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Lanckohr C, Horn D, Roßlenbroich S, Raschke MJ, Hirsch T, Stolberg-Stolberg J. [Necrotizing soft tissue infections]. DIE ANAESTHESIOLOGIE 2024; 73:608-616. [PMID: 39133289 DOI: 10.1007/s00101-024-01442-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/05/2024] [Indexed: 08/13/2024]
Abstract
Necrotizing soft tissue infections are a heterogeneous group of severe infections of the skin, connective tissue and muscles in which necrotic destruction of the tissue occurs at the site of infection. Various bacteria are known as "typical" triggering pathogens and the infection can occur on the entire surface of the body. Necrotizing soft tissue infections are always a time-sensitive emergency associated with high mortality. Many affected patients are critically ill and require treatment in an intensive care unit. The rapid and radical surgical treatment is an essential part of management and in addition an adequate and timely antimicrobial treatment is of great importance. The health consequences for surviving patients are often severe, as extensive soft tissue damage leads to functional impairments. In many cases extensive plastic surgery follow-up is necessary. Therefore, necrotizing soft tissue infections are "complicated" in every phase of the disease and require interprofessional treatment. This review article provides a current overview of various aspects of the diagnostics, treatment and aftercare of necrotizing soft tissue infections.
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Affiliation(s)
- Christian Lanckohr
- Antibiotic Stewardship (ABS)-Team, Institut für Hygiene, Universitätsklinikum Münster, Robert-Koch-Straße 41, 48149, Münster, Deutschland.
| | - Dagmar Horn
- Geschäftsbereich Apotheke, Universitätsklinikum Münster, Münster, Deutschland
| | - Steffen Roßlenbroich
- Klinik für Unfall‑, Hand- und Wiederherstellungschirurgie, Universitätsklinikum Münster, Münster, Deutschland
| | - Michael J Raschke
- Klinik für Unfall‑, Hand- und Wiederherstellungschirurgie, Universitätsklinikum Münster, Münster, Deutschland
| | - Tobias Hirsch
- Klinik für Plastische Chirurgie, Universitätsklinikum Münster, Münster, Deutschland
| | - Josef Stolberg-Stolberg
- Klinik für Unfall‑, Hand- und Wiederherstellungschirurgie, Universitätsklinikum Münster, Münster, Deutschland
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Coluccio A, Lopez Palomera F, Spero MA. Anaerobic bacteria in chronic wounds: Roles in disease, infection and treatment failure. Wound Repair Regen 2024. [PMID: 39129662 DOI: 10.1111/wrr.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/09/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
Infection is among the most common factors that impede wound healing, yet standard treatments routinely fail to resolve chronic wound infections. The chronic wound environment is largely hypoxic/anoxic, and wounds are predominantly colonised by facultative and obligate anaerobic bacteria. Oxygen (O2) limitation is an underappreciated driver of microbiota composition and behaviour in chronic wounds. In this perspective article, we examine how anaerobic bacteria and their distinct physiologies support persistent, antibiotic-recalcitrant infections. We describe the anaerobic energy metabolisms bacteria rely on for long-term survival in the wound environment, and why many antibiotics become less effective under hypoxic conditions. We also discuss obligate anaerobes, which are among the most prevalent taxa to colonise chronic wounds, yet their potential roles in influencing the microbial community and wound healing have been overlooked. All of the most common obligate anaerobes found in chronic wounds are opportunistic pathogens. We consider how these organisms persist in the wound environment and interface with host physiology to hinder wound healing processes or promote chronic inflammation. Finally, we apply our understanding of anaerobic physiologies to evaluate current treatment practices and to propose new strategies for treating chronic wound infections.
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Affiliation(s)
- Alison Coluccio
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | | | - Melanie A Spero
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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Marchand S, Rodriguez C, Woerther PL. [High-throughput sequencing for infectious disease diagnoses: Example of shotgun metagenomics in central nervous system infections]. Rev Med Interne 2024; 45:166-173. [PMID: 37230923 DOI: 10.1016/j.revmed.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The advent of high-throughput sequencing in clinical microbiology is opening the way to new diagnostic and prognostic approaches in infectious diseases. Detection, identification and characterisation of pathogenic microorganisms are essential steps in diagnosis and implementation of appropriate antimicrobial therapy. However, standard methods of microbiological diagnosis are failing in some cases. In addition, the emergence of new infections, facilitated by international travel and global warming, requires the implementation of innovative diagnostic methods. Among the different strategies used in clinical microbiology and reviewed in this article, shotgun metagenomics is the only technique that allows today a panpathogenic and unbiased detection of all microorganisms potentially responsible for an infectious disease, including those still unknown. The aims of this article are to present the different possible strategies of high-throughput sequencing used in the microbiological diagnosis of infectious diseases and to highlight the diagnostic contribution of shotgun metagenomics in the field of central nervous system infections.
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Affiliation(s)
- S Marchand
- Département de microbiologie, hôpital Henri Mondor, AP-HP, Créteil, France; Plateforme de génomique, hôpital Henri Mondor, AP-HP, Créteil, France.
| | - C Rodriguez
- Département de microbiologie, hôpital Henri Mondor, AP-HP, Créteil, France; Plateforme de génomique, hôpital Henri Mondor, AP-HP, Créteil, France; Inserm U955, université Paris-Est Créteil, Créteil, France
| | - P-L Woerther
- Département de microbiologie, hôpital Henri Mondor, AP-HP, Créteil, France; Plateforme de génomique, hôpital Henri Mondor, AP-HP, Créteil, France; EA 7380 Dynamyc, université Paris-Est Créteil, Créteil, France
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Yu J, Zhang L, Gao D, Wang J, Li Y, Sun N. Comparison of metagenomic next-generation sequencing and blood culture for diagnosis of bloodstream infections. Front Cell Infect Microbiol 2024; 14:1338861. [PMID: 38328669 PMCID: PMC10847245 DOI: 10.3389/fcimb.2024.1338861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Objectives This study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis. Methods A total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records. Results Using blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively. Conclusion Compared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.
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Affiliation(s)
- Juan Yu
- Department of Clinical Laboratory, Nanjing Lishui People’s Hospital, Nanjing, China
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Li Zhang
- Department of Clinical Laboratory, Nanjing Lishui People’s Hospital, Nanjing, China
| | - Deyu Gao
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jie Wang
- Clinical Medicine Research Center, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Yi Li
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ning Sun
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Bay P, Rodriguez C, Caruso S, Demontant V, Boizeau L, Soulier A, Woerther PL, Mekontso-Dessap A, Pawlotsky JM, de Prost N, Fourati S. Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in critically ill COVID-19 patients. J Med Virol 2023; 95:e29268. [PMID: 38050838 DOI: 10.1002/jmv.29268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
Severe coronavirus disease 2019 (COVID-19) is related to dysregulated immune responses. We aimed to explore the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on the immune response by nasopharyngeal transcriptomic in critically-ill patients. This prospective monocentric study included COVID-19 patients requiring intensive care unit (ICU) admission between March 2020 and 2022. Patients were classified according to VOC (ancestral, Alpha, Delta, and Omicron). Eighty-eight patients with severe COVID-19 were included after matching (on prespecified clinical criteria). Profiling of gene expression markers of innate and adaptive immune responses were investigated by respiratory transcriptomics at ICU admission. Eighty-eight patients were included in the study after matching (ancestral [n = 24], Alpha [n = 24], Delta [n = 22], and Omicron [n = 18] variants). Respiratory transcriptomic analysis revealed distinct innate and adaptive immune profiling between variants. In comparison with the ancestral variant, there was a reduced expression of neutrophil degranulation, T cell activation, cytokines signalling pathways in patients infected with Alpha and Delta variants. In contrast, there was a higher expression of neutrophil degranulation, T and B cells activation, and inflammatory interleukins pathways in patients infected with Omicron. To conclude, Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in patients with severe COVID-19, pointing to an evolving pathophysiology of severe COVID-19 in the Omicron era.
