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Andersson M, Wu J, Wullimann D, Gao Y, Aberg M, Muschiol S, Healy K, Naud S, Bogdanovic G, Palma M, Mellstedt H, Chen P, Ljunggren HG, Hansson L, Sallberg Chen M, Buggert M, Ingelman-Sundberg HM, Osterborg A. Local and Systemic Immunity During Five Vaccinations Against SARS-CoV-2 in Zanubrutinib-Treated Patients With Chronic Lymphocytic Leukemia. J Hematol 2023; 12:170-175. [PMID: 37692865 PMCID: PMC10482612 DOI: 10.14740/jh1140] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023] Open
Abstract
Background Patients with chronic lymphocytic leukemia (CLL) are vulnerable to coronavirus disease 2019 (COVID-19) and are at risk of inferior response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination, especially if treated with the first-generation Bruton's tyrosine kinase inhibitor (BTKi) ibrutinib. We aimed to evaluate the impact of the third-generation BTKi, zanubrutinib, on systemic and mucosal response to SARS-CoV-2 vaccination. Methods Nine patients with CLL with ongoing zanubrutinib therapy were included and donated blood and saliva during SARS-CoV-2 vaccination, before vaccine doses 3 and 5 and 2 - 3 weeks after doses 3, 4, and 5. Ibrutinib-treated control patients (n = 7) and healthy aged-matched controls (n = 7) gave blood 2 - 3 weeks after vaccine dose 5. We quantified reactivity and neutralization capacity of SARS-CoV-2-specific IgG and IgA antibodies (Abs) in both serum and saliva, and reactivity of T cells activated with viral peptides. Results Both zanubrutinib- and ibrutinib-treated patients had significantly, up to 1,000-fold, lower total spike-specific Ab levels after dose 5 compared to healthy controls (P < 0.01). Spike-IgG levels in serum from zanubrutinib-treated patients correlated well to neutralization capacity (r = 0.68; P < 0.0001) and were thus functional. Mucosal immunity (specific IgA in serum and saliva) was practically absent in zanubrutinib-treated patients even after five vaccine doses, whereas healthy controls had significantly higher levels (tested in serum after vaccine dose 5) (P < 0.05). In contrast, T-cell reactivity against SARS-CoV-2 peptides was equally high in zanubrutinib- and ibrutinib-treated patients as in healthy control donors. Conclusions In our small cohort of zanubrutinib-treated CLL patients, we conclude that up to five doses of SARS-CoV-2 vaccination induced no detectable IgA mucosal immunity, which likely will impair the primary barrier defence against the infection. Systemic IgG responses were also impaired, whereas T-cell responses were normal. Further and larger studies are needed to evaluate the impact of these findings on disease protection.
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Affiliation(s)
- Maria Andersson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
- These authors contributed equally to this article
| | - Jinghua Wu
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- These authors contributed equally to this article
| | - David Wullimann
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Yu Gao
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Aberg
- Department of Medical Sciences, Clinical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sandra Muschiol
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Katie Healy
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Sabrina Naud
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Gordana Bogdanovic
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marzia Palma
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Hakan Mellstedt
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Puran Chen
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lotta Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
| | | | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hanna M. Ingelman-Sundberg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Karolinska University Hospital Solna, Stockholm, Sweden
- These authors contributed equally to this article
| | - Anders Osterborg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
- These authors contributed equally to this article
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Naud S, Valles C, Abdillah A, Abou Chacra L, Mekhalif FZ, Ibrahim A, Caputo A, Baudoin JP, Gouriet F, Bittar F, Lagier JC, Ranque S, Fenollar F, Tidjani Alou M, Raoult D. Preliminary landscape of Candidatus Saccharibacteria in the human microbiome. Front Cell Infect Microbiol 2023; 13:1195679. [PMID: 37577371 PMCID: PMC10414567 DOI: 10.3389/fcimb.2023.1195679] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date. Methods In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics. Results Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples. Conclusion This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.
