logistic regression indicates that the Firmicutes (AUC 0.918), Bacteroidetes (AUC 0.856), body mass index (BMI) (AUC 0.777), and age (AUC 0.710) and their combined factors (AUC 0.942) are effective for CRC detection. And the best kernel type is RBF, which achieves an accuracy of 90.1% when k = 5, and 91.2% when k = 10. This study provides a new method for colorectal cancer prediction based on independent risky factors. Graphical abstract Flow chart depicting the method adopted in the study. LR (logistic regression) and ROC curve are used to select independent features as input of SVM. SVM kernel selection aims to find the best kernel function for classification by comparing Linear, RBF, Sigmoid, and Polynomial kernel types of SVM, and the result shows the best kernel is RBF. Classification performance of LR + RF, LR + NB, LR + KNN, and LR + ANNs models are compared with LR + SVM. After these steps, the cancer and healthy individuals can be classified, and the best model is selected.
Collapse
|
30
|
Siddharthan R, Chapek M, Warren M, Martindale R. Probiotics in Prevention of Surgical Site Infections. Surg Infect (Larchmt) 2018; 19:781-784. [PMID: 30394861 DOI: 10.1089/sur.2018.231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Despite significant improvements in peri-operative care, surgical site infections (SSIs) remain an important contributor to morbidity, cost, and death. The human gastrointestinal tract is a complex microenvironment linking host cells and the indigenous microflora or "microbiome," creating a "super-organism" that engages in macro-nutrient and micro-nutrient extraction for the host while serving as a barrier to toxins and other detrimental bacterial end-products. Maintaining a healthy microbiome in the peri-operative period may enable control of multi-drug resistance (MDR) organisms, whereas use of antibiotics simply resets the dysbiotic relation by eliminating multiple strains of bacteria. Such loss of microbial diversity or abundance can slow wound healing. Use of pro-biotics to prevent infection has been evaluated in several studies, but their utility is not yet clear. There is a clear need for randomized trials to draw firm conclusions about their efficacy and to make clinical recommendations.
Collapse
Affiliation(s)
- Ragavan Siddharthan
- Department of Surgery, Oregon Health and Science University , Portland, Oregon
| | - Michael Chapek
- Department of Surgery, Oregon Health and Science University , Portland, Oregon
| | - Malissa Warren
- Department of Surgery, Oregon Health and Science University , Portland, Oregon
| | - Robert Martindale
- Department of Surgery, Oregon Health and Science University , Portland, Oregon
| |
Collapse
|
31
|
Brown JRM, Flemer B, Joyce SA, Zulquernain A, Sheehan D, Shanahan F, O'Toole PW. Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection. BMC Gastroenterol 2018; 18:131. [PMID: 30153805 PMCID: PMC6114236 DOI: 10.1186/s12876-018-0860-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/15/2018] [Indexed: 12/12/2022] Open
Abstract
Background Alteration of the gut microbiota by repeated antibiotic treatment increases susceptibility to Clostridioides difficile infection. Faecal microbiota transplantation from donors with a normal microbiota effectively treats C. difficile infection. Methods The study involved 10 patients with recurrent C. difficile infection, nine of whom received transplants from individual donors and one who received a donor unit from a stool bank (OpenBiome). Results All individuals demonstrated enduring post-transplant resolution of C. difficile- associated diarrhoea. Faecal microbiota diversity of recipients significantly increased, and the composition of the microbiota resembled that of the donor. Patients with C. difficile infection exhibited significantly lower faecal levels of secondary/ bile acids and higher levels of primary bile acids. Levels of secondary bile acids were restored in all transplant recipients, but to a lower degree with the OpenBiome transplant. The abundance increased of bacterial genera known from previous studies to confer resistance to growth and germination of