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d’Humières C, Gaïa N, Gueye S, de Lastours V, Leflon-Guibout V, Maataoui N, Duprilot M, Lecronier M, Rousseau MA, Gamany N, Lescure FX, Senard O, Deconinck L, Dollat M, Isernia V, Le Hur AC, Petitjean M, Nazimoudine A, Le Gac S, Chalal S, Ferreira S, Lazarevic V, Guigon G, Gervasi G, Armand-Lefèvre L, Schrenzel J, Ruppé E. Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections. Front Microbiol 2022; 13:863777. [PMID: 35531285 PMCID: PMC9069157 DOI: 10.3389/fmicb.2022.863777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2022] [Indexed: 11/20/2022] Open
Abstract
Bone and joint infections (BJIs) are complex infections that require precise microbiological documentation to optimize antibiotic therapy. Currently, diagnosis is based on microbiological culture, sometimes complemented by amplification and sequencing of the 16S rDNA gene. Clinical metagenomics (CMg), that is, the sequencing of the entire nucleic acids in a sample, was previously shown to identify bacteria not detected by conventional methods, but its actual contribution to the diagnosis remains to be assessed, especially with regard to 16S rDNA sequencing. In the present study, we tested the performance of CMg in 34 patients (94 samples) with suspected BJIs, as compared to culture and 16S rDNA sequencing. A total of 94 samples from 34 patients with suspicion of BJIs, recruited from two sites, were analyzed by (i) conventional culture, (ii) 16S rDNA sequencing (Sanger method), and (iii) CMg (Illumina Technology). Two negative controls were also sequenced by CMg for contamination assessment. Based on the sequencing results of negative controls, 414 out of 539 (76.7%) bacterial species detected by CMg were considered as contaminants and 125 (23.2%) as truly present. For monomicrobial infections (13 patients), the sensitivity of CMg was 83.3% as compared to culture, and 100% as compared to 16S rDNA. For polymicrobial infections (13 patients), the sensitivity of CMg was 50% compared to culture, and 100% compared to 16S rDNA. For samples negative in culture (8 patients, 21 samples), CMg detected 11 bacteria in 10 samples from 5 different patients. In 5/34 patients, CMg brought a microbiological diagnosis where conventional methods failed, and in 16/34 patients, CMg provided additional information. Finally, 99 antibiotic resistance genes were detected in 24 patients (56 samples). Provided sufficient genome coverage (87.5%), a correct inference of antibiotic susceptibility was achieved in 8/8 bacteria (100%). In conclusion, our study demonstrated that the CMg provides complementary and potentially valuable data to conventional methods of BJIs diagnosis.
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Affiliation(s)
- Camille d’Humières
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
- INSERM, Université de Paris Cité, IAME, Paris, France
- *Correspondence: Camille d’Humières,
| | - Nadia Gaïa
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Signara Gueye
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
| | - Victoire de Lastours
- INSERM, Université de Paris Cité, IAME, Paris, France
- AP-HP, Hôpital Beaujon, Service de Médecine Interne, Paris, France
| | | | - Naouale Maataoui
- AP-HP, Hôpital Beaujon, Laboratoire de Bactériologie, Paris, France
| | - Marion Duprilot
- AP-HP, Hôpital Beaujon, Laboratoire de Bactériologie, Paris, France
| | - Marie Lecronier
- AP-HP, Hôpital Beaujon, Service de Médecine Interne, Paris, France
| | | | - Naura Gamany
- AP-HP, Hôpital Beaujon, Service de Médecine Interne, Paris, France
| | - François-Xavier Lescure
- INSERM, Université de Paris Cité, IAME, Paris, France
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Olivia Senard
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Laurène Deconinck
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Marion Dollat
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Valentina Isernia
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | | | | | | | - Sylvie Le Gac
- AP-HP, Hôpital Bichat, Département d’Epidémiologie Biostatistique et Recherche Clinique, Paris, France
| | - Solaya Chalal
- AP-HP, Hôpital Bichat, Département d’Epidémiologie Biostatistique et Recherche Clinique, Paris, France
| | | | - Vladimir Lazarevic
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | | | | | - Laurence Armand-Lefèvre
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
- INSERM, Université de Paris Cité, IAME, Paris, France
| | - Jacques Schrenzel
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Etienne Ruppé
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
- INSERM, Université de Paris Cité, IAME, Paris, France
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Deconinck L, Gschwind R, Petitjean M, Gueye S, Leflon-Guibout V, Maataoui N, Rondinaud E, Suard A, Gallais K, Richaud R, Fuchs A, Iung B, Alkhoder S, Ismaël S, Herrou J, Prié H, Armand-Lefèvre L, d’Humières C, Ruppé E. Endocarditis caused by Thalassospira sp. IDCases 2021; 24:e01109. [PMID: 33948436 PMCID: PMC8080455 DOI: 10.1016/j.idcr.2021.e01109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/20/2022] Open
Abstract
We report a case of an infective endocarditis caused by a Thalassospira sp. in a 53-year-old man with pre-existing valvular lesions and living in French Polynesia as a fisherman. The strain was identified with DNA-sequecing methods while it was not by mass spectrometry.
