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Top J, Verschuuren TD, Viveen MC, Riccio ME, Harbarth S, Kluytmans JAJW, Willems RJL, Paganelli FL. Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts. Microbiol Spectr 2023; 11:e0127523. [PMID: 37888982 PMCID: PMC10714770 DOI: 10.1128/spectrum.01275-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Colonization with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) often precedes infections and is therefore considered as a great threat for public health. Here, we studied the gut microbiome dynamics in eight index patients colonized with ESBL-PE after hospital discharge and the impact of exposure to this index patient on the gut microbiome dynamics of their household contacts. We showed that the microbiome composition from index patients is different from their household contacts upon hospital discharge and that, in some of the index patients, their microbiome composition over time shifted toward the composition of their household contacts. In contrast, household contacts showed a stable microbiome composition over time irrespective of low-level extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) gut colonization, suggesting that, in healthy microbiomes, colonization resistance is able to prevent ESBL-PE expansion.
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Affiliation(s)
- Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Marco C. Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M. Eugenia Riccio
- University of Geneva Hospitals and Faculty of Medicine, Infection Control Program, WHO Collaborating Center, Geneva, Switzerland
| | - Stephan Harbarth
- University of Geneva Hospitals and Faculty of Medicine, Infection Control Program, WHO Collaborating Center, Geneva, Switzerland
| | - Jan A. J. W. Kluytmans
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
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2
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Stege PB, Hordijk J, Sandholt AKS, Zomer AL, Viveen MC, Rogers MRC, Salomons M, Wagenaar JA, Mughini-Gras L, Willems RJL, Paganelli FL. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition. Microbiol Spectr 2023; 11:e0006323. [PMID: 37404183 PMCID: PMC10434115 DOI: 10.1128/spectrum.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.
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Affiliation(s)
- Paul B. Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joost Hordijk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arnar K. S. Sandholt
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Marco C. Viveen
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Moniek Salomons
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
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3
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de Vor L, van Dijk B, van Kessel K, Kavanaugh JS, de Haas C, Aerts PC, Viveen MC, Boel EC, Fluit AC, Kwiecinski JM, Krijger GC, Ramakers RM, Beekman FJ, Dadachova E, Lam MGEH, Vogely HC, van der Wal BCH, van Strijp JAG, Horswill AR, Weinans H, Rooijakkers SHM. Human monoclonal antibodies against Staphylococcus aureus surface antigens recognize in vitro and in vivo biofilm. eLife 2022; 11:e67301. [PMID: 34989676 PMCID: PMC8751199 DOI: 10.7554/elife.67301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
Implant-associated Staphylococcus aureus infections are difficult to treat because of biofilm formation. Bacteria in a biofilm are often insensitive to antibiotics and host immunity. Monoclonal antibodies (mAbs) could provide an alternative approach to improve the diagnosis and potential treatment of biofilm-related infections. Here, we show that mAbs targeting common surface components of S. aureus can recognize clinically relevant biofilm types. The mAbs were also shown to bind a collection of clinical isolates derived from different biofilm-associated infections (endocarditis, prosthetic joint, catheter). We identify two groups of antibodies: one group that uniquely binds S. aureus in biofilm state and one that recognizes S. aureus in both biofilm and planktonic state. Furthermore, we show that a mAb recognizing wall teichoic acid (clone 4497) specifically localizes to a subcutaneously implanted pre-colonized catheter in mice. In conclusion, we demonstrate the capacity of several human mAbs to detect S. aureus biofilms in vitro and in vivo.