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Affiliation(s)
- Pierre Bay
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Stefano Caruso
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Vanessa Demontant
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Laure Boizeau
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Alexandre Soulier
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Paul L Woerther
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- EA 7380 Dynamic, Université Paris-Est-Créteil (UPEC), École Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Armand Mekontso-Dessap
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Jean-Michel Pawlotsky
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Slim Fourati
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
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Kimseng H, Rossi G, Danjean M, Jimenez-Araya B, Chaligne C, Galy A, Souhail B, Bert F, Leflon V, Fihman V, Caillault A, Demontant V, Seng S, Trawinski E, N 'Debi M, Boizeau L, Jacquier H, Ronot M, Reizine E, Le Roy V, Lefort A, Rodriguez C, Lepeule R, Woerther PL. Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses. J Infect 2023; 87:365-372. [PMID: 37604210 DOI: 10.1016/j.jinf.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA. METHODS In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae, we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture. RESULTS Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p<0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing. DISCUSSION Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future.
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Affiliation(s)
- Hadrien Kimseng
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Geoffrey Rossi
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Maxime Danjean
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Bryan Jimenez-Araya
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Camille Chaligne
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Adrien Galy
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Bérénice Souhail
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Frédéric Bert
- Department of Microbiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Véronique Leflon
- Department of Microbiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Vincent Fihman
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | | | | | - Sarah Seng
- NGS Platform, IMRB Institute, Créteil, France
| | | | | | | | - Hervé Jacquier
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Maxime Ronot
- Department of Radiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Edouard Reizine
- Department of Radiology, Henri Mondor Hospital, AP-HP, Créteil, France
| | - Vincent Le Roy
- Department of Hepatology, Henri Mondor Hospital, AP-HP, Créteil, France
| | - Agnès Lefort
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France; IAME, UMR1137, Université Paris-Cité, Paris, France
| | - Christophe Rodriguez
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; INSERM U955, IMRB Institute, Créteil, France; NGS Platform, IMRB Institute, Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; NGS Platform, IMRB Institute, Créteil, France.
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Cunningham SA, Rodriguez C, Woerther PL, Menigaux C, Bauer T, Herrmann JL, Rottman M, Roux AL, Gaillard JL, Patel R, El Sayed F. In Vivo Emergence of Dual Resistance to Rifampin and Levofloxacin in Osteoarticular Cutibacterium avidum. Microbiol Spectr 2023; 11:e0368722. [PMID: 37289061 PMCID: PMC10434181 DOI: 10.1128/spectrum.03687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Cutibacterium avidum is an emerging causative agent of orthopedic device-related infections (ODRIs). There are no guidelines for the antimicrobial treatment of C. avidum ODRI, but oral rifampin is frequently used in combination with a fluoroquinolone following intravenous antibiotics. We describe the in vivo emergence of combined resistance to rifampin and levofloxacin in a C. avidum strain isolated from a patient with early-onset ODRI treated with debridement, antibiotic treatment, and implant retention (DAIR) using rifampin combined with levofloxacin as the oral treatment. Whole-genome sequencing of C. avidum isolates before and after antibiotic exposure confirmed strain identity and identified new mutations in rpoB and gyrA, leading to amino acid substitutions previously reported to be associated with resistance to rifampin (S446P) and fluoroquinolones (S101L), respectively, in other microbial agents, in the posttherapy isolate. Aside from the molecular insights reported here, this study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing a DAIR procedure for C. avidum ODRI and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens. IMPORTANCE In this study, we report for the first time the in vivo emergence of dual resistance to levofloxacin and rifampin in C. avidum isolated from a patient who received both antibiotics orally in the setting of a salvage debridement and implant retention of an ODRI. Aside from the molecular insights reported here, this study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing these surgical procedures and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens.
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Affiliation(s)
- Scott A. Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christophe Rodriguez
- NGS Platform, IMRB, CHU Henri Mondor, Créteil, France
- Institut Mondor de Recherche Biomédicale, Inserm U955, Créteil, France
| | - Paul-Louis Woerther
- NGS Platform, IMRB, CHU Henri Mondor, Créteil, France
- Institut Mondor de Recherche Biomédicale, Inserm U955, Créteil, France
| | - Christophe Menigaux
- APHP, GHU Paris Saclay, Hôpital Ambroise Paré, Orthopedic Surgery Department, Boulogne-Billancourt, France
| | - Thomas Bauer
- APHP, GHU Paris Saclay, Hôpital Ambroise Paré, Orthopedic Surgery Department, Boulogne-Billancourt, France
| | - Jean-Louis Herrmann
- APHP, GHU Paris Saclay, Hôpital Raymond Poincaré, Microbiology Department, Garches, France
- Université Paris-Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-Le-Bretonneux, France
| | - Martin Rottman
- APHP, GHU Paris Saclay, Hôpital Raymond Poincaré, Microbiology Department, Garches, France
- Université Paris-Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-Le-Bretonneux, France
| | - Anne-Laure Roux
- Université Paris-Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-Le-Bretonneux, France
- APHP, GHU Paris Saclay, Hôpital Ambroise Paré, Microbiology Department, Boulogne-Billancourt, France
| | - Jean-Louis Gaillard
- Université Paris-Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-Le-Bretonneux, France
- APHP, GHU Paris Saclay, Hôpital Ambroise Paré, Microbiology Department, Boulogne-Billancourt, France
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Faten El Sayed
- Université Paris-Saclay, UVSQ, Inserm, Infection et Inflammation, Montigny-Le-Bretonneux, France
- APHP, GHU Paris Saclay, Hôpital Ambroise Paré, Microbiology Department, Boulogne-Billancourt, France
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8
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Mizusawa M, Carroll KC. Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA. Expert Rev Mol Diagn 2023; 23:679-699. [PMID: 37419696 DOI: 10.1080/14737159.2023.2234823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management. AREAS COVERED A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance. EXPERT OPINION Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.
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Affiliation(s)
- Masako Mizusawa
- Monmouth Medical Center, Rutgers University Robert Wood Johnson Medical School, Long Branch, NJ, USA
| | - Karen C Carroll
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Barbier F, Woerther PL, Timsit JF. Rapid diagnostics for skin and soft tissue infections: the current landscape and future potential. Curr Opin Infect Dis 2023; 36:57-66. [PMID: 36718917 DOI: 10.1097/qco.0000000000000901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
PURPOSE OF REVIEW Managing antimicrobial therapy in patients with complicated skin and soft tissue infections (SSTI) constitutes a growing challenge due to the wide spectrum of potential pathogens and resistance phenotypes. Today, microbiological documentation relies on cultural methods. This review summarizes the available evidence regarding the clinical input of rapid microbiological diagnostic tools (RMDT) and their impact on the management of antimicrobial therapy in SSTI. RECENT FINDINGS Accurate tools are already available for the early detection of methicillin-resistant Staphylococcus aureus (MRSA) in SSTI samples and may help avoiding or shortening empirical anti-MRSA coverage. Further research is necessary to develop and evaluate RMDT detecting group A streptococci (e.g., antigenic test) and Gram-negative pathogens (e.g., multiplex PCR assays), including through point-of-care utilization. Next-generation sequencing (NGS) methods could provide pivotal information for the stewardship of antimicrobial therapy, especially in case of polymicrobial or fungal SSTI and in the immunocompromised host; however, a shortening in the turnaround time and prospective data regarding their therapeutic input are needed to better appraise the clinical positioning of these promising approaches. SUMMARY The clinical input of RMDT in SSTI is currently limited due to the scarcity of available dedicated assays and the polymicrobial feature of certain cases. NGS appears as a relevant tool but requires further developments before its implementation in routine clinical practice.