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Affiliation(s)
- Sabrina Naud
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Camille Valles
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Abdourahim Abdillah
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Linda Abou Chacra
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Fatima Zouina Mekhalif
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Florence Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
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3
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Ghorbani M, Al-Manei K, Naud S, Healy K, Gabarrini G, Sobkowiak MJ, Chen P, Ray S, Akber M, Muschiol S, Bogdanovic G, Bergman P, Ljungman P, Buggert M, Ljunggren HG, Pin E, Nowak P, Aleman S, Sällberg Chen M. Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV. Front Immunol 2023; 13:1079995. [PMID: 36703980 PMCID: PMC9871925 DOI: 10.3389/fimmu.2022.1079995] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/28/2022] [Indexed: 01/12/2023] Open
Abstract
Coevolution of microbiome and immunity at mucosal sites is essential for our health. Whether the oral microbiome, the second largest community after the gut, contributes to the immunogenicity of COVID-19 vaccines is not known. We investigated the baseline oral microbiome in individuals in the COVAXID clinical trial receiving the BNT162b2 mRNA vaccine. Participants (n=115) included healthy controls (HC; n=57) and people living with HIV (PLHIV; n=58) who met the study selection criteria. Vaccine-induced Spike antibodies in saliva and serum from 0 to 6 months were assessed and comparative analyses were performed against the individual salivary 16S ASV microbiome diversity. High- versus low vaccine responders were assessed on general, immunological, and oral microbiome features. Our analyses identified oral microbiome features enriched in high- vs. low-responders among healthy and PLHIV participants. In low-responders, an enrichment of Gram-negative, anaerobic species with proteolytic activity were found including Campylobacter, Butyrivibrio, Selenomonas, Lachnoanaerobaculum, Leptotrichia, Megasphaera, Prevotella and Stomatobaculum. In high-responders, enriched species were mainly Gram-positive and saccharolytic facultative anaerobes: Abiotrophia, Corynebacterium, Gemella, Granulicatella, Rothia, and Haemophilus. Combining identified microbial features in a classifier using the area under the receiver operating characteristic curve (ROC AUC) yielded scores of 0.879 (healthy controls) to 0.82 (PLHIV), supporting the oral microbiome contribution in the long-term vaccination outcome. The present study is the first to suggest that the oral microbiome has an impact on the durability of mucosal immunity after Covid-19 vaccination. Microbiome-targeted interventions to enhance long-term duration of mucosal vaccine immunity may be exploited.
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Affiliation(s)
- Mahin Ghorbani
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Khaled Al-Manei
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden,Department of Restorative Dental Science, College of Dentistry, King Saud University, Riyadh, Saudi Arabia
| | - Sabrina Naud
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Katie Healy
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden,Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Giorgio Gabarrini
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | | | - Puran Chen
- Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Shilpa Ray
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Mira Akber
- Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Sandra Muschiol
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Gordana Bogdanovic
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Bergman
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden,Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Huddinge, Sweden
| | - Per Ljungman
- Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden,Department of Cellular Therapy and Allogeneic Stem Cell Transplantation, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Huddinge, Sweden
| | - Marcus Buggert
- Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden
| | | | - Elisa Pin
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Piotr Nowak
- Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden,Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
| | - Soo Aleman
- Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden,Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
| | - Margaret Sällberg Chen
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden,*Correspondence: Margaret Sällberg Chen,
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4
