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1. Conception and validation of A 3d printed learning model of supra condylar fracture of children

Author

Alexis Lubet, Mariette Renaux-Petel, Laurent Delbreilh, Agnès Liard-Zmuda, Annabelle Auble, and Mathilde Payen

Subjects
3D printing, Supra condylar fracture, Learning model, Surgical education, Science (General), Q1-390, Social sciences (General), H1-99
Abstract

The supracondylar fracture of the child is a common fracture. Its physiology, physiopathology and treatment use periosteum. As far as we know, there is no 3D printed model of this typical fracture in children with periosteum. The purposes of the research are to present the concept of an educational 3D printed supra condylar model with periosteum of the child and its expert validation. Materials and methods: The basis for the paediatric elbow model was a 3D scan of a four-year-old girl. Once the data had been extracted, the models were constructed using 3D Slicer®, Autodesk fusion 360® and Ultimaker Cura® software's. The Creality 3D Ender 6 SE Printer® used PLA filaments to print bone and TPU for periosteum. Printing took place at the University Hospital and the steps were modelled by hand. 3D printed bones and 3D printed periosteum were manually assembled. Participants: Expert validation with twelve paediatric orthopaedic surgeons took place in three University hospitals of the North of France. Results: Four Lagrange and Rigault 3D printed models of supracondylar fractures with periosteum were obtained with 200 h of design, printing and manual assembly based on a four-year-old elbow. According to the paediatric orthopaedic surgery experts, the size of the model is very good, but the model itself is of little interest compared to the information provided by the reconstruction of a 3D scanner. In total, with 9 out of 12 questions scoring higher than 8/10, the model was considered to be a good model for informing parents and teaching students. Conclusions: This study details the design of the first 3D-printed supra condylar fracture model in children with a full-size physeal and periosteum. The model has been validated by paediatric orthopaedic surgery experts.

Published
2024
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2. Evaluation of an Antibiotic Susceptibility Testing Method on Enterobacterales-Positive Blood Cultures in Less Than 8 h Using the Rapid Mueller-Hinton Diffusion Method in Conjunction with the SIRscan 2000 Automatic Reading Device

Author

Mathilde Payen, Alice Gaudart, Kevin Legueult, James Kasprzak, Audrey Emery, Grégoire Mutambayi, Christian Pradier, Frédéric Robin, Romain Lotte, and Raymond Ruimy

Subjects
antibiotic susceptibility testing, rapid AST, bacteremia, Biology (General), QH301-705.5
Abstract

Enterobacterales bloodstream infections are life-threatening and require rapid, targeted antibiotherapy based on antibiotic susceptibility testing (AST). A new method using Muller-Hinton Rapid-SIR (MHR-SIR) agar (i2a, Montpellier, France) allows complete direct AST (dAST) to be read from positive blood culture bottles (BCBs) for all Enterobacterales species after 6–8 h of incubation. We evaluated (i) the performance of dAST from positive BCBs on MHR-SIR agar using two different inoculum protocols; (ii) the categorical agreement between dAST results obtained with MHR-SIR agar vs. those obtained with Muller-Hinton (MH) agar; and (iii) the ability of the MHR-SIR medium to detect β-lactam resistant Enterobacterales. Finally, we estimated the saved turnaround time (TAT) with MHR-SIR compared with MH agar in our 24/7 laboratory. Our results showed that the most suitable inoculation protocol for dAST on MHR-SIR agar was 1 drop of BCB/5 mL H2O. For monomicrobial Enterobacterales BCBs, dAST performed on MHR-SIR medium showed 99.3% categorical agreement with AST on MH agar. Furthermore, MHR-SIR agar allows early detection of β-lactam resistance mechanisms, including AmpC hyperproduction, extended-spectrum β-lactamase, and carbapenemase. Finally, TAT reduction in our 24/7 laboratory was 16 h, enabling a significantly faster provision of antibiotic advice.