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Affiliation(s)
- François Barbier
- Médecine Intensive - Réanimation, Centre Hospitalier Régional d'Orléans, Orléans
- CEPR/INSERM U1100, Université de Tours, Tours
| | - Paul-Louis Woerther
- Département de Microbiologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique - Hôpitaux de Paris
- DYNAMYC/EA7380, Université Paris Est - Créteil, Créteil
| | - Jean-François Timsit
- Réanimation Médicale et des Maladies Infectieuses, Centre Hospitalier Universitaire Bichat - Claude Bernard, Assistance Publique - Hôpitaux de Paris
- DeSCID/IAME/INSERM U1137, Université Paris Cité, Paris, France
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10
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Hua C, Urbina T, Bosc R, Parks T, Sriskandan S, de Prost N, Chosidow O. Necrotising soft-tissue infections. THE LANCET. INFECTIOUS DISEASES 2023; 23:e81-e94. [PMID: 36252579 DOI: 10.1016/s1473-3099(22)00583-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/05/2022] [Accepted: 08/22/2022] [Indexed: 11/07/2022]
Abstract
The incidence of necrotising soft-tissue infections has increased during recent decades such that most physicians might see at least one case of these potentially life-threatening infections in their career. Despite advances in care, necrotising soft-tissue infections are still associated with high morbidity and mortality, underlining a need for continued education of the medical community. In particular, failure to suspect necrotising soft-tissue infections, fuelled by poor awareness of the disease, promotes delays to first surgical debridement, amplifying disease severity and adverse outcomes. This Review will focus on practical approaches to management of necrotising soft-tissue infections including prompt recognition, initiation of specific management, exploratory surgery, and aftercare. Increased alertness and awareness for these infections should improve time to diagnosis and early referral to specialised centres, with improvement in the prognosis of necrotising soft-tissue infections.
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Affiliation(s)
- Camille Hua
- Service de Dermatologie, Assistance Publique-Hôpitaux de Paris, Créteil, France; Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France; Epidemiology in Dermatology and Evaluation of Therapeutics, Université Paris Est Créteil, Créteil, France; Groupe Infectiologie Dermatologique-Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France
| | - Tomas Urbina
- Service de Médecine Intensive Réanimation, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Romain Bosc
- Service de Chirurgie Plastique, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Tom Parks
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Diseases, Imperial College London, London, UK; MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, Assistance Publique-Hôpitaux de Paris, Créteil, France; CARMAS Research Group, UPEC-Université Paris-Est Créteil Val de Marne, Faculté de médecine de Créteil, Créteil, France
| | - Olivier Chosidow
- Service de Dermatologie, Assistance Publique-Hôpitaux de Paris, Créteil, France; Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France; Groupe Infectiologie Dermatologique-Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France; Research group Dynamyc, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.
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11
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Valyraki N, Maillart E, Pourcher V, Shor N, Tran S, Boudot de la Motte M, Houiller C, Domont F, Morvan E, Touat M, Del Mar Amador M, Aboab J, Mathon B, Hesters A, Vignal-Clermont C, Dehais C, Bonnin S, Lafitte F, Villain N, Varnous S, Gout O, Eloit M, Rodriguez C, Deschamps R. Human pegivirus identified in severe myelitis and optic neuritis in immunocompromised patients: A pathogenic role for a forgotten virus? Rev Neurol (Paris) 2022; 179:361-367. [PMID: 36302709 DOI: 10.1016/j.neurol.2022.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 11/05/2022]
Abstract
The role of Human pegivirus (HPgV) in patients with encephalitis has been recently questioned. We present cases of 4 patients with similar clinical, biological, and radiological characteristics, including a past history of transplantation with long-term immunosuppression and a progressive course of severe and predominantly myelitis, associated in 3 cases with optic neuropathy causing blindness. Extensive workup was negative but analysis of the CSF by use of pan-microorganism DNA- and RNA-based shotgun metagenomics was positive for HPgV. This case series further supports the hypothesis of HPgV CNS infection and highlights the utility of metagenomic next-generation sequencing of CSF in immunocompromised patients.
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12
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Yang WT, Chiang I, Tseng CH, Cheng C, Lin JH, Liu PY, Huang YT. Metagenomic Sequencing and Histology on a Chronic Wound Identified Epstein-Barr Virus-Associated Lymphoma. Evol Bioinform Online 2022; 18:11769343221110663. [PMID: 35874624 PMCID: PMC9297456 DOI: 10.1177/11769343221110663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
Accurate diagnosis of chronic, non-healing wounds is challenging and time-consuming because it can be caused by a variety of etiologies. This brief report presents an unusual case of a chronic wound lasting for 10 months investigated by deep metagenomic sequencing. Epstein-Barr virus (EBV) was identified in the wound and subsequently validated by in situ hybridization. Histopathologic examination eventually revealed that the non-healing wound was due to an EBV-associated NK/T cell lymphoma. By identifying mutations across the viral genome, the virus was classified as Type I EBV and clustered with others of geographic proximity. Our results suggest that metagenomic shotgun sequencing can not only rapidly and accurately identify the presence of underlying pathogens but also provide strain-level resolution for the surveillance of viral epidemiology.
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Affiliation(s)
- Wan-Ting Yang
- Department of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - I Chiang
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chien-Hao Tseng
- Department of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chun Cheng
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Jyun-Hong Lin
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Po-Yu Liu
- Department of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
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13
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Genetic and Phenotypic Study of the Pectobacterium versatile Beta-Lactamase, the Enzyme Most Similar to the Plasmid-Encoded TEM-1. Appl Environ Microbiol 2022; 88:e0022022. [PMID: 35575550 DOI: 10.1128/aem.00220-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genus Pectobacterium bacteria include important agricultural pathogens. Pectobacterium versatile isolates contain a chromosome-borne beta-lactamase, PEC-1. This enzyme is the closest relative of TEM-1, a plasmid-borne beta-lactamase widespread in the Enterobacterales. We performed bioinformatics and phenotypic analyses to investigate the genetic and phenotypic features of PEC-1 and its frequency and ability to spread within genus Pectobacterium. We also compared the characteristics of PEC-1 and TEM-1 and evaluated the likelihood of transfer. We found that blaPEC-1 was present principally in a small number of genetic environments in P. versatile. Identical blaPEC-1 genetic environments were present in closely related species, consistent with the high frequency of genetic exchange within the genus Pectobacterium. Despite the similarities between PEC-1 and TEM-1, their genetic environments displayed no significant identity, suggesting an absence of recent transfer. Phenotypic analyses on clonal constructs revealed similar hydrolysis spectra. Our results suggest that P. versatile is the main reservoir of PEC-1, which seems to transfer to closely related species. The genetic distance between PEC-1 and TEM-1, and the lack of conserved elements in their genetic environments, suggest that any transfer that may have occurred must have taken place well before the antibiotic era. IMPORTANCE This study aimed to compare the chromosomal beta-lactamase from Pectobacterium versatile, PEC-1, with the well-known and globally distributed TEM-1 in terms of genetic and functional properties. Despite the similarities between the enzymes, we obtained no definitive proof of gene transfer for the emergence of blaPEC-1 from blaTEM-1. Indeed, given the limited degree of sequence identity and the absence of a common genetic environment, it seems unlikely that any transfer of this gene has occurred recently. However, although blaPEC-1 was found mostly in one specific clade of the P. versatile species, certain isolates from other closely related species, such as Pectobacterium brasiliense and Pectobacterium polaris, may also carry this gene inserted into common genetic environments. This observation suggests that genetic exchanges are frequent, accounting for the diffusion of blaPEC-1 between isolates from different Pectobacterium species and, potentially, to exogenous mobile genetic elements.