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Affiliation(s)
- Lisanne de Vor
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Bruce van Dijk
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
| | - Kok van Kessel
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Jeffrey S Kavanaugh
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
| | - Carla de Haas
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Piet C Aerts
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Edwin C Boel
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Jakub M Kwiecinski
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
| | - Gerard C Krijger
- Department of Radiology and Nuclear Medicine, University Medical Centre UtrechtUtrechtNetherlands
| | - Ruud M Ramakers
- MILabs B.VUtrechtNetherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical CenterUtrechtNetherlands
- Department of Radiation Science and Technology, Delft University of TechnologyDelftNetherlands
| | - Freek J Beekman
- MILabs B.VUtrechtNetherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical CenterUtrechtNetherlands
- Department of Radiation Science and Technology, Delft University of TechnologyDelftNetherlands
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of SaskatchewanSaskatoonCanada
| | - Marnix GEH Lam
- Department of Radiology and Nuclear Medicine, University Medical Centre UtrechtUtrechtNetherlands
| | - H Charles Vogely
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
| | - Bart CH van der Wal
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
| | - Jos AG van Strijp
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
- Department of Veterans Affairs, Eastern Colorado Health Care SystemDenverUnited States
| | - Harrie Weinans
- Department of Orthopedics, University Medical Centre UtrechtUtrechtNetherlands
- Department of Biomechanical engineering, TU DelftDelftNetherlands
| | - Suzan HM Rooijakkers
- Department of Medical Microbiology, University Medical Centre UtrechtUtrechtNetherlands
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4
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Langedijk AC, Lebbink RJ, Naaktgeboren C, Evers A, Viveen MC, Greenough A, Heikkinen T, Stein RT, Richmond P, Martinón-Torres F, Nunes M, Hosoya M, Keller C, Bauck M, Cohen R, Papenburg J, Pernica J, Hennus MP, Jin H, Tabor DE, Tovchigrechko A, Ruzin A, Abram ME, Wilkins D, Wildenbeest JG, Kragten-Tabatabaie L, Coenjaerts FEJ, Esser MT, Bont LJ. Global molecular diversity of RSV - the "INFORM RSV" study. BMC Infect Dis 2020; 20:450. [PMID: 32591017 PMCID: PMC7316634 DOI: 10.1186/s12879-020-05175-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/17/2020] [Indexed: 11/30/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is a global cause of severe respiratory morbidity and mortality in infants. While preventive and therapeutic interventions are being developed, including antivirals, vaccines and monoclonal antibodies, little is known about the global molecular epidemiology of RSV. INFORM is a prospective, multicenter, global clinical study performed by ReSViNET to investigate the worldwide molecular diversity of RSV isolates collected from children less than 5 years of age. Methods The INFORM study is performed in 17 countries spanning all inhabited continents and will provide insight into the molecular epidemiology of circulating RSV strains worldwide. Sequencing of > 4000 RSV-positive respiratory samples is planned to detect temporal and geographical molecular patterns on a molecular level over five consecutive years. Additionally, RSV will be cultured from a subset of samples to study the functional implications of specific mutations in the viral genome including viral fitness and susceptibility to different monoclonal antibodies. Discussion The sequencing and functional results will be used to investigate susceptibility and resistance to novel RSV preventive or therapeutic interventions. Finally, a repository of globally collected RSV strains and a database of RSV sequences will be created.
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Affiliation(s)
- Annefleur C Langedijk
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christiana Naaktgeboren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anouk Evers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anne Greenough
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,ReSViNET foundation, Zeist, the Netherlands
| | - Terho Heikkinen
- ReSViNET foundation, Zeist, the Netherlands.,Department of Paediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Renato T Stein
- Centro INFANT at Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil
| | - Peter Richmond
- Department of Paediatrics, The University of Queensland, Brisbane, Australia
| | | | - Marta Nunes
- ReSViNET foundation, Zeist, the Netherlands.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, Faculty of health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mitsuaki Hosoya
- Department of Paediatrics, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Christian Keller
- Department of Virology, University Hospital Giessen and Marburg, Marburg, Germany
| | - Monika Bauck
- Department of Paediatrics, University Hospital Giessen and Marburg, Marburg, Germany
| | - Robert Cohen
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, CHI Créteil, GRC Gemini, Université Paris XII, Créteil, France
| | - Jesse Papenburg
- Department of Paediatrics, Division of Pediatric Infectious Diseases, Montreal Children's Hospital, McGill University Health Centre, Montreal, Canada
| | - Jeffrey Pernica
- Department of Paediatrics, McMaster University, Hamilton, Canada
| | - Marije P Hennus
- Paediatric Intensive Care Unit, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hong Jin
- AstraZeneca, Gaithersburg/South San Francisco, USA
| | | | | | - Alexey Ruzin
- AstraZeneca, Gaithersburg/South San Francisco, USA
| | | | | | - Joanne G Wildenbeest
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Frank E J Coenjaerts
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark T Esser
- AstraZeneca, Gaithersburg/South San Francisco, USA
| | - Louis J Bont
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands. .,ReSViNET foundation, Zeist, the Netherlands.