C. difficile. These were significantly negatively associated with primary bile acid levels and positively related with secondary bile acid levels. Although reduced levels of the short chain fatty acids, butyrate, propionate and acetate, have been previously reported, here we report elevations in SCFA, pyruvic and lactic fatty acids, saturated, ω-6, monounsaturated, ω-3 and ω-6 polyunsaturated fatty acids (PUFA) in C. difficile infection. This potentially indicates one or a combination of increased dietary FA intake, microbial modification of FAs or epithelial cell damage and inflammatory cell recruitment. No reversion to donor FA profile occurred post-FMT but ω-3 to ω-6 PUFA ratios were altered in the direction of the donor. Archaeal metabolism genes were found in some samples post FMT. Conclusion A consistent metabolic signature was identified in the post-transplant microbiota, with reduced primary bile acids and substantial restoration of secondary bile acid production capacity. Total FA levels were unchanged but the ratio of inflammatory to non-inflammatory FAs decreased. Electronic supplementary material The online version of this article (10.1186/s12876-018-0860-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jillian R-M Brown
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Burkhardt Flemer
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, National University of Ireland, Cork, Ireland
| | - Akbar Zulquernain
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Donal Sheehan
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland. .,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| |
Collapse
|
32
|
Thorpe CM, Kane AV, Chang J, Tai A, Vickers RJ, Snydman DR. Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel Clostridium difficile-targeting antibacterial, compared to vancomycin. PLoS One 2018; 13:e0199810. [PMID: 30071046 PMCID: PMC6071993 DOI: 10.1371/journal.pone.0199810] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022] Open
Abstract
Ridinilazole, a novel targeted antibacterial being developed for the treatment of C. difficile infection (CDI) and prevention of recurrence, was shown in a recent Phase 2 study to be superior to vancomycin with regard to the primary efficacy measure, sustained clinical response (SCR), with the superiority being driven primarily by marked reductions in the rates of CDI recurrence within 30 days. Tolerability of ridinilazole was comparable to that of vancomycin. The current nested cohort study compared the effects of ridinilazole and vancomycin on fecal microbiota during and after treatment among participants in the Phase 2 study. Changes in the microbiota were assessed using qPCR and high-throughput sequencing on participants' stools collected at multiple time-points (baseline [Day 1], Day 5, end-of-treatment [EOT; Day 10], Day 25, end-of-study [EOS; Day 40], and at CDI recurrence). qPCR analyses showed profound losses of Bacteroides, C. coccoides, C. leptum, and Prevotella groups at EOT with vancomycin treatment, while ridinilazole-treated participants had a modest decrease in C. leptum group levels at EOT, with levels recovering by Day 25. Vancomycin-treated participants had a significant increase in the Enterobacteriaceae group, with this increase persisting beyond EOT. At EOT, alpha diversity decreased with both antibiotics, though to a significantly lesser extent with ridinilazole (p <0.0001). Beta diversity analysis showed a significantly larger weighted Unifrac distance from baseline-to-EOT with vancomycin. Taxonomically, ridinilazole had a markedly narrower impact, with modest reductions in relative abundance in Firmicutes taxa. Microbiota composition returned to baseline sooner with ridinilazole than with vancomycin. Vancomycin treatment resulted in microbiome-wide changes, with significant reductions in relative abundances of Firmicutes, Bacteroidetes, Actinobacteria, and a profound increase in abundance of Proteobacteria. These findings demonstrate that ridinilazole is significantly less disruptive to microbiota than vancomycin, which may contribute to the reduced CDI recurrence observed in the Phase 2 study.