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14
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Lamoureux C, Surgers L, Fihman V, Gricourt G, Demontant V, Trawinski E, N'Debi M, Gomart C, Royer G, Launay N, Le Glaunec JM, Wemmert C, La Martire G, Rossi G, Lepeule R, Pawlotsky JM, Rodriguez C, Woerther PL. Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections. Front Microbiol 2022; 13:761873. [PMID: 35464955 PMCID: PMC9020828 DOI: 10.3389/fmicb.2022.761873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
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Affiliation(s)
- Claudie Lamoureux
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Laure Surgers
- GHU AP-HP Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Vincent Fihman
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France
| | - Guillaume Gricourt
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Elisabeth Trawinski
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Melissa N'Debi
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Camille Gomart
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Guilhem Royer
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Nathalie Launay
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jeanne-Marie Le Glaunec
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Charlotte Wemmert
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Giulia La Martire
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Geoffrey Rossi
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Raphaël Lepeule
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jean-Michel Pawlotsky
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Christophe Rodriguez
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France.,NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Paul-Louis Woerther
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France.,Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
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15
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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] [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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16
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Courbin V, Riller Q, Amegnizin JL, Gricourt G, Demontant V, Fihman V, Angebault C, Mahevas M, Gaube G, Coutte L, Pawlotsky JM, Lepeule R, Rodriguez C, Woerther PL. Case Report: Cerebral Nocardiosis Caused by Nocardia cyriacigeorgica Detected by Metagenomics in an Apparently Immunocompetent Patient. Front Immunol 2022; 13:719124. [PMID: 35185867 PMCID: PMC8852340 DOI: 10.3389/fimmu.2022.719124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/20/2022] [Indexed: 01/26/2023] Open
Abstract
We report a case of meningoencephalitis due to Nocardia cyriacigeorgica diagnosed with metagenomics, while all the standard methods were negative. This diagnosis made adaptation of antimicrobial treatment possible and led to the discovery of a rare, acquired immunodeficiency syndrome.
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Affiliation(s)
- Virginie Courbin
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Quentin Riller
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Jean-Louis Amegnizin
- Department of Radiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Guillaume Gricourt
- NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Vanessa Demontant
- NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Vincent Fihman
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA Dynamyc 7380, Université Paris Est Créteil-Ecole nationale Vétérinaire de Maisons-Alfort, Créteil, France
| | - Cecile Angebault
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA Dynamyc 7380, Université Paris Est Créteil-Ecole nationale Vétérinaire de Maisons-Alfort, Créteil, France
| | - Matthieu Mahevas
- Internal Medicine Department, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Géraldine Gaube
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Laëtitia Coutte
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Christophe Rodriguez
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA Dynamyc 7380, Université Paris Est Créteil-Ecole nationale Vétérinaire de Maisons-Alfort, Créteil, France
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17
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Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
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18
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Carbo EC, Blankenspoor I, Goeman JJ, Kroes ACM, Claas ECJ, De Vries JJC. Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield. Expert Rev Mol Diagn 2021; 21:1139-1146. [PMID: 34607520 DOI: 10.1080/14737159.2021.1985467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ivar Blankenspoor
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C De Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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19
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Urbina T, Razazi K, Ourghanlian C, Woerther PL, Chosidow O, Lepeule R, de Prost N. Antibiotics in Necrotizing Soft Tissue Infections. Antibiotics (Basel) 2021; 10:antibiotics10091104. [PMID: 34572686 PMCID: PMC8466904 DOI: 10.3390/antibiotics10091104] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Necrotizing soft tissue infections (NSTIs) are rare life-threatening bacterial infections characterized by an extensive necrosis of skin and subcutaneous tissues. Initial urgent management of NSTIs relies on broad-spectrum antibiotic therapy, rapid surgical debridement of all infected tissues and, when present, treatment of associated organ failures in the intensive care unit. Antibiotic therapy for NSTI patients faces several challenges and should (1) carry broad-spectrum activity against gram-positive and gram-negative pathogens because of frequent polymicrobial infections, considering extended coverage for multidrug resistance in selected cases. In practice, a broad-spectrum beta-lactam antibiotic (e.g., piperacillin-tazobactam) is the mainstay of empirical therapy; (2) decrease toxin production, typically using a clindamycin combination, mainly in proven or suspected group A streptococcus infections; and (3) achieve the best possible tissue diffusion with regards to impaired regional perfusion, tissue necrosis, and pharmacokinetic and pharmacodynamic alterations. The best duration of antibiotic treatment has not been well established and is generally comprised between 7 and 15 days. This article reviews the currently available knowledge regarding antibiotic use in NSTIs.