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5
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Berbers RM, Mohamed Hoesein FAA, Ellerbroek PM, van Montfrans JM, Dalm VASH, van Hagen PM, Paganelli FL, Viveen MC, Rogers MRC, de Jong PA, Uh HW, Willems RJL, Leavis HL. Low IgA Associated With Oropharyngeal Microbiota Changes and Lung Disease in Primary Antibody Deficiency. Front Immunol 2020; 11:1245. [PMID: 32636843 PMCID: PMC7318304 DOI: 10.3389/fimmu.2020.01245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Common Variable Immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA) are primary antibody deficiencies characterized by hypogammaglobulinemia and recurrent infections, which can lead to structural airway disease (AD) and interstitial lung disease (ILD). We investigated associations between serum IgA, oropharyngeal microbiota composition and severity of lung disease in these patients. In this cross-sectional multicentre study we analyzed oropharyngeal microbiota composition of 86 CVID patients, 12 XLA patients and 49 healthy controls (HC) using next-generation sequencing of the 16S rRNA gene. qPCR was used to estimate bacterial load. IgA was measured in serum. High resolution CT scans were scored for severity of AD and ILD. Oropharyngeal bacterial load was increased in CVID patients with low IgA (p = 0.013) and XLA (p = 0.029) compared to HC. IgA status was associated with distinct beta (between-sample) diversity (p = 0.039), enrichment of (Allo)prevotella, and more severe radiographic lung disease (p = 0.003), independently of recent antibiotic use. AD scores were positively associated with Prevotella, Alloprevotella, and Selenomonas, and ILD scores with Streptococcus and negatively with Rothia. In clinically stable patients with CVID and XLA, radiographic lung disease was associated with IgA deficiency and expansion of distinct oropharyngeal bacterial taxa. Our findings highlight IgA as a potential driver of upper respiratory tract microbiota homeostasis.
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Affiliation(s)
- Roos-Marijn Berbers
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | | | - Pauline M Ellerbroek
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Joris M van Montfrans
- Department of Paediatric Immunology and Infectious Diseases, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Virgil A S H Dalm
- Division of Clinical Immunology, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (RIDC), Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - P Martin van Hagen
- Division of Clinical Immunology, Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Immunology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (RIDC), Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Pim A de Jong
- Department of Radiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Hae-Won Uh
- Department of Biostatistics and Research Support, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
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6
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Paganelli FL, Luyer M, Hazelbag CM, Uh HW, Rogers MRC, Adriaans D, Berbers RM, Hendrickx APA, Viveen MC, Groot JA, Bonten MJM, Fluit AC, Willems RJL, Leavis HL. Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of surgery type. Sci Rep 2019; 9:10979. [PMID: 31358818 PMCID: PMC6662812 DOI: 10.1038/s41598-019-47332-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/08/2019] [Indexed: 02/07/2023] Open
Abstract
Bariatric surgery in morbid obesity, either through sleeve gastrectomy (SG) or Roux-Y gastric bypass (RYGB), leads to sustainable weight loss, improvement of metabolic disorders and changes in intestinal microbiota. Yet, the relationship between changes in gut microbiota, weight loss and surgical procedure remains incompletely understood. We determined temporal changes in microbiota composition in 45 obese patients undergoing crash diet followed by SG (n = 22) or RYGB (n = 23). Intestinal microbiota composition was determined before intervention (baseline, S1), 2 weeks after crash diet (S2), and 1 week (S3), 3 months (S4) and 6 months (S5) after surgery. Relative to S1, the microbial diversity index declined at S2 and S3 (p < 0.05), and gradually returned to baseline levels at S5. Rikenellaceae relative abundance increased and Ruminococcaceae and Streptococcaceae abundance decreased at S2 (p < 0.05). At S3, Bifidobacteriaceae abundance decreased, whereas those of Streptococcaceae and Enterobacteriaceae increased (p < 0.05). Increased weight loss between S3-S5 was not associated with major changes in microbiota composition. No significant differences appeared between both surgical procedures. In conclusion, undergoing a crash diet and bariatric surgery were associated with an immediate but temporary decline in microbial diversity, with immediate and permanent changes in microbiota composition, independent of surgery type.