Collapse
Affiliation(s)
- Cheleste M. Thorpe
- Tufts Medical Center, Boston, MA, United States of America
- Tufts University School of Medicine, Boston, MA, United States of America
| | - Anne V. Kane
- Tufts Medical Center, Boston, MA, United States of America
| | - Justin Chang
- Tufts University School of Medicine, Boston, MA, United States of America
| | - Albert Tai
- Tufts University School of Medicine, Boston, MA, United States of America
| | | | - David R. Snydman
- Tufts Medical Center, Boston, MA, United States of America
- Tufts University School of Medicine, Boston, MA, United States of America
| |
Collapse
|
33
|
Horvat S, Rupnik M. Interactions Between Clostridioides difficile and Fecal Microbiota in in Vitro Batch Model: Growth, Sporulation, and Microbiota Changes. Front Microbiol 2018; 9:1633. [PMID: 30087660 PMCID: PMC6066498 DOI: 10.3389/fmicb.2018.01633] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Disturbance in gut microbiota is crucial for the development of Clostridioides difficile infection (CDI). Different mechanisms through which gut microbiota influences C. difficile colonization are known. However, C. difficile could also affect gut microbiota balance as previously demonstrated by cultivation of fecal microbiota in C. difficile conditioned medium. In current study, the interactions of C. difficile cells with gut microbiota were addressed. Three different strains (ribotypes 027, 014/020, and 010) were co-cultivated with two types of fecal microbiota (healthy and dysbiotic) using in vitro batch model. While all strains showed higher sporulation frequency in the presence of dysbiotic fecal microbiota, the growth was strain dependent. C. difficile either proliferated to comparable levels in the presence of dysbiotic and healthy fecal microbiota or grew better in co-culture with dysbiotic microbiota. In co-cultures with any C. difficile strain fecal microbiota showed decreased richness and diversity. Dysbiotic fecal microbiota was more affected after co-culture with C. difficile than healthy microbiota. Altogether, 62 OTUs were significantly changed in co-cultures of dysbiotic microbiota/C. difficile and 45 OTUs in co-cultures of healthy microbiota/C. difficile. However, the majority of significantly changed OTUs in both types of microbiota belonged to the phylum Firmicutes with Lachnospiraceae and Ruminococcaceae origin.
Collapse
Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Centre for Medical Microbiology, National Laboratory for Health, Environment and Food, Maribor, Slovenia
| |
Collapse
|
34
|
Fecal Microbiome Among Nursing Home Residents with Advanced Dementia and Clostridium difficile. Dig Dis Sci 2018; 63:1525-1531. [PMID: 29594967 PMCID: PMC6434537 DOI: 10.1007/s10620-018-5030-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/15/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND/OBJECTIVES Patients colonized with toxinogenic strains of Clostridium difficile have an increased risk of subsequent infection. Given the potential role of the gut microbiome in increasing the risk of C. difficile colonization, we assessed the diversity and composition of the gut microbiota among long-term care facility (LTCF) residents with advanced dementia colonized with C. difficile. DESIGN Retrospective analysis of rectal samples collected during a prospective observational study. SETTING Thirty-five nursing homes in Boston, Massachusetts. PARTICIPANTS Eighty-seven LTCF residents with advanced dementia. MEASUREMENTS Operational taxonomic units were identified using 16S rRNA sequencing. Samples positive for C. difficile were matched to negative controls in a 1:3 ratio and assessed for differences in alpha diversity, beta diversity, and differentially abundant features. RESULTS Clostridium difficile sequence variants were identified among 7/87 (8.04%) residents. No patient had evidence of C. difficile infection. Demographic characteristics and antimicrobial exposure were similar between the seven cases and 21 controls. The overall biodiversity among cases and controls was reduced with a median Shannon index of 3.2 (interquartile range 2.7-3.9), with no statistically significant differences between groups. The bacterial community structure was significantly different among residents with C. difficile colonization versus those without and included a predominance of Akkermansia spp., Dermabacter spp., Romboutsia spp., Meiothermus spp., Peptoclostridium spp., and Ruminococcaceae UGC 009. CONCLUSION LTCF residents with advanced dementia have substantial dysbiosis of their gut microbiome. Specific taxa characterized C. difficile colonization status.