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Affiliation(s)
- Tomas Urbina
- Médecine Intensive Réanimation, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris (AP-HP), 75571 Paris, France;
- Sorbonne Université, Université Pierre-et-Marie Curie, 75001 Paris, France
| | - Keyvan Razazi
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France;
- Groupe de Recherche Clinique CARMAS, Faculté de Médecine, Université Paris Est Créteil, 94010 Créteil, France
| | - Clément Ourghanlian
- Service de Pharmacie, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France;
- Unité Transversale de Traitement des Infections, Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France;
| | - Paul-Louis Woerther
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France;
- Research Group Dynamic, Faculté de Santé de Créteil, Université Paris-Est Créteil Val de Marne (UPEC), 94010 Créteil, France;
| | - Olivier Chosidow
- Research Group Dynamic, Faculté de Santé de Créteil, Université Paris-Est Créteil Val de Marne (UPEC), 94010 Créteil, France;
- Service de Dermatologie, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France
| | - Raphaël Lepeule
- Unité Transversale de Traitement des Infections, Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France;
| | - Nicolas de Prost
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor-Albert Chenevier, Assistance Publique-Hôpitaux de Paris (AP-HP), 94010 Créteil, France;
- Groupe de Recherche Clinique CARMAS, Faculté de Médecine, Université Paris Est Créteil, 94010 Créteil, France
- Correspondence: ; Tel.: +33-1-49-81-23-94
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20
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Beydon M, Rodriguez C, Karras A, Cez A, Rafat C, Jourde-Chiche N, Fain O, Philipponnet C, Puéchal X, Dossier A, Dupin N, Levy D, Aureau I, Guillevin L, Terrier B. Bartonella and Coxiella infections presenting as systemic vasculitis: case series and review of literature. Rheumatology (Oxford) 2021; 61:2609-2618. [PMID: 34500468 DOI: 10.1093/rheumatology/keab691] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/02/2021] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Coxiella and Bartonella sp. display particular tropism for endothelial or endocardial tissues and an abnormal host response to infections with induced autoimmunity. We aimed, through a case series combined with a comprehensive literature review, to outline characteristics of Coxiella and Bartonella infections presenting as systemic vasculitis. METHODS We retrospectively included cases of definite Coxiella and Bartonella infections presenting with vasculitis features and performed a comprehensive literature review. RESULTS Six cases of Bartonella infections were added to 18 cases from literature review. Causative pathogens were mainly B. henselae. Bartonella infection mimicked anti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitis in 83% with PR3-ANCA and presented as cryoglobulinemic vasculitis in 8%. Glomerulonephritis was present in 92%, and 88% had endocarditis. Complement fractions were low in 82% and rheumatoid factor positive in 85%. Kidney biopsies showed cell proliferation, mostly crescentic, with pauci-immune glomerulonephritis in 29%. Outcome was favorable, with the use of antibiotics alone in one third. Five cases of Coxiella infections were added to 16 from literature review. Sixteen had small-vessel vasculitides, mainly cryoglobulinemia vasculitis in 75%. One patient had polyarteritis nodosa-like vasculitis and four large-vessel vasculitis. Outcome was good except for one death. A highly sensitive next generation sequencing analysis on 3 Coxiella and 2 Bartonella-related vasculitides biopsies did not find any bacterial DNA. CONCLUSION Coxiella and Bartonella are both able to induce vasculitis but display distinct vasculitis features. Bartonella mimics PR3-ANCA-associated vasculitis in the setting of endocarditis, whereas Coxiella may induce vasculitis involving all vessel sizes.
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Affiliation(s)
- Maxime Beydon
- Département de Médecine Interne, Centre de Référence National pour les maladies auto-immunes systémiques rares, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Christophe Rodriguez
- Departement de Virologie, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Alexandre Karras
- Unité de Néphrologie, Hôpital Européen Georges-Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université de Paris, Paris, F-75006, France
| | - Alexandre Cez
- Service de néphrologie et dialyse, Hôpital Tenon (AP-HP), Paris, France
| | - Cédric Rafat
- Service des urgences Néphrologiques et Transplantation rénale, Assistance Publique-Hôpital de Paris, Paris, France
| | - Noémie Jourde-Chiche
- Aix-Marseille Univ, C2VN, INSERM, INRAE, Centre de Néphrologie et de Transplantation Rénale, Hôpital de la Conception AP-HM, Marseille, France
| | - Olivier Fain
- Département de Médecine interne, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Carole Philipponnet
- Département de néphrologie et de dialyse CHU Clermont Ferrand, Clermont Ferrand, France
| | - Xavier Puéchal
- Département de Médecine Interne, Centre de Référence National pour les maladies auto-immunes systémiques rares, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Antoine Dossier
- Service de médecine interne, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Dupin
- Département de Dermatologie, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Dan Levy
- Service de rhumatologie, CHU Strasbourg, Strasbourg, France
| | - Inès Aureau
- Service de médecine interne, Centre Hospitalier de Pau, Pau, France
| | - Loïc Guillevin
- Département de Médecine Interne, Centre de Référence National pour les maladies auto-immunes systémiques rares, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Benjamin Terrier
- Département de Médecine Interne, Centre de Référence National pour les maladies auto-immunes systémiques rares, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université de Paris, Paris, F-75006, France
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21
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Lavaud J, Hüssler S, Gricourt G, de Prost N, Rodriguez C, Ingen-Housz-Oro S, Chosidow O, Bernigaud C, Woerther PL. 16S metagenomic assessment of the skin microbiota dynamic and possible association with the risk of infection in patients with epidermal necrolysis. J Eur Acad Dermatol Venereol 2021; 35:e914-e917. [PMID: 34365683 DOI: 10.1111/jdv.17584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J Lavaud
- Department of Dermatology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France.,EA7380 Dynamic, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France
| | - S Hüssler
- Department of Microbiology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France
| | - G Gricourt
- Department of Microbiology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France.,NGS Platform, IMRB Institute, Université Paris-Est Créteil Val-de-Marne, Créteil, France
| | - N de Prost
- Department of Medical Intensive Care Unit, Assistance Publique-Hôpitaux de Paris, hôpital Henri Mondor, Créteil, France.,Reference Center for Toxic Bullous Dermatoses and severe drug reactions TOXIBUL, Créteil, France
| | - C Rodriguez
- NGS Platform, IMRB Institute, Université Paris-Est Créteil Val-de-Marne, Créteil, France.,INSERM U955, Université Paris-Est Créteil Val-de-Marne, Créteil, France
| | - S Ingen-Housz-Oro
- Department of Dermatology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France.,Reference Center for Toxic Bullous Dermatoses and severe drug reactions TOXIBUL, Créteil, France.,EpiDermE, Université Paris-Est Créteil, Créteil, France
| | - O Chosidow
- Department of Dermatology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France.,EA7380 Dynamic, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.,Reference Center for Toxic Bullous Dermatoses and severe drug reactions TOXIBUL, Créteil, France
| | - C Bernigaud
- Department of Dermatology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France.,EA7380 Dynamic, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.,Reference Center for Toxic Bullous Dermatoses and severe drug reactions TOXIBUL, Créteil, France
| | - P L Woerther
- EA7380 Dynamic, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.,Department of Microbiology, Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Faculté de Santé, Créteil, France.,NGS Platform, IMRB Institute, Université Paris-Est Créteil Val-de-Marne, Créteil, France
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22
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Grodner C, Bernigaud C, Lapadula S, Beringuer H, Billiet PA, Woerther PL, Billon R, Derhy H, Haye B, Hotz C, Pressiat C, Vodovar D, Rodriguez C, Fabresse N, de Prost N, Hua C, Chosidow O. Health products e-sale should be regulated: a case of necrotizing soft-tissue infection of the abdomen linked to self-injection of slimming products purchased on the internet. Int J Dermatol 2021; 61:e52-e54. [PMID: 34351634 DOI: 10.1111/ijd.15818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/15/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Camille Grodner