Published
2022
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3. Spontaneous Bacterial Peritonitis: The Incremental Value of a Fast and Direct Bacterial Identification from Ascitic Fluids Inoculated in Blood Culture Bottles by MALDI-TOF MS for a Better Management of Patients

Author

Romain Lotte, Audrey Courdurié, Alice Gaudart, Audrey Emery, Alicia Chevalier, Albert Tran, Mathilde Payen, and Raymond Ruimy

Subjects
direct identification of bacteria, MALDI-TOF, ascites, Biology (General), QH301-705.5
Abstract

Spontaneous bacterial peritonitis (SBP) is a severe infection that requires fast and accurate antibiotic therapy to improve the patient outcome. Direct bacterial identification using MALDI-TOF mass spectrometry from ascitic fluid inoculated in blood culture bottles (BCBs) could therefore improve patients’ management. We evaluated the impact of the implementation of this method for the treatment of patients. Our identification protocol was performed on 136 positive BCBs collected from 61 patients between December 2018 and December 2020. The therapeutic impact of our protocol was evaluated using a before (2015–2016) and after (2019–2020) case–control study in two populations of 41 patients diagnosed with SBP and treated with antibiotics. The decrease in time to first identification and the optimization of antibiotic therapy following communication of the identification result were evaluated. Our protocol allowed us to identify 78% of bacteria in ascitic fluids. The transmission of the direct identification allowed the introduction or adaption of the antibiotic therapy early in 37% of SBP, with a mean decrease in time to first antibiotic change of 17 h. Our direct identification protocol for positive inoculated ascitic fluids is fast, reliable and inexpensive. Its routine integration into a microbiology laboratory allows the early introduction of appropriate antibiotic therapy and improves the management of patients with SBP.

Published
2022
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4. Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter?

Author

Cécile Angebault, Mathilde Payen, Paul-Louis Woerther, Christophe Rodriguez, and Françoise Botterel

Subjects
Medicine, Science
Abstract

BACKGROUND:High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota. METHODS:Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results. RESULTS:AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3-11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa. CONCLUSION:Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.

Published
2020
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5. La cerise dans le labo !: Des femmes de sciences inspirées et inspirantes

Author

Lucie Le Moine, Charline Forns, Judith Lorne, Laura Cardoso, Lorène Gaydon, Lucie Albrecht, Mathilde Payen, Reine Dibussi, Victoria Denys, Kei Lam, Line Hachem, Marine Joumard, Lalex Andrea, Léonie Massot Floury and Lucie Le Moine, Charline Forns, Judith Lorne, Laura Cardoso, Lorène Gaydon, Lucie Albrecht, Mathilde Payen, Reine Dibussi, Victoria Denys, Kei Lam, Line Hachem, Marine Joumard, Lalex Andrea, Léonie Massot Floury

Published
2023

6. Evaluation of non-traumatic brachial plexus using Diffusion Tensor Imaging

Author

Mathilde PAYEN, Mélanie DIDIER, Raphaël VIALLE, Stéphane Lehericy, Franck Fitoussi, and Manon BACHY

Abstract

BACKGROUND: Clinical examination is the gold standard for surgical indication. Electromyogram and conventional MRI are insufficient to understand the highly variable clinical presentation of neonatal brachial plexus (BP) lesions. Diffusion Tensor Imaging is based on motion of water molecules and can explore nerve function. PURPOSE: This pilot study of healthy subjects aimed to develop a new method for BP exploration using MRI. The main objective was to obtain complete and accurate BP mapping using DTI and MRI tractography. METHODS: Six healthy volunteers had MRI (3T PRISMA) with anatomical 3D STIR, SPACE and RESOLVE diffusion sequences. Image analysis and processing was performed with MATLAB software. Diffusion parametric maps of fractional anisotropy (FA) were extracted from RESOLVE acquisitions. A reproducible method for root volume and angle measurements was created using 3DSlicer. Regions Of Interest were segmented on Mean B0 sequences. FA measurements were obtained with ROI on Mean B0 sequences. RESULTS: RESOLVE sequence was adapted to the BP. Mean FA was 0.30. Angle measurements on 3D STIR SPACE sequences showed increasing values from proximal to distal roots with an ICC of 0.6. Volume measurements on anatomical sequences varied widely from one root to another but no significant difference was shown on laterality. CONCLUSION: A new and reproducible method for BP exploration was developed using MRI RESOLVE diffusion sequences. Complete mapping was obtained despite low track density imaging resolution. The whole BP was visualized. Extraction of diffusion, volume and angle parameters of the plexus roots, and script creation for image processing was adapted to the healthy BP.