Collapse
|
35
|
Fareed S, Sarode N, Stewart FJ, Malik A, Laghaie E, Khizer S, Yan F, Pratte Z, Lewis J, Immergluck LC. Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children. PeerJ 2018; 6:e4663. [PMID: 29868248 PMCID: PMC5984579 DOI: 10.7717/peerj.4663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/02/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fecal Microbiota Transplantation (FMT) is an innovative means of treating recurrent Clostridium difficile infection (rCDI), through restoration of gut floral balance. However, there is a lack of data concerning the efficacy of FMT and its impact on the gut microbiome among pediatric patients. This study analyzes clinical outcomes and microbial community composition among 15 pediatric patients treated for rCDI via FMT. METHODS This is a prospective, observational, pilot study of 15 children ≤18 years, who presented for rCDI and who met inclusion criteria for FMT at a pediatric hospital and pediatric gastroenterology clinic. Past medical history and demographics were recorded at enrollment and subsequent follow-up. Specimens of the donors' and the patients' pre-FMT and post-FMT fecal specimen were collected and used to assess microbiome composition via 16S rRNA gene sequencing. RESULTS FMT successfully prevented rCDI episodes for minimum of 3 months post-FMT in all patients, with no major adverse effects. Three patients reported continued GI bleeding; however, all three also had underlying Inflammatory Bowel Disease (IBD). Our analyses confirm a significant difference between pre-and post-FMT gut microbiome profiles (Shannon diversity index), whereas no significant difference was observed between post-FMT and donor microbiome profiles. At the phyla level, post-FMT profiles showed significantly increased levels of Bacteroidetes and significantly decreased levels of Proteobacteria. Subjects with underlying IBD showed no difference in their pre-and post-FMT profiles. CONCLUSION The low rate of recurrence or re-infection by C. difficile, coupled with minimal adverse effects post-FMT, suggests that FMT is a viable therapeutic means to treat pediatric rCDI. Post-FMT microbiomes are different from pre-FMT microbiomes, and similar to those of healthy donors, suggesting successful establishment of a healthier microbiome.
Collapse
Affiliation(s)
- Shaaz Fareed
- Department of Microbiology/Biochemistry/Immunology, Morehouse School of Medicine, Atlanta, GA, United States of America
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Neha Sarode
- Department of Organismic & Evolutionary Biology, Harvard University, Boston, MA, United States of America
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Aneeq Malik
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Elham Laghaie
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Saadia Khizer
- Clinical Research, Children’s Healthcare of Atlanta, Atlanta, GA, United States of America
| | - Fengxia Yan
- Department of Community Health & Preventive Medicine, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Zoe Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Jeffery Lewis
- Pediatric Gastroenterology, Children’s Center for Digestive Health Care, LLC, Atlanta, GA, United States of America
| | - Lilly Cheng Immergluck
- Department of Microbiology/Biochemistry/Immunology, Morehouse School of Medicine, Atlanta, GA, United States of America
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| |
Collapse
|
36
|
Dong D, Ni Q, Wang C, Zhang L, Li Z, Jiang C, EnqiangMao, Peng Y. Effects of intestinal colonization by Clostridium difficile and Staphylococcus aureus on microbiota diversity in healthy individuals in China. BMC Infect Dis 2018; 18:207. [PMID: 29724187 PMCID: PMC5934869 DOI: 10.1186/s12879-018-3111-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/25/2018] [Indexed: 12/16/2022] Open
Abstract
Background Intestinal colonization by pathogenic bacteria is a risk factor for infection, and contributes to environmental contamination and disease dissemination. Alteration of gut microbiota also plays a pivotal role in the development of disease. Although Clostridium difficile and Staphylococcus aureus are well-recognized pathogens causing nosocomial and community infections, the intestinal colonization was not fully investigated. Herein, we explored their overall carriage rates in healthy adults from the community, and characterized the gut microbiomes of C. difficile and S. aureus carriers. Methods Fecal samples were collected from 1709 healthy volunteers from communities in