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Al-Manei K, Ghorbani M, Naud S, Al-Manei KK, Sobkowiak MJ, Lund B, Hazirolan G, Sällberg Chen M, Özenci V. Clinical Microbial Identification of Severe Oral Infections by MALDI-TOF Mass Spectrometry in Stockholm County: an 11-Year (2010 to 2020) Epidemiological Investigation. Microbiol Spectr 2022; 10:e0248722. [PMID: 36420577 PMCID: PMC9769555 DOI: 10.1128/spectrum.02487-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/19/2022] [Indexed: 11/25/2022] Open
Abstract
Growing evidence suggests that oral infections can modify the course of systemic diseases. To date, epidemiological data on microbial oral infections are scarce. Here, we performed a comprehensive analysis of the trend and microbial diversity in oral infection specimens referred for clinical microbiology analysis from 2010 to 2020. The microbes were isolated by culture and were identified via matrix-assisted laser desorption ionization-time of flight mass spectrometry technology (MALDI-TOF MS) throughout the study period. A total of 1,014 referred samples from dental clinics in Stockholm County with dentoalveolar abscesses and jaw osteomyelitis being the main reason were identified. Overall, the microbial composition was dominated by Firmicutes (51%), followed by Bacteroidetes (19%), Proteobacteria (12%), and Actinobacteria (5%). At the genus level, Streptococcus spp. (36%), Prevotella spp. (18%), and Staphylococcus spp. (11%) were among the most frequently reported. Interestingly, a strong increase in trend was noted for Streptococcus anginosus, Streptococcus mitis, Streptococcus sanguinis, Eikenella corrodens, Actinomyces spp., Aggregatibacter aphrophilus, Staphylococcus epidermidis, and Granulicatella adiacens during the study time (R = 0.66 to 0.89, P < 0.05), and a minor increase was noted for Enterococcus faecalis and Klebsiella spp., whereas steady levels were noted for most of the others. The present study shows the diversity of bacteria that have been involved in dental infections during the last decade in the capital of Sweden, as well as the emerging oral microbiota trend, with clear clinical implications on the oral-systemic link. IMPORTANCE Oral diseases and associated microbes are a risk factor for systemic diseases and can change the courses of these diseases. To date, epidemiological data on microbial oral infections are scarce, and longitudinal reports are lacking. We present for the first time the microbial composition of severe oral bacterial infections determined via the MALDI-TOF mass spectrometry technique in a comprehensive study between 2010 and 2020 (11 years) in Stockholm County. The trend and microbial diversity of oral infections were analyzed on referred clinical microbiological samples and were processed by standardized protocols. Trend increase was noted for Streptococcus anginosus, Streptococcus mitis, Streptococcus sanguinis, Eikenella corrodens, Actinomyces spp., Aggregatibacter aphrophilus, Staphylococcus epidermidis, Granulicatella adiacens, Enterococcus faecalis, and Klebsiella spp. Our results provide new insights into the diversity and trend of oral microbiota that were involved in serious oral infections over the past decade in the capital of Sweden and may influence the oral-systemic link.
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Affiliation(s)
- Khaled Al-Manei
- Unit of Oral Diagnostics and Surgery, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
- Division of Endodontics, Department of Restorative Dental Science, College of Dentistry, King Saud University, Riyadh, Saudi Arabia
| | - Mahin Ghorbani
- Unit of Oral Diagnostics and Surgery, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Sabrina Naud
- Unit of Oral Diagnostics and Surgery, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Kholod Khalil Al-Manei
- Division of Endodontics, Department of Restorative Dental Science, College of Dentistry, King Saud University, Riyadh, Saudi Arabia
| | - Michał J. Sobkowiak
- Unit of Oral Diagnostics and Surgery, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Bodil Lund
- Unit of Oral Diagnostics and Surgery, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
- Medical Unit of Plastic Surgery and Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Surgery and Jaw Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Gulsen Hazirolan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Margaret Sällberg Chen
- Unit of Oral Diagnostics and Surgery, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Volkan Özenci
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Clinical Microbiology F 72, Karolinska University Hospital, Huddinge, Sweden
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5
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Ibrahim A, Colson P, Merhej V, Zgheib R, Maatouk M, Naud S, Bittar F, Raoult D. Rhizomal Reclassification of Living Organisms. Int J Mol Sci 2021; 22:5643. [PMID: 34073251 PMCID: PMC8199106 DOI: 10.3390/ijms22115643] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 03/23/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 12/11/2022] Open
Abstract
Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.