Published
2023

9. Surgical treatment of congenital pseudarthrosis of the clavicle: a series of 10 cases

Author

Mathilde, Payen, Nicolas, Mainard, Franck, Accadbled, Jérôme Sales de, Gauzy, and Abdelaziz, Abid

Subjects
Orthopedics and Sports Medicine, Surgery
Abstract

Congenital pseudarthrosis of the clavicle (CPC) is a rare congenital malformation. We describe the outcomes of surgical treatment of CPC in a series of 10 patients. The hypothesis was that surgical treatment is an acceptable solution that will lead to satisfactory healing in asymptomatic patients. The aims were to determine if 1) surgical treatment of CPC will produce a satisfactory union rate, 2) surgical treatment causes complications and impacts the postoperative outcomes and 3) risk factors can be identified that affect the success of the surgical care.Ten patients with CPC who were treated by resection and bone grafting were included in this case series. The CPC was always in the right clavicle. All patients except one were asymptomatic preoperatively. The mean age at the time of the procedure was 5.1 years (range, 1.7-13.4). The initial fixation consisted of a K-wire in 9 patients and a plate in 1 patient. Iliac crest autograft was harvested in all patients. The mean length of postoperative immobilization was 10 weeks (range, 6-18 weeks).At a mean follow-up of 29 months (range, 3-129 months), all patients were pain-free and had full range of motion. Bone union was achieved in 70% (7/10) after revision at a mean of 3.8 months (range, 1.1-13.3). Three clavicles did not heal, two of which had been revised surgically. Four patients suffered a complication: three cases of K-wire migration and one case of infection. Among them, two patients had the fixation changed to a plate while preserving the graft, while the fixation device was removed in two patients, one of whom was undergoing revision for infection. The patients who had complications were all under 5 years of age at the time of surgery (mean 3.7 years, range 1.7-5 years).Surgical treatment of CPC generates a moderate union rate with a complication risk that is not insignificant. Age at the time of surgery appears to affect the outcomes. Thus, we propose waiting until the patient is at least 5 years of age before implementing surgical treatment.IV, Retrospective study.

Published
2022

10. Study of the latency of transcranial motor evoked potentials in spinal cord monitoring during surgery for adolescent idiopathic scoliosis

Author

François Luc, Nicolas Mainard, Mathilde Payen, Isabelle Bernardini, Mathias El-Ayoubi, Andreas Friberg, Natalia Delgado Piccoli, and Anne-Laure Simon

Subjects
Neurology, Adolescent, Scoliosis, Spinal Cord, Physiology (medical), Monitoring, Intraoperative, Humans, Neurology (clinical), General Medicine, Evoked Potentials, Motor, Neurosurgical Procedures
Abstract

An increase in the latency of a motor evoked potential might be as significant as a decrease in amplitude to predict a significant and clinically symptomatic neurological injury in spinal surgery for adolescent idiopathic scoliosis. The aim of the study was to investigate the impact of monitoring of latency of motor evoked potentials during spinal surgery for adolescent idiopathic scoliosis by describing intraoperative data.Preoperative recordings of 50 patients undergoing posterior spinal fusion for idiopathic scoliosis were studied. Latencies of appearance of the motor evoked potential curves on the right and left side were recorded for each group of muscles at several key moments during the procedure (basal, before the first implant, before and after corrective maneuvers).Mean latencies were approximately the same in each muscle group on the right and the left side, before and after correction. There was no significant increase in latency during surgery. Overall results showed that the measured latency did not differ significantly between the two age groups (p=0.07). Negative correlation between height and the means of latencies was recorded in the abductor pollicis brevis and abductor digiti minimi (r=0.4; p=0.009), rectus femoris (r=0.4; p=0.01), tibialis anterior (r=0.4; p=0.007), and abductor hallucis (r=0.5; p=0.0004). No significant correlation was found between age and intraoperative parameters.Intraoperative latency could be a reliable intraoperative monitoring criteria with low variability, that might be used to predict postoperative motor deficits in surgery for adolescent idiopathic scoliosis.