Shanghai, China, and tested for the presence of C. difficile, methicillin-sensitive S. aureus (MSSA), and methicillin-resistant S. aureus (MRSA) using culture-based techniques. To explore differences in the gut microbiome, 16S rRNA gene sequencing was conducted using samples from non-carriers (CH), C. difficile carriers (CCD), MRSA carriers (CM), and MSSA carriers (CS). Results Overall, we detected 12 C. difficile and 60 S. aureus isolates, accounting for 0.70% and 3.51% of total isolates, respectively. Eight isolates were determined to be MRSA, accounting for 13.3% of the S. aureus population. Sequencing data revealed that the microbial diversity and richness were similar among the four groups. However, at the phylum level, carriage of C. difficile or MRSA was associated with a paucity of Bacteroidetes and an overabundance of Proteobacteria compared with non-carriers. At the genus level, the prevalence of the genera Bacteroides, Prevotella, Faecalibacterium, and Roseburia was decreased in C. difficile-positive samples compared with the controls, while the proportion of Clostridium cluster XIVa species was increased. MRSA carriers exhibited a higher proportion of the genera Parasutterella and Klebsiella, but a decreased prevalence of Bacteroides. Compared with MSSA carriers, Klebsiella was the only genus found to be significantly enriched in MRSA carriers. Conclusions In healthy adults, colonization by C. difficile or S. aureus did not significantly affect gut microbiota diversity. However, the alteration of the gut microbiota composition in C. difficile carriers could indicate a predisposition to further infection. Our study provides essential data on the prevalence and effects of C. difficile and S. aureus colonization on gut microbiota composition in healthy adults. Electronic supplementary material The online version of this article (10.1186/s12879-018-3111-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Qi Ni
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Chen Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - Lihua Zhang
- Department of Laboratory Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Zhen Li
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Medicine, No725 South Wanping Road, Shanghai, 200032, China
| | - Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China
| | - EnqiangMao
- Department of Emergency Intensive Care Unit, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China.
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin ER Road, Shanghai, 200025, China.
| |
Collapse
|
37
|
Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure. Sci Rep 2017; 7:16448. [PMID: 29180685 PMCID: PMC5703886 DOI: 10.1038/s41598-017-15434-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/26/2017] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile infection (CDI) is typically associated with disturbed gut microbiota and changes related to decreased colonization resistance against C. difficile are well described. However, nothing is known about possible effects of C. difficile on gut microbiota restoration during or after CDI. In this study, we have mimicked such a situation by using C. difficile conditioned medium of six different C. difficile strains belonging to PCR ribotypes 027 and 014/020 for cultivation of fecal microbiota. A marked decrease of microbial diversity was observed in conditioned medium of both tested ribotypes. The majority of differences occurred within the phylum Firmicutes, with a general decrease of gut commensals with putative protective functions (i.e. Lactobacillus, Clostridium_XIVa) and an increase in opportunistic pathogens (i.e. Enterococcus). Bacterial populations in conditioned medium differed between the two C. difficile ribotypes, 027 and 014/020 and are likely associated with nutrient availability. Fecal microbiota cultivated in medium conditioned by E. coli, Salmonella Enteritidis or Staphylococcus epidermidis grouped together and was clearly different from microbiota cultivated in C. difficile conditioned medium suggesting that C. difficile effects are specific. Our results show that the changes observed in microbiota of CDI patients are partially directly influenced by C. difficile.
Collapse
|
38
|
Papanicolas LE, Gordon DL, Wesselingh SL, Rogers GB. Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? Trends Microbiol 2017; 26:393-400. [PMID: 29146383 DOI: 10.1016/j.tim.2017.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 01/04/2023]
Abstract
The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.