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Charlotte Bernigaud
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Research Group Dynamyc, EA7380, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.,GrIDIST, Groupe Infectiologie Dermatologique - Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France
| | - Simone Lapadula
- Department of Maxillofacial and Plastic, Reconstructive, and Aesthetic Surgery, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Helene Beringuer
- Intensive Care Unit, AP-HP, Henri Mondor Hospital, Créteil, France
| | | | - Paul-Louis Woerther
- Research Group Dynamyc, EA7380, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.,Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Raphaelle Billon
- Department of Maxillofacial and Plastic, Reconstructive, and Aesthetic Surgery, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Henri Derhy
- Department of Maxillofacial and Plastic, Reconstructive, and Aesthetic Surgery, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Benjamin Haye
- Department of Maxillofacial and Plastic, Reconstructive, and Aesthetic Surgery, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Claire Hotz
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Claire Pressiat
- Pharmacology-Toxicology Department, Pôle de Biologie, CHU Henri Mondor, Créteil, France
| | - Dominique Vodovar
- Centre AntiPoison de Paris - Fédération de toxicologie de l'APHP, Hôpital Fernand-Widal (APHP), Paris, France.,UFR de Médecine, Université de Paris, Paris, France.,UMRS 1144, INSERM, Paris, France
| | | | - Nicolas Fabresse
- Pharmacology-Toxicology Department, CH Raymond Poincaré, Garches, France
| | - Nicolas de Prost
- Intensive Care Unit, AP-HP, Henri Mondor Hospital, Créteil, France
| | - Camille Hua
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,GrIDIST, Groupe Infectiologie Dermatologique - Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France
| | - Oliver Chosidow
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Research Group Dynamyc, EA7380, Faculté de Santé de Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, Université Paris-Est Créteil, Créteil, France.,GrIDIST, Groupe Infectiologie Dermatologique - Infections Sexuellement Transmissibles, Société Française de Dermatologie, Paris, France
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23
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de Vries JJ, Brown JR, Fischer N, Sidorov IA, Morfopoulou S, Huang J, Munnink BBO, Sayiner A, Bulgurcu A, Rodriguez C, Gricourt G, Keyaerts E, Beller L, Bachofen C, Kubacki J, Cordey S, Laubscher F, Schmitz D, Beer M, Hoeper D, Huber M, Kufner V, Zaheri M, Lebrand A, Papa A, van Boheemen S, Kroes AC, Breuer J, Lopez-Labrador FX, Claas EC. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples. J Clin Virol 2021; 141:104908. [PMID: 34273858 PMCID: PMC7615111 DOI: 10.1016/j.jcv.2021.104908] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/18/2021] [Accepted: 06/30/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. METHODS Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed. RESULTS Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. CONCLUSION A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
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Affiliation(s)
- Jutte J.C. de Vries
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Julianne R. Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | - Igor A. Sidorov
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Jiabin Huang
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany
| | | | - Arzu Sayiner
- Dokuz Eylul University, Medical Faculty, Izmir, Turkey
| | | | | | | | - Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Belgium
| | - Leen Beller
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Belgium
| | | | - Jakub Kubacki
- Institute of Virology, University of Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland
| | - Dennis Schmitz
- RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany
| | - Dirk Hoeper
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Switzerland
| | | | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | | | - Aloys C.M. Kroes
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith Breuer
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - F. Xavier Lopez-Labrador
- Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana and Microbiology & Ecology Department, University of Valencia, Spain
- CIBERESP, Instituto de Salud Carlos III, Spain
| | - Eric C.J. Claas
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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24
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d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
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Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
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25
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Rodriguez C, Gricourt G, Ndebi M, Demontant V, Poiteau L, Burrel S, Boutolleau D, Woerther PL, Calvez V, Stroer S, Pawlotsky JM. Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France. Emerg Infect Dis 2021; 26:1287-1290. [PMID: 32441621 PMCID: PMC7258463 DOI: 10.3201/eid2606.191431] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report the discovery of a new orthobunyavirus, Cristoli virus, by means of shotgun metagenomics. The virus was identified in an immunodepressed patient with fatal encephalitis. Full-length genome sequencing revealed high-level expression of a virulence factor, possibly explaining the severity of the infection. The patient’s recent history suggests circulation in France.
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26
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Rodriguez C, Gouilh MA, Weiss N, Stroer S, Mokhtari K, Seilhean D, Mathon B, Demontant V, N'Debi M, Gricourt G, Woerther PL, Pawlotsky JM, Stefic K, Marlet J, Dequin PF, Guillon A, Pourcher V, Boutolleau D, Vabret A, Burrel S. Fatal Measles Inclusion-Body Encephalitis in Adult with Untreated AIDS, France. Emerg Infect Dis 2021; 26:2231-2234. [PMID: 32818389 PMCID: PMC7454109 DOI: 10.3201/eid2609.200366] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We report a fatal case of measles inclusion-body encephalitis occurring in a woman from Romania with AIDS. After an extensive but unsuccessful diagnostic evaluation, a pan-pathogen shotgun metagenomic approach revealed a measles virus infection. We identified no mutations previously associated with neurovirulence.
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27
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Monnet P, Rodriguez C, Gaudin O, Cirotteau P, Papouin B, Dereure O, Tetart F, Lalevee S, Colin A, Lebrun-Vignes B, Abe E, Alvarez JC, Demontant V, Gricourt G, de Prost N, Barau C, Chosidow O, Wolkenstein P, Hue S, Ortonne N, Milpied B, Ingen-Housz-Oro S. Towards a better understanding of adult idiopathic epidermal necrolysis: a retrospective study of 19 cases. J Eur Acad Dermatol Venereol 2021; 35:1569-1576. [PMID: 33834541 DOI: 10.1111/jdv.17274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/24/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Most cases of Stevens-Johnson syndrome and toxic epidermal necrolysis are drug-induced. A small subset of cases remain with unknown aetiology (idiopathic epidermal necrolysis [IEN]). OBJECTIVE We sought to better describe adult IEN and understand the aetiology. METHODS This retrospective study was conducted in 4 centres of the French national reference centre for epidermal necrolysis. Clinical data were collected for the 19 adults hospitalized for IEN between January 2015 and December 2019. Wide toxicology analysis of blood samples was performed. Histology of IEN cases was compared with blinding to skin biopsies of drug-induced EN (DIEN, 'controls'). Available baseline skin biopsies were analysed by shotgun metagenomics and transcriptomics and compared to controls. RESULTS IEN cases represented 15.6% of all EN cases in these centres. The median age of patients was 38 (range 16-51) years; 68.4% were women. Overall, 63.2% (n = 12) of cases required intensive care unit admission and 15.8% (n = 3) died at the acute phase. Histology showed the same patterns of early- to late-stage EN with no difference between DIEN and IEN cases. One toxicology analysis showed unexpected traces of carbamazepine; results for other cases were negative. Metagenomics analysis revealed no unexpected pathological microorganism. Transcriptomic analysis highlighted a different pro-apoptotic pathway in IEN compared to DIEN, with an overexpression of apoptosis effectors TWEAK/TRAIL. CONCLUSIONS IEN affects young people and is a severe form of EN. A large toxicologic investigation is warranted. Different pathways seem involved in IEN and DIEN, leading to the same apoptotic effect, but the primary trigger remains unknown.