Published
2021

14. Diagnostic challenge of gastrointestinal infection due to lactose-fermenting Salmonella enterica subsp. enterica serovar 4,5:I

Author

Philippe Bidet, Maria Pardos de la Gandara, Mathilde Payen, Stéphane Bonacorsi, Alix Massiot, François-Xavier Weill, Aurélie Cointe, AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris], Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Institut Pasteur [Paris] (IP), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord

Subjects
0301 basic medicine, Microbiology (medical), Serotype, Salmonella typhimurium, Salmonella, Gastrointestinal Diseases, 030106 microbiology, lac operon, Lactose, medicine.disease_cause, C8-esterase, Polymerase Chain Reaction, Microbiology, Agar plate, Feces, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, medicine, Humans, 030212 general & internal medicine, Child, Lactose-fermenting Salmonella, Bacteriological Techniques, biology, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Monophasic Salmonella, Infectious Diseases, chemistry, Salmonella enterica, Salmonella Infections, bacteria, Female, Salmonella enterica subsp. enterica, Bacteria, Lac operon
Abstract

International audience; Here, we describe a case of a nontyphoidal Salmonella disease caused by a Salmonella enterica serovar 4,5:i:- (monophasic Salmonella typhimurium) which acquired a Lac operon. This lactose-fermenting bacterium presents a major challenge for phenotypical detection of Salmonella. Only specific agar plates or molecular techniques allow reliable detection.

Published
2020

15. Medical features of COVID-19 and influenza infection: A comparative study in Paris, France

Author

Sonia Burrel, Aude Jary, Hélène Faury, Marc Wirden, Vincent Calvez, Martin Dres, Anne-Geneviève Marcelin, Charles-Edouard Luyt, Basma Abdi, David Boutolleau, Pierre Hausfater, Valérie Pourcher, Mathilde Payen, Camille Courboulès, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), BIOSFAST [CHU Pitié-Salpêtrière] (GRC 14), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Institut de cardiologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Neurophysiologie Respiratoire Expérimentale et Clinique (UMRS 1158), dres, martin, Service de virologie [CHU Pitié-Salpêtrière], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service des Urgences [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Neurophysiologie Respiratoire Expérimentale et Clinique, Service de Pneumologie et Réanimation Médicale [CHU Pitié-Salpêtrière] (Département ' R3S '), Gestionnaire, HAL Sorbonne Université 5, Service de Virologie [CHU Pitié-Salpêtrière], and Service d'Accueil des Urgences [CHU Pitié-Salpêtrière] (SAU)

Subjects
0301 basic medicine, Microbiology (medical), 2019-20 coronavirus outbreak, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), [SDV]Life Sciences [q-bio], 030106 microbiology, Death risk, Overweight, Article, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Diabetes mellitus, medicine, 030212 general & internal medicine, Risk factor, ComputingMilieux_MISCELLANEOUS, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, References: 10, business.industry, Mortality rate, COVID-19, medicine.disease, Influenza, 3. Good health, [SDV] Life Sciences [q-bio], Infectious Diseases, Respiratory failure, Risk factors, Severe clinical forms, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, medicine.symptom, business
Abstract

• COVID-19 and influenza patients share overweight as a risk factor for severe infection. • Higher death rate was reported in COVID-19 group than in influenza group. • COVID-19 patients developed preferentially secondary respiratory failure. • Older age and diabetes were confirmed as major contributing death risk factors in COVID-19.

Published
2020

16. Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity

Author

Jérôme Le Goff, Ioannis Nicolis, Béatrice Berçot, David Michonneau, Clotilde Rousseau, Nathalie Kapel, Marie Robin, Marie-José Butel, Mathilde Payen, Johanne Delannoye, Gérard Socié, Camille Mayeur, Laboratoire de Microbiologie, Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Physiopathologie et pharmacotoxicologie placentaire humaine : Microbiote pré & post natal (3PHM - UMR-S 1139), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Biostatistique, traitement et modélisation des données biologiques (BioSDTM - URP_7537), Université de Paris (UP), Hematology Transplantation, Immunologie humaine, physiopathologie & immunothérapie (HIPI (UMR_S_976 / U976)), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Coprologie Fonctionnelle [Pitié-Salpêtrière], Sorbonne Université (SU), Lallemant, Christopher, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), and Université Paris Cité (UPCité)

Subjects
medicine.medical_treatment, [SDV]Life Sciences [q-bio], Graft vs Host Disease, Disease, Butyrate, Hematopoietic stem cell transplantation, Gut flora, 03 medical and health sciences, Feces, 0302 clinical medicine, immune system diseases, hemic and lymphatic diseases, medicine, Humans, Phylogeny, 030304 developmental biology, 0303 health sciences, Transplantation, biology, integumentary system, business.industry, Lachnospiraceae, Hematopoietic Stem Cell Transplantation, Hematology, biology.organism_classification, medicine.disease, 3. Good health, Gastrointestinal Microbiome, [SDV] Life Sciences [q-bio], Real-time polymerase chain reaction, Graft-versus-host disease, surgical procedures, operative, 030220 oncology & carcinogenesis, Immunology, Anaerobic bacteria, business
Abstract