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Affiliation(s)
- Laurène Deconinck
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses et Tropicales, F-75018 Paris, France
| | - Rémi Gschwind
- INSERM, Université de Paris, IAME, F-75018 Paris, France
| | | | - Signara Gueye
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | | | - Naouale Maataoui
- INSERM, Université de Paris, IAME, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Emilie Rondinaud
- INSERM, Université de Paris, IAME, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Augustin Suard
- Centre de Cardiologie du Taaone, BP1640 Papeete, Tahiti, French Polynesia
| | - Katell Gallais
- Centre de Cardiologie du Taaone, BP1640 Papeete, Tahiti, French Polynesia
| | - Rainui Richaud
- Centre de Cardiologie du Taaone, BP1640 Papeete, Tahiti, French Polynesia
| | - Adeline Fuchs
- AP-HP, Hôpital Bichat, Service de Cardiologie, F-75018 Paris, France
| | - Bernard Iung
- AP-HP, Hôpital Bichat, Service de Cardiologie, F-75018 Paris, France
- INSERM, Université de Paris, LVTS, F75108 Paris, France
| | - Soleiman Alkhoder
- AP-HP, Hôpital Bichat, Service de Chirurgie Cardiaque et Vasculaire, F-75018 Paris, France
| | - Sophie Ismaël
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses et Tropicales, F-75018 Paris, France
| | - Julia Herrou
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses et Tropicales, F-75018 Paris, France
| | - Héloïse Prié
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses et Tropicales, F-75018 Paris, France
| | - Laurence Armand-Lefèvre
- INSERM, Université de Paris, IAME, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Camille d’Humières
- INSERM, Université de Paris, IAME, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Etienne Ruppé
- INSERM, Université de Paris, IAME, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
- Corresponding author at: Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018 Paris, France.
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d’Humières C, Patrier J, Lortat-Jacob B, Tran-dinh A, Chemali L, Maataoui N, Rondinaud E, Ruppé E, Burdet C, Ruckly S, Montravers P, Timsit JF, Armand-Lefevre L. Two original observations concerning bacterial infections in COVID-19 patients hospitalized in intensive care units during the first wave of the epidemic in France. PLoS One 2021; 16:e0250728. [PMID: 33914786 PMCID: PMC8084132 DOI: 10.1371/journal.pone.0250728] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/12/2021] [Indexed: 12/28/2022] Open
Abstract
Among 197 COVID-19 patients hospitalized in ICU, 88 (44.7%) experienced at least one bacterial infection, with pneumonia (39.1%) and bloodstream infections (15,7%) being the most frequent. Unusual findings include frequent suspicion of bacterial translocations originating from the digestive tract as well as bacterial persistence in the lungs despite adequate therapy.