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Affiliation(s)
- Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Misha Luyer
- Department of Surgery, Catharina Hospital Eindhoven, Eindhoven, The Netherlands
| | - C Marijn Hazelbag
- Department of Biostatistics and Research Support, Julius Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hae-Won Uh
- Department of Biostatistics and Research Support, Julius Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danielle Adriaans
- Department of Surgery, Catharina Hospital Eindhoven, Eindhoven, The Netherlands
| | - Roos-Marijn Berbers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - James A Groot
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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7
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Sachs N, Papaspyropoulos A, Zomer-van Ommen DD, Heo I, Böttinger L, Klay D, Weeber F, Huelsz-Prince G, Iakobachvili N, Amatngalim GD, de Ligt J, van Hoeck A, Proost N, Viveen MC, Lyubimova A, Teeven L, Derakhshan S, Korving J, Begthel H, Dekkers JF, Kumawat K, Ramos E, van Oosterhout MF, Offerhaus GJ, Wiener DJ, Olimpio EP, Dijkstra KK, Smit EF, van der Linden M, Jaksani S, van de Ven M, Jonkers J, Rios AC, Voest EE, van Moorsel CH, van der Ent CK, Cuppen E, van Oudenaarden A, Coenjaerts FE, Meyaard L, Bont LJ, Peters PJ, Tans SJ, van Zon JS, Boj SF, Vries RG, Beekman JM, Clevers H. Long-term expanding human airway organoids for disease modeling. EMBO J 2019; 38:embj.2018100300. [PMID: 30643021 PMCID: PMC6376275 DOI: 10.15252/embj.2018100300] [Citation(s) in RCA: 514] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 12/30/2022] Open
Abstract
Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here, we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar resections or lavage material. The pseudostratified airway organoids consist of basal cells, functional multi-ciliated cells, mucus-producing secretory cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoids established from lung cancer resections and metastasis biopsies retain tumor histopathology as well as cancer gene mutations and are amenable to drug screening. Respiratory syncytial virus (RSV) infection recapitulates central disease features, dramatically increases organoid cell motility via the non-structural viral NS2 protein, and preferentially recruits neutrophils upon co-culturing. We conclude that human airway organoids represent versatile models for the in vitro study of hereditary, malignant, and infectious pulmonary disease.
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Affiliation(s)
- Norman Sachs
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Inha Heo
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Lena Böttinger
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Dymph Klay
- St. Antonius Hospital Nieuwegein, Nieuwegein, The Netherlands
| | - Fleur Weeber
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Natalie Proost
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Anna Lyubimova
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Luc Teeven
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Sepideh Derakhshan
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Jeroen Korving
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Johanna F Dekkers
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | - Kuldeep Kumawat
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Emilio Ramos
- Hubrecht Organoid Technology, Utrecht, The Netherlands
| | | | | | - Dominique J Wiener
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Egbert F Smit
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Mouse Clinic for Cancer and Aging (MCCA) Preclinical Intervention Unit, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Emile E Voest
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Linde Meyaard
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Louis J Bont
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Sylvia F Boj
- Hubrecht Organoid Technology, Utrecht, The Netherlands
| | | | - Jeffrey M Beekman
- Wilhelmina Children's Hospital and UMC Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW and UMC Utrecht, Utrecht, The Netherlands .,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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8
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Nieuwkamp DJ, Murk JL, van Oosten BW, Cremers CHP, Killestein J, Viveen MC, Van Hecke W, Frijlink DW, Wattjes MP. PML in a patient without severe lymphocytopenia receiving dimethyl fumarate. N Engl J Med 2015; 372:1474-6. [PMID: 25853764 DOI: 10.1056/nejmc1413724] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Majchrzykiewicz-Koehorst JA, Heikens E, Trip H, Hulst AG, de Jong AL, Viveen MC, Sedee NJA, van der Plas J, Coenjaerts FEJ, Paauw A. Rapid and generic identification of influenza A and other respiratory viruses with mass spectrometry. J Virol Methods 2015; 213:75-83. [PMID: 25500183 PMCID: PMC7113647 DOI: 10.1016/j.jviromet.2014.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/13/2014] [Accepted: 11/18/2014] [Indexed: 12/03/2022]
Abstract
The rapid identification of existing and emerging respiratory viruses is crucial in combating outbreaks and epidemics. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and reliable identification method in bacterial diagnostics, but has not been used in virological diagnostics. Mass spectrometry systems have been investigated for the identification of respiratory viruses. However, sample preparation methods were laborious and time-consuming. In this study, a reliable and rapid sample preparation method was developed allowing identification of cultured respiratory viruses. Tenfold serial dilutions of ten cultures influenza A strains, mixed samples of influenza A virus with human metapneumovirus or respiratory syncytial virus, and reconstituted clinical samples were treated with the developed sample preparation method. Subsequently, peptides were subjected to MALDI-TOF MS and liquid chromatography tandem mass spectrometry (LC-MS/MS). The influenza A strains were identified to the subtype level within 3h with MALDI-TOF MS and 6h with LC-MS/MS, excluding the culturing time. The sensitivity of LC-MS/MS was higher compared to MALDI-TOF MS. In addition, LC-MS/MS was able to discriminate between two viruses in mixed samples and was able to identify virus from reconstituted clinical samples. The development of an improved and rapid sample preparation method allowed generic and rapid identification of cultured respiratory viruses by mass spectrometry.