Acute graft-versus-host disease (aGVHD) is the main complication of hematopoietic stem cell transplantation (HSCT). Changes in gut microbiota composition have been associated with subsequent aGVHD, and reconstitution of healthy microbiota is currently being explored as a therapeutic approach. However, the specific actors in the intestinal ecosystem involved in the pathologic process at the time of aGVHD onset are not yet fully known. We prospectively collected stool samples from patients who underwent allogeneic HSCT. Patients sampled at aGVHD onset were compared with non-GVHD patients. To identify phylogenetic and functional signatures of the disease process, we determined fecal short-chain fatty acid (SFCA) profiles and used high-throughput DNA sequencing and real-time quantitative polymerase chain reaction to assess the microbiota composition. Microbiota alterations were highly specific of gastrointestinal (GI) aGVHD severity. Bacterial biomass and a-diversity were lower in severe aGVHD. We identified several bacterial signatures associated with severe aGVHD at disease onset; a negative correlation was observed with anaerobic bacteria of the Lachnospiraceae, especially the Blautia genus, and Ruminococcaceae families. In parallel, in severe aGVHD patients, we showed a dramatic decrease in the levels of the main SFCAs: acetate (75.8%), propionate (95.8%), and butyrate (94.6%). Mild aGVHD patients were characterized by conserved levels of propionate and Blautia propionate producers. Butyrate was significantly decreased in all GI aGVHD stages, representing a potential diagnostic marker of the disease. Specific microbiota and metabolic alterations were thus associated with aGVHD severity and may be useful for diagnostic and pathophysiologic purposes., Stem-cell Transplantation; Diversity

Published
2020

18. The Microbiome in Graft Versus Host Disease

Author

Clotilde Rousseau and Mathilde Payen

Subjects
Graft-versus-host disease, business.industry, Immunology, Medicine, Microbiome, business, medicine.disease
Published
2019

19. Contributors

Author

Nur Elina Abdul Mutalib, Bianca de Almeida-Pittito, Ana Clara Matoso Montuori de Andrade, José Luiz de Brito Alves, L. Caetano M. Antunes, M.J. Arias-Tellez, Panduro Arturo, R. Awais, Camille de Moura Balarini, Dibyajyoti Banerjee, Thais Fernanda Bartelli, Paulo José Basso, Soumeya Bekri, Rajasri Bhattacharyya, Aleksandr Birg, Natália Alvarenga Borges, Valdir de Andrade Braga, Nicholas Buys, Niels Olsen Saraiva Câmara, Agostinho Carvalho, Maria Dolores Luque de Castro, Luiz Gonzaga Vaz Coelho, Nathaniel Aviv Cohen, Kevin C. Conlon, Ramon V. Cortez, Cláudia A. Couto, Josiane de Campos Cruz, Cristina Cunha, P. D'Amelio, Dinesh Kumar Dahiya, Arun Kumar Dangi, Emmanuel Dias-Neto, Cláudio Duarte-Oliveira, Sinead N. Duggan, Alex Escalona, Joel Faintuch, Jacob J. Faintuch, Salomao Faintuch, Luciana Costa Faria, Carla Fernández-Reynoso, Silvia M. Ferolla, Maria de Lourdes A. Ferrari, Teresa C.A. Ferrari, Nicole V. Ferreira, Sandra Roberta G. Ferreira, Rosana B.R. Ferreira, Manuel Ferrer, Jarlei Fiamoncini, Hooi Ling Foo, Damodar Gajurel, Daniel Garrido, A. Gil, Shailendra Giri, Thaís Glatthardt, Samuel M. Gonçalves, Alexandra Grill, Emily K. Hendrix, Aline Ignacio, M. Íñiguez, Rosa Jorba, N. Kapel, Trevor O. Kirby, Anastasios Koulaouzidis, Deepak Kumar, Fulvio Lauretani, Henry C. Lin, Iara M. Linhares, Teck Chwen Loh, Igor Loniewski, Mateus Eustáquio Moura Lopes, Denise Mafra, Marciane Magnani, Nitsan Maharshak, Danish J. Malik, Ashutosh Mangalam, Kunal Maniar, Wojciech Marlicz, M.Carmen. Martínez-Cuesta, Robert Memba, Tiziana Meschi, Christian Milani, Evelyn Minis, Amal Moideen, Ana Carolina F. Moraes, Luana N. Moreira, Carlos G. Moscoso, Marcelle M. Nascimento, Andrew Nelson, E. Neumann, Krista M. Newman, J.R. Nicoli, Antonio Nouvenne, Javier Ochoa-Repáraz, Claudia Ojeda-Granados, Gislane Lellis Vilela de Oliveira, J.A. Oteo, L.R. Pace, Rigoberto Pallares-Méndez, R.D. Parker, Kalpesh G. Patel, Heidi Pauer, Mathilde Payen, Carmen. Peláez, Murilo Pereira, Marina Perez-Gordo, P. Pérez-Matute, J. Plaza-Diaz, F. Priego-Capote, Anil Kumar Puniya, Nikolaos T. Pyrsopoulos, Beata Anna Raczkowska, Raha Abdul Rahim, Christoph Reinhardt, null Renuka, Teresa Requena, J. Reygner, Nathaniel L. Ritz, Ingrid Rivera-Iñiguez, Renata Robial, David Rojo, Sonia Roman, Clotilde Rousseau, F.J. Ruiz-Ojeda, M.J. Saez-Lara, Liliane Martins dos Santos, F. Sassi, Umesh K. Shandilya, P. Shrestha, Pratyoosh Shukla, Vandana Singh, Karolina Skonieczna-Żydecka, Camila Solar, P. Solis-Urra, Evandro Leite de Souza, Charikleia Stefanaki, Christopher J. Stewart, Jing Sun, Carla R. Taddei, Claudio Tana, Abdellah Tebani, Fernanda Fernandes Terra, Andrea Ticinesi, Byron P. Vaughn, Marco Ventura, Hubert Vidal, L.Q. Vieira, M.J. Villanueva-Millán, Ingrid Kazue Mizuno Watanabe, C.M. Wells, Steven S. Witkin, T.Y. Wong, Chenghong Yin, and Elisa Zubeldia-Varela