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Affiliation(s)
- Camille d’Humières
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Bacteriology, Paris, France
| | - Juliette Patrier
- AP-HP, Hôpital Bichat, Medical and Infectious Diseases ICU (MI2), Paris, France
| | - Brice Lortat-Jacob
- Department of Anesthesiology and Surgical Critical Care, AP-HP, Hôpital Bichat, Paris, France
| | - Alexy Tran-dinh
- Department of Anesthesiology and Surgical Critical Care, AP-HP, Hôpital Bichat, Paris, France
- Université de Paris, INSERM U 1148, Paris, France
| | | | - Naouale Maataoui
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Bacteriology, Paris, France
| | - Emilie Rondinaud
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Bacteriology, Paris, France
| | - Etienne Ruppé
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Bacteriology, Paris, France
| | - Charles Burdet
- Université de Paris, INSERM, IAME, Paris, France
- Département d’Epidémiologie, Biostatistique et Recherche Clinique, AP-HP, Hôpital Bichat, Paris, France
| | - Stéphane Ruckly
- AP-HP, Hôpital Bichat, Medical and Infectious Diseases ICU (MI2), Paris, France
| | - Philippe Montravers
- Department of Anesthesiology and Surgical Critical Care, AP-HP, Hôpital Bichat, Paris, France
- INSERM 1152 –ANR-10-LABX-17, Paris, France
| | - Jean-François Timsit
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Medical and Infectious Diseases ICU (MI2), Paris, France
| | - Laurence Armand-Lefevre
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Bacteriology, Paris, France
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Rodrigues C, d’Humières C, Papin G, Passet V, Ruppé E, Brisse S. Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage. Microb Genom 2020; 6:mgen000419. [PMID: 32749955 PMCID: PMC7641421 DOI: 10.1099/mgen.0.000419] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/17/2020] [Indexed: 01/23/2023] Open
Abstract
Klebsiella pneumoniae (Kp) reference strain Kp52.145 is widely used in experimental Klebsiella pathophysiology. Since 1935, only one other strain of the same sublineage (sequence type ST66, capsular serotype K2) was isolated (AJ210, Australia). Here, we describe a community-acquired invasive infection caused by a ST66-K2 Kp strain in France. Four hypermucoviscous Kp isolates responsible for acute otitis media, meningitis, bacteraemia and bacteriuria, respectively, were obtained from a patient with a history of chronic alcoholism and diabetes mellitus, and infected with HIV. The isolates were characterized by phenotypic and genomic methods. The four genetically identical ST66-K2 isolates presented a full antimicrobial susceptibility profile, including to ampicillin, corresponding to a single strain (SB5881), which was more closely related to AJ210 (135 SNPs) than to Kp52.145 (388 SNPs). Colibactin and yersiniabactin gene clusters were present on the integrative and conjugative element ICEKp10 in the chromosome. The two plasmids from Kp52.145 were detected in SB5881. In addition to carrying genes for virulence factors RmpA, aerobactin and salmochelin, plasmid II has acquired in SB5881, the conjugation machinery gene cluster from plasmid I. We report the first case of community-acquired infection caused by a hypervirulent ST66-K2 Kp strain in Europe. This demonstrates the long-term persistence of the high-virulence and laboratory model ST66-K2 sublineage. The combination of a conjugative apparatus and major virulence genes on a single plasmid may contribute to the co-occurrence of hypervirulence and multidrug resistance in single Kp strains.
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Affiliation(s)
- Carla Rodrigues
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Camille d’Humières
- INSERM, IAME, UMR 1137, 75018 Paris, France
- Université de Paris, Paris, France
- AP-HP, Hôpitaux Universitaires Paris Nord Val-de-Seine, Laboratoire de Bacteriologie, Site Bichat, 75018 Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, 75015 Paris, France
- CNRS, UMR3525, 75015 Paris, France
| | - Grégory Papin
- AP-HP, Hôpitaux Universitaires Paris Nord Val-de-Seine, Service de Réanimation Médicale, Site Bichat, F-75018 Paris, France
| | - Virginie Passet
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Etienne Ruppé
- INSERM, IAME, UMR 1137, 75018 Paris, France
- Université de Paris, Paris, France
- AP-HP, Hôpitaux Universitaires Paris Nord Val-de-Seine, Laboratoire de Bacteriologie, Site Bichat, 75018 Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
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d’Humières C, Birgy A, Doit C, Bidet P, Arlet G, Bingen E. Use of a new screening medium to detect carbapenem-non-susceptible members of the Enterobacteriaceae. J Med Microbiol 2012; 61:878-880. [DOI: 10.1099/jmm.0.042127-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Camille d’Humières
- Laboratoire de Microbiologie, AP-HP, Hôpital Robert-Debré, Paris, France
| | - André Birgy
- Laboratoire de Microbiologie, AP-HP, Hôpital Robert-Debré, Paris, France
| | - Catherine Doit
- Laboratoire de Microbiologie, AP-HP, Hôpital Robert-Debré, Paris, France
| | - Philippe Bidet
- Laboratoire de Microbiologie, AP-HP, Hôpital Robert-Debré, Paris, France
| | - Guillaume Arlet
- Laboratoire de Microbiologie, AP-HP, Hôpital Tenon, Paris, France
| | - Edouard Bingen
- Laboratoire de Microbiologie, AP-HP, Hôpital Robert-Debré, Paris, France
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Bidet P, Liguori S, Plainvert C, Bonacorsi S, Courroux C, d’Humières C, Poyart C, Efstratiou A, Bingen E. Identification of group A streptococcal emm types commonly associated with invasive infections and antimicrobial resistance by the use of multiplex PCR and high-resolution melting analysis. Eur J Clin Microbiol Infect Dis 2012; 31:2817-26. [DOI: 10.1007/s10096-012-1635-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 04/25/2012] [Indexed: 10/28/2022]
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