Collapse
Affiliation(s)
- Lito E Papanicolas
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University, Adelaide, South Australia, Australia
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
| |
Collapse
|
39
|
Lee YJ, Arguello ES, Jenq RR, Littmann E, Kim GJ, Miller LC, Ling L, Figueroa C, Robilotti E, Perales MA, Barker JN, Giralt S, van den Brink MRM, Pamer EG, Taur Y. Protective Factors in the Intestinal Microbiome Against Clostridium difficile Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation. J Infect Dis 2017; 215:1117-1123. [PMID: 28498996 DOI: 10.1093/infdis/jix011] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Clostridium difficile infection (CDI) is a frequent complication in recipients of allogeneic hematopoietic stem cell transplantation (allo-HSCT), who receive intensive treatments that significantly disrupt the intestinal microbiota. In this study, we examined the microbiota composition of allo-HSCT recipients to identify bacterial colonizers that confer protection against CDI after engraftment. Methods Feces collected from adult recipients allo-HSCT at engraftment were analyzed; 16S ribosomal RNA genes were sequenced and analyzed from each sample. Bacterial taxa with protective effects against development of CDI were identified by means of linear discriminant analysis effect size analysis and then further assessed with clinical predictors of CDI using survival analysis. Results A total of 234 allo-HSCT recipients were studied; postengraftment CDI developed in 53 (22.6%). Within the composition of the microbiota, the presence of 3 distinct bacterial taxa was correlated with protection against CDI: Bacteroidetes, Lachnospiraceae, and Ruminococcaceae. Colonization with these groups at engraftment was associated with a 60% lower risk of CDI, independent of clinical factors. Conclusions Colonization with these 3 bacterial groups is associated with a lower risk of CDI. These groups have been shown to be vital components of the intestinal microbiota. Targeted efforts to maintain them may help minimize the risk of CDI in this at-risk population.
Collapse
Affiliation(s)
- Yeon Joo Lee
- Infectious Diseases Service and.,Weill Cornell Medical College, New York, New York
| | | | - Robert R Jenq
- Adult Bone Marrow Transplantation Service, Department of Medicine, and.,Weill Cornell Medical College, New York, New York
| | - Eric Littmann
- Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center
| | - Grace J Kim
- Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center
| | - Liza C Miller
- Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center
| | - Lilan Ling
- Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center
| | - Cesar Figueroa
- Infectious Diseases Service and.,Weill Cornell Medical College, New York, New York
| | - Elizabeth Robilotti
- Infectious Diseases Service and.,Weill Cornell Medical College, New York, New York
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, and.,Weill Cornell Medical College, New York, New York
| | - Juliet N Barker
- Adult Bone Marrow Transplantation Service, Department of Medicine, and.,Weill Cornell Medical College, New York, New York
| | - Sergio Giralt
- Adult Bone Marrow Transplantation Service, Department of Medicine, and.,Weill Cornell Medical College, New York, New York
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, and.,Weill Cornell Medical College, New York, New York
| | - Eric G Pamer
- Infectious Diseases Service and.,Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center.,Immunology Program, Sloan-Kettering Institute, and.,Weill Cornell Medical College, New York, New York
| | - Ying Taur
- Infectious Diseases Service and.,Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center.,Weill Cornell Medical College, New York, New York
| |
Collapse
|
40
|
Silverman MA, Konnikova L, Gerber JS. Impact of Antibiotics on Necrotizing Enterocolitis and Antibiotic-Associated Diarrhea. Gastroenterol Clin North Am 2017; 46:61-76. [PMID: 28164853 PMCID: PMC5314436 DOI: 10.1016/j.gtc.2016.09.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibiotic treatment alters the composition and metabolic function of the intestinal microbiota. These alterations may contribute to the pathogenesis of necrotizing enterocolitis (NEC) and antibiotic-associated diarrhea (AAD). Recent studies are beginning to unravel the contribution of specific groups of microbes and their metabolic pathways to these diseases. Probiotics or other microbiota-targeted therapies may provide effect strategies to prevent and treat NEC and AAD.