Published
2019

20. Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter?

Author

Christophe Rodriguez, Mathilde Payen, Paul Louis Woerther, Françoise Botterel, Cécile Angebault, Unité de Parasitologie-Mycologie [Créteil], Département de Prévention, Diagnostic et Traitement des Infections [Créteil], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Henri Mondor-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Henri Mondor, Dynamic Microbiology - EA 7380 (DYNAMIC), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est (UPE)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Unité de Bactériologie-Hygiène [Créteil], Next-Generation Sequencing Platform [Créteil] (Génomiques), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work is an ancillary project of a larger study entitled 'Ecologie et dynamique des communautés bactériennes et fongiques des voies aériennes supérieures des patients atteints de mucoviscidose: Exploration prospective des discordances clinico-biologiques lors des traitements anti-infectieux par pyroséquençage à haut débit', which received a grant from 'Vaincre La Mucoviscidose' Fondation (Grant Number attributed to FB: 2013/2013-047/03, https://www.vaincrelamuco.org/)., Bodescot, Myriam, École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10

Subjects
Lysis, Molecular biology, Respiratory System, Yeast and Fungal Models, Pathology and Laboratory Medicine, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Sequencing techniques, Medicine and Health Sciences, DNA sequencing, DNA, Fungal, DNA extraction, Candida, Fungal Pathogens, 0303 health sciences, Multidisciplinary, biology, Microbiota, Eukaryota, High-Throughput Nucleotide Sequencing, Genomics, Biodiversity, Amplicon, Aspergillus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Real-time polymerase chain reaction, Experimental Organism Systems, Fungal Molds, Medical Microbiology, Medicine, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], France, Pathogens, Research Article, DNA, Bacterial, Science, Microbial Genomics, Mycology, Real-Time Polymerase Chain Reaction, Microbiology, 03 medical and health sciences, Extraction techniques, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Candida Albicans, Humans, Microbial Pathogens, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 030304 developmental biology, Bacteria, 030306 microbiology, Organisms, Fungi, Sputum, Biology and Life Sciences, Sequence Analysis, DNA, biology.organism_classification, Yeast, Research and analysis methods, Molecular biology techniques, Metagenomics, Animal Studies, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Microbiome
Abstract

International audience; Background: High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota.Methods: Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results.Results: AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3-11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa.Conclusion: Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.

Published
2020

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