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Affiliation(s)
- Ahmad Ibrahim
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Vicky Merhej
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Rita Zgheib
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, 13005 Marseille, France
| | - Mohamad Maatouk
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Sabrina Naud
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Fadi Bittar
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
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6
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Naud S, Khelaifia S, Mbogning Fonkou MD, Dione N, Lagier JC, Raoult D. Proof of Concept of Culturomics Use of Time of Care. Front Cell Infect Microbiol 2020; 10:524769. [PMID: 33330116 PMCID: PMC7719802 DOI: 10.3389/fcimb.2020.524769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/06/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022] Open
Abstract
Culturomics, a high throughput culture method with rapid identification of the colonies by Matrix Assisted Laser Desorption Ionization/Time Of Flight Mass Spectrometry (MALDI-TOF MS), has demonstrated its contribution to the exploration of the gut microbiota over the past 10 years. However, the cost, work time and workload, considerably limit its use on a large scale or emergency context. Here, by testing two different stool samples, including a stool sample from a patient requiring rapid immunotherapy treatment, we tested a new fast culturomic protocol using two pre-incubation media, blood culture bottle and YCFA modified medium. Both media were supplemented with 2 ml of rumen fluid filtered at 0.2 μm and 2 ml of defibrinated and sterile sheep blood. Unlike the standard culturomics, subculturing of blood culture bottle were performed at reduced incubation time (3 h, 6 h, 9 h, 24 h) and at a longer incubation time (3 days, 7 days, and 10 days) at 37°C. By testing 5,200 colonies per MALDI-TOF MS and obtaining a comparable number of cultured bacterial species (131 to 143) in a stool sample, this new protocol reduced the number of colonies tested by 57%, working time by 78.6% and cost by 72.2%. In addition, we highlighted that the proportion of strict anaerobic species has increased by 24%, known to be the preferential targets for biotherapy, including Faecalibacterium prausnitzii, Akkermansia muciniphila, Christensenella minuta, and Phascolarctobacterium faecium. Finally, this work showed that some bacterial species grew earlier but disappeared with prolonged incubation times.
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Affiliation(s)
- Sabrina Naud
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Maxime Descartes Mbogning Fonkou
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Niokhor Dione
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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7
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Benabdelkader S, Naud S, Lo CI, Fadlane A, Traore SI, Aboudharam G, La Scola B. Parabacteroides pacaensis sp. nov. and Parabacteroides provencensis sp. nov., two new species identified from human gut microbiota. New Microbes New Infect 2020; 34:100642. [PMID: 32071723 PMCID: PMC7013006 DOI: 10.1016/j.nmni.2019.100642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/10/2019] [Accepted: 12/27/2019] [Indexed: 12/12/2022] Open
Abstract
Strains Marseille-P4001 and Marseille-P3668 are new species from the order Bacteroidales isolated from healthy French volunteers. They are anaerobic Gram-negative rod-shaped bacteria. They exhibited 92.68% and 96.68% 16S rRNA sequence identities with Parabacteroides gordonii strain MS-1 and Parabacteroides chinchillae JCM 17104, respectively, the phylogenetically closest species. Their respective draft genomes measured 5.23 Mb and 3.73 Mb with 39.2 mol% and 40.8 mol% of G + C content. Using a taxonogenomics method, we propose here a brief description of Parabacteroides pacaensis sp. nov., strain Marseille-P4001T and Parabacteroides provencensis sp. nov., strain Marseille-P3668T as new bacterial species.
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Affiliation(s)
- S Benabdelkader
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Naud
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A Fadlane
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S I Traore
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - G Aboudharam
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,UFR Odontologie, Aix-Marseille Université, Marseille, France
| | - B La Scola
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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8
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Takakura T, Francis R, Anani H, Naud S, Raoult D, Bou Khalil J. Dorea phocaeensis sp. nov., a new bacterium isolated from the stool of a healthy 29-year-old male. New Microbes New Infect 2019; 32:100600. [PMID: 31641515 PMCID: PMC6796640 DOI: 10.1016/j.nmni.2019.100600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/30/2019] [Indexed: 11/06/2022] Open
Abstract
Dorea phocaeensis strain Marseille-P4003T (= CSURP4003T; = CCUG71359T) is a new species isolated from the stool of a healthy 29-year-old male from France.
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9
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Bellali S, Lo C, Naud S, Fonkou M, Armstrong N, Raoult D, Fournier PE, Fenollar F. Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen. New Microbes New Infect 2019; 32:100602. [PMID: 31641517 PMCID: PMC6796604 DOI: 10.1016/j.nmni.2019.100602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022] Open
Abstract
Parabacteroides massiliensis sp. nov., strain Marseille-P2231T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It was isolated from a stool specimen of a 25-year-old healthy woman. Its genome was 5 013 798 bp long with a 45.7 mol% G+C content. The closest species based on 16S rRNA sequence was Parabacteroides merdae strain JCM 9497T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides.