Collapse
Affiliation(s)
- Michael A. Silverman
- Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Liza Konnikova
- Department of Pediatric and Newborn Medicine, Brigham and Women’s Hospital, Boston, MA 02115 and Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jeffrey S. Gerber
- Center for Pediatric Clinical Effectiveness, Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
41
|
Freedberg DE, Salmasian H, Cohen B, Abrams JA, Larson EL. Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed. JAMA Intern Med 2016; 176:1801-1808. [PMID: 27723860 PMCID: PMC5138095 DOI: 10.1001/jamainternmed.2016.6193] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To assess whether receipt of antibiotics by prior hospital bed occupants is associated with increased risk for CDI in subsequent patients who occupy the same bed. DESIGN, SETTING, AND PARTICIPANTS This is a retrospective cohort study of adult patients hospitalized in any 1 of 4 facilities between 2010 and 2015. Patients were excluded if they had recent CDI, developed CDI within 48 hours of admission, had inadequate follow-up time, or if their prior bed occupant was in the bed for less than 24 hours. MAIN OUTCOMES AND MEASURES The primary exposure was receipt of non-CDI antibiotics by the prior bed occupant and the primary outcome was incident CDI in the subsequent patient to occupy the same bed. Incident CDI was defined as a positive result from a stool polymerase chain reaction for the C difficile toxin B gene followed by treatment for CDI. Demographics, comorbidities, laboratory data, and medication exposures are reported. RESULTS Among 100 615 pairs of patients who sequentially occupied a given hospital bed, there were 576 pairs (0.57%) in which subsequent patients developed CDI. Receipt of antibiotics in prior patients was significantly associated with incident CDI in subsequent patients (log-rank P < .01). This relationship remained unchanged after adjusting for factors known to influence risk for CDI including receipt of antibiotics by the subsequent patient (adjusted hazard ratio [aHR], 1.22; 95% CI, 1.02-1.45) and also after excluding 1497 patient pairs among whom the prior patients developed CDI (aHR, 1.20; 95% CI, 1.01-1.43). Aside from antibiotics, no other factors related to the prior bed occupants were associated with increased risk for CDI in subsequent patients. CONCLUSIONS AND RELEVANCE Receipt of antibiotics by prior bed occupants was associated with increased risk for CDI in subsequent patients. Antibiotics can directly affect risk for CDI in patients who do not themselves receive antibiotics.
Collapse
Affiliation(s)
- Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York
| | - Hojjat Salmasian
- Department of Biomedical Informatics, New York-Presbyterian Hospital, New York, New York
| | - Bevin Cohen
- Department of Epidemiology, Mailman School of Public Health, School of Nursing, Columbia University, New York, New York
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, New York
| | - Elaine L Larson
- Department of Epidemiology, Mailman School of Public Health, School of Nursing, Columbia University, New York, New York
| |
Collapse
|
42
|
Leelahavanichkul A, Panpetch W, Worasilchai N, Somparn P, Chancharoenthana W, Nilgate S, Finkelman M, Chindamporn A, Tumwasorn S. Evaluation of gastrointestinal leakage using serum (1→3)-β-D-glucan in a Clostridium difficile murine model. FEMS Microbiol Lett 2016; 363:fnw204. [PMID: 27573235 DOI: 10.1093/femsle/fnw204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2016] [Indexed: 12/26/2022] Open
Abstract
Gastrointestinal (GI) leakage in Clostridium difficile-associated diarrhea (CDAD) is well known but is not routinely assessed in clinical practice. Serum (1→3)-β-D-glucan (BG), a fungal cell wall component used as a biomarker for invasive fungal disease, was tested in a CDAD mouse model with and without probiotics. Higher serum fluorescein isothiocyanate-dextran (FITC-dextran) and spontaneous gram-negative bacteremia, GI leakage indicators, were frequently found in CDAD mice, which died compared with those which survived. BG, serum macrophage inflammatory protein-2 and FITC-dextran but not quantitative blood bacterial count differentiated the clinical severity. Interestingly, a specific dose of Lactobacillus rhamnosus L34 attenuated CDAD and decreased serum BG and FITC-dextran, but not other parameters. BG also showed a higher area under the receiver operating characteristic curve for 7-day mortality than FITC-dextran. Fifty-five percent of CDAD mice with BG ≥ 60 pg/ml (the human negative cut-off value for invasive fungal disease) at 1 day after C. difficile gavage died within 7 days. In conclusion, S: erum BG was elevated in mice with severe CDAD, an established model of GI leakage with a strong association with mortality rate. BG monitoring in patients with CDAD is of interest as both a potential prognostic tool and a therapeutic efficacy indicator.
