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Rodriguez-Ruiz JP, Lin Q, Van Heirstraeten L, Lammens C, Stewardson AJ, Godycki-Cwirko M, Coenen S, Goossens H, Harbarth S, Malhotra-Kumar S. Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses. Int J Antimicrob Agents 2024; 64:107259. [PMID: 38936492 DOI: 10.1016/j.ijantimicag.2024.107259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Urinary tract infections (UTIs) are one of the main reasons for antibiotic prescriptions in primary care. Recent studies demonstrate similar clinical outcomes with short vs. long antibiotics courses. The aim of this study was to investigate the differential collateral effect of ciprofloxacin treatment duration on the gastrointestinal and oropharyngeal microbiome in patients presenting with uncomplicated UTI to primary care practices in Switzerland, Belgium and Poland. METHODS Stool and oropharyngeal samples were obtained from 36 treated patients and 14 controls at the beginning of antibiotic therapy, end of therapy and one month after the end of therapy. Samples underwent shotgun metagenomics. RESULTS At the end of therapy, patients treated with both short (≤7 days) and long (>7 days) ciprofloxacin courses showed similar changes in the gastrointestinal microbiome compared to non-treated controls. After one month, most changes in patients receiving short courses were reversed; however, long courses led to increased abundance of the genera Roseburia, Faecalicatena and Escherichia. Changes in the oropharynx were minor and reversed to baseline levels within one month. Ciprofloxacin resistance encoding mutations in gyrA/B and parC/E reads were observed in both short and long treatment groups but decreased to baseline levels after one month. An increased abundance of resistance genes was observed in the gastrointestinal microbiome after longer treatment, and correlated to increased prevalence of aminoglycoside, β-lactam, sulphonamide, and tetracycline resistance genes. CONCLUSION Collateral effects on the gastrointestinal community, including an increased prevalence of antimicrobial resistance genes, persists for up to at least one month following longer ciprofloxacin therapy. These data support the use of shorter antimicrobial treatment duration.
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Affiliation(s)
- J P Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Q Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - L Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - C Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - A J Stewardson
- Department of Infectious Diseases, The Alfred and Central Clinical School, Monash University, Melbourne, Australia
| | - M Godycki-Cwirko
- Centre for Family and Community Medicine, Medical University of Lodz, Lodz, Poland
| | - S Coenen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - H Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - S Harbarth
- Infection Control Program & Division of Infectious Diseases, University of Geneva and Faculty of Medicine, Geneva
| | - S Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
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3
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Zeamer AL, Salive MC, An X, Beaudoin FL, House SL, Stevens JS, Zeng D, Neylan TC, Clifford GD, Linnstaedt SD, Rauch SL, Storrow AB, Lewandowski C, Musey PI, Hendry PL, Sheikh S, Jones CW, Punches BE, Swor RA, Hudak LA, Pascual JL, Seamon MJ, Harris E, Pearson C, Peak DA, Merchant RC, Domeier RM, Rathlev NK, O'Neil BJ, Sergot P, Sanchez LD, Bruce SE, Kessler RC, Koenen KC, McLean SA, Bucci V, Haran JP. Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure. Transl Psychiatry 2023; 13:354. [PMID: 37980332 PMCID: PMC10657470 DOI: 10.1038/s41398-023-02643-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biological mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition after trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether the gut microbiomes of trauma-exposed emergency department patients who develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms. We performed metagenomic analysis on stool samples (n = 51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Two-, eight- and twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and encoded metabolic pathways from stool metagenomics. Microbial species, including Flavonifractor plautii, Ruminococcus gnavus and, Bifidobacterium species, which are prevalent commensal gut microbes, were found to be important in predicting worse APNS outcomes from microbial abundance data. Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. Common commensal microbial species are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, a metabolic change that has also been demonstrated in the plasma of patients with PTSD.