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Affiliation(s)
- P Monnet
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - C Rodriguez
- Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,INSERM U955, Université Paris Est Créteil Val de Marne, UPEC, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France
| | - O Gaudin
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France
| | - P Cirotteau
- Dermatology Department, Saint André Hospital, Bordeaux, France
| | - B Papouin
- Pathology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - O Dereure
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Dermatology Department, Saint Eloi Hospital, Montpellier, France
| | - F Tetart
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Dermatology Department, Charles Nicole Hospital, Rouen, France
| | - S Lalevee
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Immunology Department, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, AP-HP, Henri Mondor Hospital, Créteil, France
| | - A Colin
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France
| | - B Lebrun-Vignes
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Pharmacovigilance Department, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - E Abe
- Pharmacology and Toxicology Department, AP-HP, Raymond Poincaré Hospital, Garches, France
| | - J-C Alvarez
- Pharmacology and Toxicology Department, AP-HP, Raymond Poincaré Hospital, Garches, France
| | - V Demontant
- Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,INSERM U955, Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - G Gricourt
- Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,INSERM U955, Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - N de Prost
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Intensive Care Unit, AP-HP, Henri Mondor Hospital, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - C Barau
- Clinical Investigation Center, Henri Mondor Hospital, Créteil, France
| | - O Chosidow
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - P Wolkenstein
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - S Hue
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Immunology Department, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, AP-HP, Henri Mondor Hospital, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - N Ortonne
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Pathology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - B Milpied
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Dermatology Department, Saint André Hospital, Bordeaux, France
| | - S Ingen-Housz-Oro
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Univ Paris Est Créteil EpidermE, Créteil, France
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28
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Rodriguez C, de Prost N, Fourati S, Lamoureux C, Gricourt G, N’debi M, Canoui-Poitrine F, Désveaux I, Picard O, Demontant V, Trawinski E, Lepeule R, Surgers L, Vindrios W, Lelièvre JD, Mongardon N, Langeron O, Cohen JL, Mekontso-Dessap A, Woerther PL, Pawlotsky JM. Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19. PLoS Pathog 2021; 17:e1009416. [PMID: 33780519 PMCID: PMC8032121 DOI: 10.1371/journal.ppat.1009416] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/08/2021] [Accepted: 02/22/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 is characterized by respiratory symptoms of various severities, ranging from mild upper respiratory signs to acute respiratory failure/acute respiratory distress syndrome associated with a high mortality rate. However, the pathophysiology of the disease is largely unknown. Shotgun metagenomics from nasopharyngeal swabs were used to characterize the genomic, metagenomic and transcriptomic features of patients from the first pandemic wave with various forms of COVID-19, including outpatients, patients hospitalized not requiring intensive care, and patients in the intensive care unit, to identify viral and/or host factors associated with the most severe forms of the disease. Neither the genetic characteristics of SARS-CoV-2, nor the detection of bacteria, viruses, fungi or parasites were associated with the severity of pulmonary disease. Severe pneumonia was associated with overexpression of cytokine transcripts activating the CXCR2 pathway, whereas patients with benign disease presented with a T helper "Th1-Th17" profile. The latter profile was associated with female gender and a lower mortality rate. Our findings indicate that the most severe cases of COVID-19 are characterized by the presence of overactive immune cells resulting in neutrophil pulmonary infiltration which, in turn, could enhance the inflammatory response and prolong tissue damage. These findings make CXCR2 antagonists, in particular IL-8 antagonists, promising candidates for the treatment of patients with severe COVID-19.
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Affiliation(s)
- Christophe Rodriguez
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Nicolas de Prost
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- CARMAS Clinical Research Group, Université Paris-Est, Créteil, France
| | - Slim Fourati
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Claudie Lamoureux
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Guillaume Gricourt
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Melissa N’debi
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Florence Canoui-Poitrine
- Université Paris-Est-Créteil, INSERM, IMRB, Créteil, France
- Public Health and Clinical Research Unit, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Isaac Désveaux
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Oriane Picard
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Vanessa Demontant
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Elisabeth Trawinski
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Laure Surgers
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - William Vindrios
- Department of Clinical Immunology and Infectious Diseases, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Jean-Daniel Lelièvre
- Department of Clinical Immunology and Infectious Diseases, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Nicolas Mongardon
- Department of Anesthesiology and Surgical Intensive Care, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Olivier Langeron
- Department of Anesthesiology and Surgical Intensive Care, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - José L. Cohen
- Center for Clinical Investigation and Biotherapies, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Immunoregulation and biotherapies”, Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - Armand Mekontso-Dessap
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- CARMAS Clinical Research Group, Université Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team DYNAMIC, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
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29
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Rampal S, Maniam S, Lim PY, Ramachandran R, Tan EK, Halim MAHA, Shamsudin Z, Singh SSS, Narayanan P, Neela VK. Necrotizing fasciitis, causative agents and management: a five-year retrospective study in two tertiary care hospitals in Central Malaysia. INTERNATIONAL ORTHOPAEDICS 2021; 45:1399-1405. [PMID: 33484294 DOI: 10.1007/s00264-020-04905-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE Necrotizing fasciitis (NF) is a rapidly progressive inflammatory infection of the fascia, with secondary necrosis of the subcutaneous tissues. The severity of the disease depends on the virulence of the organism and host immunity. There is a paucity of reports on the prevalence of NF causing pathogens and management. METHODS Retrospective data of patients treated for NF were collected from two tertiary care hospitals in Central Malaysia between January 2014 and December 2018. RESULTS A total of 469 NF patients were identified. More than half of the NF patients were males (n = 278; 59.28%). The highest number of cases was found among age groups between 30 and 79, with mean age of 56.17. The majority of the NF cases (n = 402; 85.72%) were monomicrobial. Streptococcus spp. (n = 89; 18.98%), Pseudomonas aeruginosa (n = 63; 13.44%) and Staphylococcus spp. (n = 61; 13.01%) were identified as the top three microorganisms isolated. Among the 469 NF cases, 173 (36.8%) were amputated or dead while 296 (63.1%) recovered. Proteus spp. (n = 19; 12.93%), Klebsiella pneumoniae (n = 18; 12.24%) and Escherichia coli (n = 14; 9.52%) were associated with all types of amputations. The most common antibiotic prescribed was unasyn (n = 284; 60.56%), followed by clindamycin (n = 56; 11.94%) and ceftazidime (n = 41; 8.74%). A total of 239 (61.8%) recovered while 148 (38.2%) were either amputated or dead when managed with the unasyn, clindamycin or ceftazidime. CONCLUSION This study represents the largest NF cases series in Malaysia highlighting the causative agents and management.
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Affiliation(s)
- Sanjiv Rampal
- Department of Orthopaedic, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Sandra Maniam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Poh Ying Lim
- Department of Community Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Rubenandran Ramachandran
- Department of Orthopaedic, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Eng Kee Tan
- Department of Orthopaedic, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Mohd Asyraf Hafizuddin Ab Halim
- Department of Orthopaedic, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Zulfahrizzat Shamsudin
- Orthopaedic Department, Hospital Tuanku Ja'afar, Jalan Rasah, Bukit Rasah, 70300, Seremban, Negeri Sembilan, Malaysia
| | - Sandeep Singh Sarawan Singh
- Orthopaedic Department, Hospital Ampang, Jalan Mewah Utara, Pandan Mewah, 68000, Ampang, Selangor Darul Ehsan, Malaysia
| | - Pravind Narayanan
- Department of Internal Medicine, Hospital Sarikei, Jalan Rentap, 96100, Sarikei, Sarawak, Malaysia
| | - Vasantha Kumari Neela
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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30
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Necrotizing Soft-Tissue Infections: Clinical Features and Diagnostic Aspects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33079362 DOI: 10.1007/978-3-030-57616-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2023]
Abstract
The term necrotizing soft-tissue infection (NSTI) encompasses a heterogenous group of patients with necrotizing infections, involving any body part. NSTI is diagnosed by surgical exploration, where necrosis of the subcutaneous tissue and/or muscle tissue, undermining of the skin, thrombosis of the superficial veins, and deliquescent tissue can be seen. Patients can present with vague symptoms, and approximately half of patients experience severe pain. The clinical presentation and microbiological etiology vary according to affected body site, with NSTI located to the extremities being dominated by monomicrobial group A streptococcal infections, and NSTI located to the anogenital area dominated by polymicrobial infections. No set of diagnostic criteria exists, and suspicion of the diagnosis should come from careful clinical examination and signs of local or systemic severity. Laboratory blood values show no distinct pattern but resemble those of sepsis. Imaging can aid the diagnostic process but must not delay surgical intervention.
