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A case for investment in clinical metagenomics in low-income and middle-income countries. THE LANCET. MICROBE 2023; 4:e192-e199. [PMID: 36563703 DOI: 10.1016/s2666-5247(22)00328-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.
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Lazarevic V, Gaïa N, Girard M, Mauffrey F, Ruppé E, Schrenzel J. Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing. ISME COMMUNICATIONS 2022; 2:122. [PMID: 37938717 PMCID: PMC9792467 DOI: 10.1038/s43705-022-00208-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 10/28/2023]
Abstract
Before implementing metagenomic next-generation sequencing (mNGS) in the routine diagnostic laboratory, several challenges need to be resolved. To address strengths and limitations of mNGS in bacterial detection and quantification in samples with overwhelming host DNA abundance, we used the pig muscle tissue spiked with a home-made bacterial mock community, consisting of four species from different phyla. From the spiked tissue, we extracted DNA using: (i) a procedure based on mechanical/chemical lysis (no bacterial DNA enrichment); (ii) the Ultra-Deep Microbiome Prep (Molzym) kit for bacterial DNA enrichment; and (iii) the same enrichment kit but replacing the original proteinase K treatment for tissue solubilization by a collagenases/thermolysin digestion and cell filtration. Following mNGS, we determined bacterial: 'host' read ratios and taxonomic abundance profiles. We calculated the load of each mock-community member by combining its read counts with read counts and microscopically-determined cell counts of other co-spiked bacteria. In unenriched samples, bacterial quantification and taxonomic profiling were fairly accurate but at the expense of the sensitivity of detection. The removal of 'host' DNA by the modified enrichment protocol substantially improved bacterial detection in comparison to the other two extraction procedures and generated less distorted taxonomic profiles as compared to the original enrichment protocol.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Florian Mauffrey
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Etienne Ruppé
- Université Sorbonne Paris Nord and INSERM UMR1137 IAME, Université de Paris Cité, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
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What Does 16S rRNA Gene-Targeted Next Generation Sequencing Contribute to the Study of Infective Endocarditis in Heart-Valve Tissue? Pathogens 2021; 11:pathogens11010034. [PMID: 35055982 PMCID: PMC8781873 DOI: 10.3390/pathogens11010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
Infective endocarditis (IE) is a severe and life-threatening disease. Identification of infectious etiology is essential for establishing the appropriate antimicrobial treatment and decreasing mortality. The aim of this study was to explore the potential utility of metataxonomics for improving microbiological diagnosis of IE. Here, next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene was performed in 27 heart valve tissues (18 natives, 5 intravascular devices, and 4 prosthetics) from 27 patients diagnosed with IE (4 of them with negative blood cultures). Metataxonomics matched with conventional diagnostic techniques in 24/27 cases (88.9%). The same bacterial family was assigned to 24 cases; the same genus, to 23 cases; and the same species, to 13 cases. In 22 of them, the etiological agent was represented by percentages > 99% of the reads and in two cases, by ~70%. Staphylococcus aureus was detected in a previously microbiological undiagnosed patient. Thus, microbiological diagnosis with 16S rRNA gene targeted-NGS was possible in one more sample than using traditional techniques. The remaining two patients showed no coincidence between traditional and 16S rRNA gene-targeted NGS microbiological diagnoses. In addition, 16S rRNA gene-targeted NGS allowed us to suggest coinfections that were supported by clinical data in one patient, and minority records also verified mixed infections in three cases. In our series, metataxonomics was valid for the identification of the causative agents, although more studies are needed before implementation of 16S rRNA gene-targeted NGS for the diagnosis of IE.