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Affiliation(s)
- Abigail L Zeamer
- Department of Microbiology and Physiologic Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marie-Claire Salive
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Xinming An
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesca L Beaudoin
- Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Emergency Medicine, Brown University, Providence, RI, USA
| | - Stacey L House
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer S Stevens
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Donglin Zeng
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas C Neylan
- Departments of Psychiatry and Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Gari D Clifford
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Sarah D Linnstaedt
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Many Brains Project, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Scott L Rauch
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, McLean Hospital, Belmont, MA, USA
| | - Alan B Storrow
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Paul I Musey
- Department of Emergency Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Phyllis L Hendry
- Department of Emergency Medicine, University of Florida College of Medicine-Jacksonville, Jacksonville, FL, USA
| | - Sophia Sheikh
- Department of Emergency Medicine, University of Florida College of Medicine-Jacksonville, Jacksonville, FL, USA
| | - Christopher W Jones
- Department of Emergency Medicine, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Brittany E Punches
- Department of Emergency Medicine, Ohio State University College of Medicine, Columbus, OH, USA
- Ohio State University College of Nursing, Columbus, OH, USA
| | - Robert A Swor
- Department of Emergency Medicine, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Lauren A Hudak
- Department of Emergency Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jose L Pascual
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark J Seamon
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Harris
- Department of Emergency Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - Claire Pearson
- Department of Emergency Medicine, Wayne State University, Ascension St. John Hospital, Detroit, MI, USA
| | - David A Peak
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Roland C Merchant
- Department of Emergency Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert M Domeier
- Department of Emergency Medicine, Trinity Health-Ann Arbor, Ypsilanti, MI, USA
| | - Niels K Rathlev
- Department of Emergency Medicine, University of Massachusetts Medical School-Baystate, Springfield, MA, USA
| | - Brian J O'Neil
- Department of Emergency Medicine, Wayne State University, Detroit Receiving Hospital, Detroit, MI, USA
| | - Paulina Sergot
- Department of Emergency Medicine, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Leon D Sanchez
- Department of Emergency Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
| | - Steven E Bruce
- Department of Psychological Sciences, University of Missouri - St. Louis, St. Louis, MO, USA
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | | | - Samuel A McLean
- Department of Emergency Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vanni Bucci
- Department of Microbiology and Physiologic Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - John P Haran
- Department of Microbiology and Physiologic Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Microbiome Dynamics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Deianova N, de Boer NK, Aoulad Ahajan H, Verbeek C, Aarnoudse-Moens CSH, Leemhuis AG, van Weissenbruch MM, van Kaam AH, Vijbrief DC, Hulzebos CV, Giezen A, Cossey V, de Boode WP, de Jonge WJ, Benninga MA, Niemarkt HJ, de Meij TGJ. Duration of Neonatal Antibiotic Exposure in Preterm Infants in Association with Health and Developmental Outcomes in Early Childhood. Antibiotics (Basel) 2023; 12:967. [PMID: 37370287 PMCID: PMC10295560 DOI: 10.3390/antibiotics12060967] [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: 04/24/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Over 90% of preterm neonates are, often empirically, exposed to antibiotics as a potentially life-saving measure against sepsis. Long-term outcome in association with antibiotic exposure (NABE) has insufficiently been studied after preterm birth. We investigated the association of NABE-duration with early-childhood developmental and health outcomes in preterm-born children and additionally assessed the impact of GA on outcomes. Preterm children (GA < 30 weeks) participating in a multicenter cohort study were approached for follow-up. General expert-reviewed health questionnaires on respiratory, atopic and gastrointestinal symptoms were sent to parents of children > 24 months' corrected age (CA). Growth and developmental assessments (Bayley Scales of Infant and Toddler Development (BSID) III) were part of standard care assessment at 24 months' CA. Uni- and multivariate regressions were performed with NABE (per 5 days) and GA (per week) as independent variables. Odds ratios (OR) for health outcomes were adjusted (aOR) for confounders, where appropriate. Of 1079 infants whose parents were approached, 347 (32%) responded at a mean age of 4.6 years (SD 0.9). In children with NABE (97%), NABE duration decreased by 1.6 days (p < 0.001) per week of gestation. Below-average gross-motor development (BSID-III gross-motor score < 8) was associated with duration of NABE (aOR = 1.28; p = 0.04). The aOR for constipation was 0.81 (p = 0.04) per gestational week. Growth was inversely correlated with GA. Respiratory and atopic symptoms were not associated with NABE, nor GA. We observed that prolonged NABE after preterm birth was associated with below-average gross-motor development at 24 months' CA, while a low GA was associated with lower weight and stature Z-scores and higher odds for constipation.
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Affiliation(s)
- Nancy Deianova
- Department of Pediatric Gastroenterology, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands (T.G.J.d.M.)
- Department of Pediatric Gastroenterology, Amsterdam UMC Location University of Amsterdam, Amsterdam Reproduction & Development Research Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Neonatology, Máxima Medical Center, 5504 DB Veldhoven, The Netherlands;
| | - Nanne K. de Boer
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Hafsa Aoulad Ahajan
- Department of Pediatric Gastroenterology, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands (T.G.J.d.M.)
| | - Cilla Verbeek
- Department of Pediatric Gastroenterology, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands (T.G.J.d.M.)