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31
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Charpentier C, Kouby F, Hua C, Sbidian E, Darty M, Bosc R, De Prost N, Gomart C, Woerther PL, Tazi A, Decousser JW, Chosidow O. Group B streptococcal necrotizing soft-tissue infection: role of pharyngeal and perineal carriage. J Eur Acad Dermatol Venereol 2020; 35:e227-e228. [PMID: 32931041 DOI: 10.1111/jdv.16943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C Charpentier
- Department of Dermatology, Henri Mondor Hospital, Créteil, France
| | - F Kouby
- Department of Dermatology, Henri Mondor Hospital, Créteil, France
| | - C Hua
- Department of Dermatology, Henri Mondor Hospital, Créteil, France
| | - E Sbidian
- Department of Dermatology, Henri Mondor Hospital, Créteil, France.,EA 7379 EpiDermE (Epidémiologie en Dermatologie et Evaluation des Thérapeutiques), UPEC, Créteil, France
| | - M Darty
- Sequencing platform NGS, University Hospital Henri Mondor, Créteil, France
| | - R Bosc
- Department of Plastic, Reconstructive and Aesthetic Surgery, Henri Mondor Hospital, Créteil, France
| | - N De Prost
- Department of Medical Intensive Care Unit, Henri Mondor Hospital, Créteil, France
| | - C Gomart
- Department of Bacteriology and Infection Control, Henri Mondor Hospital, Créteil, France
| | - P-L Woerther
- Department of Bacteriology and Infection Control, Henri Mondor Hospital, Créteil, France.,EA 7380 Dynamyc, Paris Est Créteil University, Créteil, France
| | - A Tazi
- CNR Streptococci, Cochin Hospital, Paris, France.,Descartes University, Sorbonne, Paris, France.,INSERM U 1016, Cochin, Paris, France
| | - J-W Decousser
- Department of Bacteriology and Infection Control, Henri Mondor Hospital, Créteil, France.,EA 7380 Dynamyc, Paris Est Créteil University, Créteil, France
| | - O Chosidow
- Department of Dermatology, Henri Mondor Hospital, Créteil, France.,EA 7379 EpiDermE (Epidémiologie en Dermatologie et Evaluation des Thérapeutiques), UPEC, Créteil, France.,INSERM CIC 1430, Créteil, France.,UPEC Université Paris-Est Créteil, Créteil, France
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32
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Understanding necrotizing soft tissue infections in the intensive care unit. Intensive Care Med 2020; 46:1739-1742. [PMID: 32394067 DOI: 10.1007/s00134-020-06071-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
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33
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Moitinho-Silva L, Rodriguez E, Weidinger S. New perspectives for necrotizing soft-tissue infections pathogen detection. Br J Dermatol 2020; 183:10. [PMID: 31957874 DOI: 10.1111/bjd.18796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L Moitinho-Silva
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - E Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - S Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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Rodriguez C, Jary A, Hua C, Woerther PL, Bosc R, Desroches M, Sitterlé E, Gricourt G, De Prost N, Pawlotsky JM, Chosidow O, Sbidian E, Decousser JW. Pathogen identification by shotgun metagenomics of patients with necrotizing soft-tissue infections. Br J Dermatol 2019; 183:105-113. [PMID: 31610037 DOI: 10.1111/bjd.18611] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Necrotizing soft-tissue infections (NSTIs) are life threatening, requiring broad-spectrum antibiotics. Their aetiological diagnosis can be limited by poor performance of cultures and administration of antibiotics before surgery. OBJECTIVES We aimed (i) to compare 16S-targeted metagenomics (TM) and unbiased semiquantitative panmicroorganism DNA- and RNA-based shotgun metagenomics (SM) with cultures, (ii) to identify patients who would best benefit from metagenomics approaches and (iii) to detect the microbial pathogens in surrounding non-necrotic 'healthy' tissues by SM-based methods. METHODS A prospective observational study was performed to assess the analytical performance of standard cultures, TM and SM on tissues from 34 patients with NSTIs. Pathogen identification obtained with these three methods was compared. RESULTS Thirty-four necrotic and 10 healthy tissues were collected from 34 patients. The performance of TM was inferior to that of the other methods (P < 0·05), whereas SM performed better than standard culture, although the result was not statistically significant (P = 0·08). SM was significantly more sensitive than TM for the detection of all bacteria (P = 0·02) and more sensitive than standard culture for the detection of anaerobic bacteria (P < 0·01). There was a strong correlation (r = 0·71, Spearman correlation coefficient) between the semiquantitative abundance of bacteria in the culture and the bacteria-to-human sequence ratio in SM. Low amounts of bacterial DNA were found in healthy tissues, suggesting a bacterial continuum between macroscopically 'healthy' and necrotic tissue. CONCLUSIONS SM showed a significantly better ability to detect a broader range of pathogens than TM and identify strict anaerobes than standard culture. Patients with diabetes with NSTIs appeared to benefit most from SM. Finally, our results suggest a bacterial continuum between macroscopically 'healthy' non-necrotic areas and necrotic tissues. What's already known about this topic? Necrotizing soft-tissue infections (NSTIs) are characterized by rapidly progressive necrosis of subcutaneous tissues and high mortality, despite surgical debridement combined with broad-spectrum antibiotics. The spectrum of potentially involved pathogens is very large, and identification is often limited by the poor performance of standard cultures, which may be impaired by previous antibiotic intake. Metagenomics-based approaches show promise for better identification of the pathogens that cause these infections, but they have not been evaluated in this medical context. What does this study add? Shotgun metagenomics (SM) showed higher sensitivity than 16S rRNA gene sequencing and a better ability than culture to detect anaerobic bacteria. As a result, a significant proportion of infections with bacteria, such as Pasteurella multocida or Clostridium perfringens, were detected only by SM. SM bacterial quantification enabled better detection of low amounts of bacterial DNA from macroscopically 'healthy' tissue, suggesting a subclinical infectious extension. What is the translational message? The high analytical performance of SM shown in this study should allow its future implementation for the diagnosis of necrotizing fasciitis, complementing or replacing routine methods. The large amount of data, including additional information on antimicrobial resistance, virulence profiles and metabolic adaptation of the pathogens, will improve microbiological documentation. Our results will improve our understanding of infectious pathophysiology in the future, leading to potentially better medical care.
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Affiliation(s)
- C Rodriguez
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,INSERM U955, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Platform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - A Jary
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - C Hua
- Department of Dermatology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - P-L Woerther
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - R Bosc
- Department of Plastic Surgery, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - M Desroches
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - E Sitterlé
- Unité de Parasitologie-Mycologie, Service de Microbiologie Clinique, Hôpital Necker-Enfants-Malades, AP-HP, Paris, France
| | - G Gricourt
- NGS Platform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - N De Prost
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,INSERM U955, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - J-M Pawlotsky
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,INSERM U955, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - O Chosidow
- Department of Dermatology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA 7379 EpiDermE (Epidémiologie en Dermatologie et Evaluation des Thérapeutiques) and INSERM CIC 1430, Université Paris-Est, Créteil, and Université Pierre et Marie Curie, Paris, France
| | - E Sbidian
- Department of Dermatology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA 7379 EpiDermE (Epidémiologie en Dermatologie et Evaluation des Thérapeutiques) and INSERM CIC 1430, Université Paris-Est, Créteil, and Université Pierre et Marie Curie, Paris, France
| | - J-W Decousser
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
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