Collapse
Affiliation(s)
- Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wimonrat Panpetch
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Navaporn Worasilchai
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Poorichaya Somparn
- Research Affairs, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Wiwat Chancharoenthana
- Division of Nephrology and Hypertension, Department of Medicine, Faculty of Medicine, Princess Chulabhorn College of Medical Sciences, Chulabhorn Royal Academy of Science (CRAS), Vipavadee road, Bangkok 10210, Thailand
| | - Sumanee Nilgate
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Malcolm Finkelman
- Department of Clinical Development, Associates of Cape Cod, Inc., 124 Bernard E. St. Jean Drive, East Falmouth, MA 02536, USA
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Somying Tumwasorn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| |
Collapse
|
43
|
Good JAD, Silver J, Núñez-Otero C, Bahnan W, Krishnan KS, Salin O, Engström P, Svensson R, Artursson P, Gylfe Å, Bergström S, Almqvist F. Thiazolino 2-Pyridone Amide Inhibitors of Chlamydia trachomatis Infectivity. J Med Chem 2016; 59:2094-108. [PMID: 26849778 DOI: 10.1021/acs.jmedchem.5b01759] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial pathogen Chlamydia trachomatis is a global health burden currently treated with broad-spectrum antibiotics which disrupt commensal bacteria. We recently identified a compound through phenotypic screening that blocked infectivity of this intracellular pathogen without host cell toxicity (compound 1, KSK 120). Herein, we present the optimization of 1 to a class of thiazolino 2-pyridone amides that are highly efficacious (EC50 ≤ 100 nM) in attenuating infectivity across multiple serovars of C. trachomatis without host cell toxicity. The lead compound 21a exhibits reduced lipophilicity versus 1 and did not affect the growth or viability of representative commensal flora at 50 μM. In microscopy studies, a highly active fluorescent analogue 37 localized inside the parasitiphorous inclusion, indicative of a specific targeting of bacterial components. In summary, we present a class of small molecules to enable the development of specific treatments for C. trachomatis.
Collapse
Affiliation(s)
- James A D Good
- Department of Chemistry, Umeå University , 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden
| | - Jim Silver
- Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden.,Department of Molecular Biology, Umeå University , 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , 901 87 Umeå, Sweden
| | - Carlos Núñez-Otero
- Department of Clinical Microbiology, Umeå University , 901 85 Umeå, Sweden
| | - Wael Bahnan
- Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden.,Department of Molecular Biology, Umeå University , 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , 901 87 Umeå, Sweden
| | - K Syam Krishnan
- Department of Chemistry, Umeå University , 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden
| | - Olli Salin
- Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , 901 87 Umeå, Sweden.,Department of Clinical Microbiology, Umeå University , 901 85 Umeå, Sweden
| | - Patrik Engström
- Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden.,Department of Molecular Biology, Umeå University , 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , 901 87 Umeå, Sweden
| | - Richard Svensson
- Department of Pharmacy, Uppsala University , SE-751 23 Uppsala, Sweden.,The Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Chemical Biology Consortium Sweden, Uppsala University , SE-751 23 Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University , SE-751 23 Uppsala, Sweden.,The Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Chemical Biology Consortium Sweden, Uppsala University , SE-751 23 Uppsala, Sweden
| | - Åsa Gylfe
- Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , 901 87 Umeå, Sweden.,Department of Clinical Microbiology, Umeå University , 901 85 Umeå, Sweden
| | - Sven Bergström
- Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden.,Department of Molecular Biology, Umeå University , 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , 901 87 Umeå, Sweden
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University , 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research, Umeå University , 901 87 Umeå, Sweden
| |
Collapse
|