| | - Cornelieke S. H. Aarnoudse-Moens
- Department of Neonatology, Emma Children’s Hospital, Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Aleid G. Leemhuis
- Department of Neonatology, Emma Children’s Hospital, Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Mirjam M. van Weissenbruch
- Department of Neonatology, Emma Children’s Hospital, Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Anton H. van Kaam
- Department of Neonatology, Emma Children’s Hospital, Amsterdam Reproduction and Development Research Institute, 1105 AZ Amsterdam, The Netherlands
| | - Daniel C. Vijbrief
- Department of Neonatology, University Medical Center Utrecht, Wilhelmina Children’s Hospital, 3584 CX Utrecht, The Netherlands
| | - Chris V. Hulzebos
- Department of Neonatology, Beatrix Children’s Hospital, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Astrid Giezen
- Department of Neonatology, Isala Hospital, Amalia Children’s Center, 8025 AB Zwolle, The Netherlands
| | - Veerle Cossey
- Department of Neonatology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Willem P. de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, 6525 XZ Nijmegen, The Netherlands
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Marc A. Benninga
- Department of Pediatric Gastroenterology, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands (T.G.J.d.M.)
| | - Hendrik J. Niemarkt
- Department of Neonatology, Máxima Medical Center, 5504 DB Veldhoven, The Netherlands;
| | - Tim G. J. de Meij
- Department of Pediatric Gastroenterology, Emma Children’s Hospital, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands (T.G.J.d.M.)
- Department of Pediatric Gastroenterology, Amsterdam UMC Location University of Amsterdam, Amsterdam Reproduction & Development Research Institute, 1105 AZ Amsterdam, The Netherlands
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Matzaras R, Nikopoulou A, Protonotariou E, Christaki E. Gut Microbiota Modulation and Prevention of Dysbiosis as an Alternative Approach to Antimicrobial Resistance: A Narrative Review. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:479-494. [PMID: 36568836 PMCID: PMC9765331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background: The importance of gut microbiota in human health is being increasingly studied. Imbalances in gut microbiota have been associated with infection, inflammation, and obesity. Antibiotic use is the most common and significant cause of major alterations in the composition and function of the gut microbiota and can result in colonization with multidrug-resistant bacteria. Methods: The purpose of this review is to present existing evidence on how microbiota modulation and prevention of gut dysbiosis can serve as tools to combat antimicrobial resistance. Results: While the spread of antibiotic-resistant pathogens requires antibiotics with novel mechanisms of action, the number of newly discovered antimicrobial classes remains very low. For this reason, the application of alternative modalities to combat antimicrobial resistance is necessary. Diet, probiotics/prebiotics, selective oropharyngeal or digestive decontamination, and especially fecal microbiota transplantation (FMT) are under investigation with FMT being the most studied. But, as prevention is better than cure, the implementation of antimicrobial stewardship programs and strict infection control measures along with newly developed chelating agents could also play a crucial role in decreasing colonization with multidrug resistant organisms. Conclusion: New alternative tools to fight antimicrobial resistance via gut microbiota modulation, seem to be effective and should remain the focus of further research and development.
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Affiliation(s)
- Rafail Matzaras
- Infectious Diseases Unit, Department of Medicine,
University General Hospital of Ioannina, University of Ioannina, Ioannina,
Greece
| | - Anna Nikopoulou
- Department of Internal Medicine, G. Papanikolaou
General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Efthimia Protonotariou
- Department of Microbiology, AHEPA University Hospital,
Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eirini Christaki
- Infectious Diseases Unit, Department of Medicine,
University General Hospital of Ioannina, University of Ioannina, Ioannina,
Greece,To whom all correspondence should be addressed:
Eirini Christaki, University General Hospital of Ioannina, St. Niarchou,
Ioannina, Greece; ; ORCID:
https://www.orcid.org/0000-0002-8152-6367
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Yahav D, Paul M, Van Nieuwkoop C, Huttner A. Is shorter always better? The pros and cons of treating Gram-negative bloodstream infections with 7 days of antibiotics. JAC Antimicrob Resist 2022; 4:dlac058. [PMID: 35719202 PMCID: PMC9201237 DOI: 10.1093/jacamr/dlac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Accumulating evidence from randomized controlled trials (RCTs) supports 7 days treatment for uncomplicated Gram-negative bacteraemia. However, some patient populations were not well represented in these RCTs, including critically ill patients, immunocompromised patients and those with MDR bacteria. In this debate document, we discuss the pros and cons for treating patients with Gram-negative bacteraemia with a 7 day antibiotic course. We surmise that the patients who were not well represented in the RCTs are probably those who have most to lose from the drawbacks of prolonged antibiotic courses, including adverse events, superinfections and resistance development. Treatment durations among these patients can be managed individually, with C-reactive protein or procalcitonin guidance or by clinical measures, and with care to discontinue antibiotics as soon as the patient recovers clinically from the infection.
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Affiliation(s)
- Dafna Yahav
- Infectious Diseases Unit, Sheba Medical Center , Ramat-Gan , Israel
- Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus , Haifa , Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology , Haifa , Israel
| | - Cees Van Nieuwkoop
- Department of Internal Medicine, Haga Teaching Hospital , The Hague , The Netherlands
| | - Angela Huttner
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine , Geneva , Switzerland
- Centre for Clinical Research, Geneva University , Geneva , Switzerland
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