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Michel C, Raimo M, Lazarevic V, Gaïa N, Leduc N, Knoop C, Hallin M, Vandenberg O, Schrenzel J, Grimaldi D, Hites M. Case Report: About a Case of Hyperammonemia Syndrome Following Lung Transplantation: Could Metagenomic Next-Generation Sequencing Improve the Clinical Management? Front Med (Lausanne) 2021; 8:684040. [PMID: 34295911 PMCID: PMC8290067 DOI: 10.3389/fmed.2021.684040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mycoplasma hominis and Ureaplasma spp. are responsible for opportunistic infections in transplant patients, sometimes causing a life-threatening hyperammonemia syndrome. Both pathogens are not identified with standard microbiology techniques, resulting in missed or delayed diagnosis. We present a clinical case that illustrates the added value that next-generation sequencing (NGS) may offer in the diagnosis of respiratory infections in immune-compromised patients. Results: A 55 years-old man with idiopathic pulmonary fibrosis underwent double lung transplantation. He received antibiotic prophylaxis with piperacillin-tazobactam and azythromycin. At day 4 post-transplantation (PTx), the patient presented an acute respiratory distress. A broncho-alveolar lavage (BAL) was performed. At day 5 PTx, the patient presented a status epilepticus due to diffuse cerebral oedema. Serum ammonia concentration was 661 μg/dL. BAL bacterial culture was negative. Because of the clinical presentation, special cultures were performed and identified 100.000 CFU/mL of M. hominis and Ureaplasma spp. and specific PCRs were positive for M. hominis and Ureaplasma parvum. Antibiotic therapy was shifted to therapeutic dose of azithromycin and doxycycline; within 48 h ammonia serum concentrations returned to normal but the coma persisted several weeks, followed by a persistent frontal lobe syndrome. A follow-up BAL was performed on day 11 Ptx. The Mycoplasma/Ureaplasma culture was negative, yet the specific PCRs remained positive. Bacterial culture found 100 CFU/mL of Staphylococcus aureus and viral culture was positive for Herpes Simplex Virus-1. These results were confirmed by metagenomic next-generation sequencing (mNGS). In the bacterial fraction, the majority of reads belonged to Corynebacterium propinquum (34.7%), S. aureus (24.1%) and Staphylococcus epidermidis (17.1%). Reads assigned to M. hominis, Ureaplasma urealyticum and parvum represented 0.71, 0.13, and 0.04% of the bacterial fraction and corresponded to 6.9 × 103, 9.7 × 102, and 3.7 × 102 genome equivalents per mL of BAL fluid, respectively. These results are in favor of a cure of the atypical infection. Conclusions: mNGS offered added diagnostic and quantitative values compared to PCR tests, which can remain positive after resolved infections. The initiation of appropriate antibiotic therapy would have occurred earlier on, possibly resulting in a better clinical outcome if mNGS had been performed in a routine fashion.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Michela Raimo
- Clinic of Infectious Diseases, Cliniques Universitaires de Bruxelles, Erasme Hospital, Brussels, Belgium
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Nina Leduc
- Department of Pneumology, Cliniques Universitaires de Bruxelles, Erasme Hospital, Brussels, Belgium
| | - Christiane Knoop
- Department of Pneumology, Cliniques Universitaires de Bruxelles, Erasme Hospital, Brussels, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivier Vandenberg
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Schrenzel
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - David Grimaldi
- Intensive Care Unit, Cliniques Universitaires de Bruxelles, Erasme Hospital, Brussels, Belgium
| | - Maya Hites
- Clinic of Infectious Diseases, Cliniques Universitaires de Bruxelles, Erasme Hospital, Brussels, Belgium
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Ai JW, Liu H, Li HX, Ling QX, Ai YQ, Sun SJ, Wang X, Zhang BY, Zheng JM, Jin JL, Zhang WH. Precise diagnosis of Neisseria macacae infective endocarditis assisted by nanopore sequencing. Emerg Microbes Infect 2021; 9:1864-1868. [PMID: 32757712 PMCID: PMC7473274 DOI: 10.1080/22221751.2020.1807411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Infective endocarditis caused by Neisseria macacae in humans is extremely rare. We presented here a case of N. macacae infective endocarditis in a 61-year-old man with a native aortic valve infection. N. macacae was isolated from blood culture and was detected by nanopore-based metagenomic sequencing in the vegetations. Finally, the patient recovered completely after surgery and antibiotic therapy.
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Affiliation(s)
- Jing-Wen Ai
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Hong Liu
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Hui-Xia Li
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Department of Infectious Diseases, No. 988. Hospital of Liberation Army, Henan, People's Republic of China
| | - Qing-Xia Ling
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Department of Infectious Diseases, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yan-Qin Ai
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Department of Infectious Diseases, Xuchang Central Hospital affiliated to Henan University of Science and Technology, Henan, People's Republic of China
| | - Si-Jia Sun
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Department of Gastroenterology, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Xuan Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Bing-Yan Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jian-Ming Zheng
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jia-Lin Jin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Wen-Hong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
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Leo S, Cherkaoui A, Renzi G, Schrenzel J. Mini Review: Clinical Routine Microbiology in the Era of Automation and Digital Health. Front Cell Infect Microbiol 2020; 10:582028. [PMID: 33330127 PMCID: PMC7734209 DOI: 10.3389/fcimb.2020.582028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Clinical microbiology laboratories are the first line to combat and handle infectious diseases and antibiotic resistance, including newly emerging ones. Although most clinical laboratories still rely on conventional methods, a cascade of technological changes, driven by digital imaging and high-throughput sequencing, will revolutionize the management of clinical diagnostics for direct detection of bacteria and swift antimicrobial susceptibility testing. Importantly, such technological advancements occur in the golden age of machine learning where computers are no longer acting passively in data mining, but once trained, can also help physicians in making decisions for diagnostics and optimal treatment administration. The further potential of physically integrating new technologies in an automation chain, combined to machine-learning-based software for data analyses, is seducing and would indeed lead to a faster management in infectious diseases. However, if, from one side, technological advancement would achieve a better performance than conventional methods, on the other side, this evolution challenges clinicians in terms of data interpretation and impacts the entire hospital personnel organization and management. In this mini review, we discuss such technological achievements offering practical examples of their operability but also their limitations and potential issues that their implementation could rise in clinical microbiology laboratories.