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Affiliation(s)
- Joanna A Majchrzykiewicz-Koehorst
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Esther Heikens
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Hein Trip
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Albert G Hulst
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Ad L de Jong
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Marco C Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Norbert J A Sedee
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands
| | - Jan van der Plas
- Expert Centre Force Health Protection, Health Care Division, Support Command, Ministry of Defence, Korte Molenweg 3, Building 37, 3941 PW Doorn, The Netherlands
| | - Frank E J Coenjaerts
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Armand Paauw
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Lange Kleiweg 137, 2288 GJ Rijswijk, The Netherlands.
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10
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Kruijsen D, Bakkers MJ, van Uden NO, Viveen MC, van der Sluis TC, Kimpen JL, Leusen JH, Coenjaerts FE, van Bleek GM. Serum antibodies critically affect virus-specific CD4+/CD8+ T cell balance during respiratory syncytial virus infections. J Immunol 2010; 185:6489-98. [PMID: 20971927 DOI: 10.4049/jimmunol.1002645] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Following infection with respiratory syncytial virus (RSV), reinfection in healthy individuals is common and presumably due to ineffective memory T cell responses. In peripheral blood of healthy adults, a higher CD4(+)/CD8(+) memory T cell ratio was observed compared with the ratio of virus-specific effector CD4(+)/CD8(+) T cells that we had found in earlier work during primary RSV infections. In mice, we show that an enhanced ratio of RSV-specific neutralizing to nonneutralizing Abs profoundly enhanced the CD4(+) T cell response during RSV infection. Moreover, FcγRs and complement factor C1q contributed to this Ab-mediated enhancement. Therefore, the increase in CD4(+) memory T cell response likely occurs through enhanced endosomal Ag processing dependent on FcγRs. The resulting shift in memory T cell response was likely amplified by suppressed T cell proliferation caused by RSV infection of APCs, a route important for Ag presentation via MHC class I molecules leading to CD8(+) T cell activation. Decreasing memory CD8(+) T cell numbers could explain the inadequate immunity during repeated RSV infections. Understanding this interplay of Ab-mediated CD4(+) memory T cell response enhancement and infection mediated CD8(+) memory T cell suppression is likely critical for development of effective RSV vaccines.
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Affiliation(s)
- Debby Kruijsen
- Department of Pediatrics, Wilhelmina Children's Hospital, Utrecht, The Netherlands
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11
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Lukens MV, van de Pol AC, Coenjaerts FEJ, Jansen NJG, Kamp VM, Kimpen JLL, Rossen JWA, Ulfman LH, Tacke CEA, Viveen MC, Koenderman L, Wolfs TFW, van Bleek GM. A systemic neutrophil response precedes robust CD8(+) T-cell activation during natural respiratory syncytial virus infection in infants. J Virol 2010; 84:2374-83. [PMID: 20015982 PMCID: PMC2820924 DOI: 10.1128/jvi.01807-09] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 12/07/2009] [Indexed: 01/09/2023] Open
Abstract
Severe primary respiratory syncytial virus (RSV) infections are characterized by bronchiolitis accompanied by wheezing. Controversy exists as to whether infants suffer from virus-induced lung pathology or from excessive immune responses. Furthermore, detailed knowledge about the development of primary T-cell responses to viral infections in infants is lacking. We studied the dynamics of innate neutrophil and adaptive T-cell responses in peripheral blood in relation to the viral load and parameters of disease in infants admitted to the intensive care unit with severe RSV infection. Analysis of primary T-cell responses showed substantial CD8(+) T-cell activation, which peaked during convalescence. A strong neutrophil response, characterized by mobilization of bone marrow-derived neutrophil precursors, preceded the peak in T-cell activation. The kinetics of this neutrophil response followed the peak of clinical symptoms and the viral load with a 2- to 3-day delay. From the sequence of events, we conclude that CD8(+) T-cell responses, initiated during primary RSV infections, are unlikely to contribute to disease when it is most severe. The mobilization of precursor neutrophils might reflect the strong neutrophil influx into the airways, which is a characteristic feature during RSV infections and might be an integral pathogenic process in the disease.
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Affiliation(s)
- Michaël V. Lukens
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Alma C. van de Pol
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Frank E. J. Coenjaerts
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Nicolaas J. G. Jansen
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Vera M. Kamp
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Jan L. L. Kimpen
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - John W. A. Rossen
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Laurien H. Ulfman
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Carline E. A. Tacke
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Marco C. Viveen
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Leo Koenderman
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Tom F. W. Wolfs
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - Grada M. van Bleek
- Department of Pediatrics, The Wilhelmina Children's Hospital, Department of Medical Microbiology, Department of Respiratory Medicine, University Medical Center, Utrecht, Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital, Tilburg, The Netherlands
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