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Affiliation(s)
- S. Bellali
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - S. Naud
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M.D.M. Fonkou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- Corresponding author: F. Fenollar, Institut Hospitalo-Universitaire Méditerranée-Infection, 19–21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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10
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Bellali S, Naud S, Ndongo S, Lo C, Anani H, Raoult D, Lagier JC. Corynebacterium pacaense sp. nov., Alistipes megaguti sp. nov., Alistipes provencensis sp. nov., 3 new bacteria isolated from fresh human stool specimens. New Microbes New Infect 2019; 32:100593. [PMID: 31641510 PMCID: PMC6796624 DOI: 10.1016/j.nmni.2019.100593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens.
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Affiliation(s)
- S. Bellali
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - S. Naud
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU–Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - H. Anani
- IHU–Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
- Corresponding author: J.-C. Lagier, IHU–Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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11
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Alaoui FE, Chevalerias A, Latouche JC, Cullie O, Jaray S, Naud S, Morizet S, Allix-Jourdan S, Rouault S, Lecharme P. Médecin du travail manager : expérience de la pluridisciplinarité dans un SST de 10 salariés. ARCH MAL PROF ENVIRO 2012. [DOI: 10.1016/j.admp.2012.03.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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van Korlaar IM, Vossen CY, Rosendaal FR, Bovill EG, Naud S, Cameron LD, Kaptein AA. Attitudes toward genetic testing for thrombophilia in asymptomatic members of a large family with heritable protein C deficiency. J Thromb Haemost 2005; 3:2437-44. [PMID: 16241941 DOI: 10.1111/j.1538-7836.2005.01619.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Little research has been performed regarding the psychological consequences of knowing that one is at an increased risk for venous thrombosis. OBJECTIVES The aim of this study was to explore attitudes toward genetic testing for protein C deficiency. METHODS Questionnaires about genetic testing attitudes, dispositional anxiety, risk perception, and thrombosis-related worry were completed by 168 asymptomatic members of a North-American kindred with a high incidence of heritable protein C deficiency conferring a high lifetime risk of venous thrombosis. A total of 76 subjects (45%) had not been tested for protein C deficiency before participating in our study whereas the other 92 subjects (55%) had been tested prior to filling in the questionnaire, of whom 34 people had protein C deficiency, while 58 did not. RESULTS Family members with protein C deficiency perceived a higher risk of suffering venous thrombosis and scored higher on thrombosis-related worry than family members without protein C deficiency. Participants who had not been tested did not report excessive thrombosis-related worry. Participants with protein C deficiency reported a belief in the psychological and health benefits of testing, and felt that they experienced low psychological distress following the genetic test. High psychological distress following the test was related to dispositional anxiety and thrombosis-related worry. Participants without protein C deficiency were relieved after finding out that they did not have the deficiency. CONCLUSION There seem to be few negative psychological consequences of knowing that one is at an increased risk for venous thrombosis, except in vulnerable individuals.
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Affiliation(s)
- I M van Korlaar
- Unit of Psychology, Leiden University Medical Center, Leiden, the Netherlands.
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13
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Emmerich J, Vossen CY, Callas PW, Demers C, Naud S, Long GL, Couture P, Rosendaal FR, Bovill EG. Chronic venous abnormalities in symptomatic and asymptomatic protein C deficiency. J Thromb Haemost 2005; 3:1428-31. [PMID: 15978099 DOI: 10.1111/j.1538-7836.2005.01452.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Thrombophilia is a frequent medical condition associated with symptomatic deep vein thrombosis (DVT). Unlike other clinical risk factors associated with DVT, such as surgery, thrombophilia has not been demonstrated to be associated with asymptomatic venous thrombotic events. Our aim was to search for asymptomatic sequelae of DVT in a protein C (PC)-deficient family. METHODS We studied 228 individuals from a large kindred with PC deficiency and performed a systematic ultrasound examination. RESULTS Among the 203 patients without a known history of venous thrombosis we found seven patients with abnormalities indicative of prior asymptomatic thrombosis: six (7.4%) in the PC-deficient group (n = 81) and only one (0.8%) in the non-deficient group (n = 122). The relative risk for these sequelae associated with PC deficiency was 9.0 (95% CI: 1.1-73.7). CONCLUSIONS These data suggest that chronic venous abnormalities are frequently present and that thrombotic events in asymptomatic individuals with familial PC deficiency may be underestimated.
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Affiliation(s)
- J Emmerich
- University of Paris 5 and INSERM U428, Paris, France
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