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Affiliation(s)
- Stefano Leo
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Abdessalam Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
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A case of infective endocarditis caused by "Neisseria skkuensis". J Infect Chemother 2020; 27:83-85. [PMID: 32861578 DOI: 10.1016/j.jiac.2020.08.013] [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: 06/22/2020] [Revised: 08/12/2020] [Accepted: 08/15/2020] [Indexed: 11/20/2022]
Abstract
"Neisseria skkuensis" is a gram-negative coccus that is endemic in the human oral cavity, with only few reports of infection in humans. Herein, we report a case of a male patient in his sixties presenting with infective endocarditis (IE) caused by "N. skkuensis". To our knowledge, this is the second case of IE confirmed using 16S rRNA gene to have been caused by "N. skkuensis". The accurate diagnosis of rare or difficult-to-identify pathogens is a major challenge for clinical microbiological laboratories. Although Neisseria spp. are common in the oral cavity and are often seen in routine tests, identification of their biochemical properties and mass spectrometric analysis are difficult. In this case report, we describe the accurate identification of "N. skkuensis" by 16S rRNA gene sequencing analysis compared to other identification methods. Further cases of "N. skkuensis" are needed to fully evaluate the clinical approach of this detection method.
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Charretier Y, Lazarevic V, Schrenzel J, Ruppé E. Messages from the Fourth International Conference on Clinical Metagenomics. Microbes Infect 2020; 22:635-641. [PMID: 32828958 DOI: 10.1016/j.micinf.2020.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Yannick Charretier
- Laboratoire de Recherche Génomique, Centre Médical Universitaire, 1 Rue Michel Servet, Genève 4 1211, Switzerland.
| | - Vladimir Lazarevic
- Laboratoire de Recherche Génomique, Centre Médical Universitaire, 1 Rue Michel Servet, Genève 4 1211, Switzerland
| | - Jacques Schrenzel
- Laboratoire de Recherche Génomique, Centre Médical Universitaire, 1 Rue Michel Servet, Genève 4 1211, Switzerland; Laboratoire de Bactériologie, Hôpitaux Universitaires de Genève, 4 Rue Gabrielle-Perret-Gentil, Geneva 14 1211, Switzerland
| | - Etienne Ruppé
- AP-HP, Hôpital Bichat - Claude Bernard, Laboratoire de Bactériologie, INSERM, IAME, UMR 1137, France; Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, 46 Rue Henri-Huchard, Paris, 75018, France
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Native valve Neisseria meningitidis endocarditis with embolic infarcts. IDCases 2020; 21:e00918. [PMID: 32775206 PMCID: PMC7399248 DOI: 10.1016/j.idcr.2020.e00918] [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: 06/03/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/04/2022] Open
Abstract
To demonstrate an unusual presentation of NM infective endocarditis (IE). To highlight the importance of considering NM endocarditis in high-risk individuals. To demonstrate challenging management of meningococcal IE.
Infective endocarditis caused by Neisseria meningitidis (NM) is a very rare manifestation of invasive meningococcal disease with only a few cases described in the literature. We report a case of a native mitral valve endocarditis caused by NM in a 61-year-old female without meningitis. Our case highlights the importance of considering NM as one of the causative organisms of infective endocarditis, even in the absence of meningitis. Even though the cases of NM endocarditis have drastically decreased with the advent of antibacterials, NM should always be considered in the differential diagnosis in certain high-risk groups, like diabetics, polysubstance abusers, and elderly individuals. The prognosis is good with early appropriate antibiotic treatment with or without surgery.
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Leo S, Lazarevic V, Girard M, Getaz-Jimenez Velasco GC, Gaïa N, Renzi G, Cherkaoui A, Hong E, Taha MK, Schrenzel J. Strain coverage of Bexsero vaccine assessed by whole-genome sequencing over a cohort of invasive meningococci of serogroups B and W isolated in Switzerland. Vaccine 2020; 38:5324-5331. [PMID: 32561121 DOI: 10.1016/j.vaccine.2020.05.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/27/2022]
Abstract
Invasive meningococcal disease (IMD), caused by Neisseria meningitidis (Nm) strains, is a life-threatening but vaccine-preventable condition. Bexsero is a four-component vaccine that offers broad protection against Nm of serogroup B (NmB), particularly common in Europe. In Switzerland, Bexsero has not yet been licensed and no information is available concerning the predicted vaccine coverage on isolates of circulating Nm. We performed genotyping of Bexsero antigen loci by whole-genome sequencing (WGS) on 104 NmB collected in Switzerland in the 2010-2015 period. We searched for antigen variants previously defined as predictors of strain coverage and estimated that 50% of IMD NmB strains were potentially covered by the vaccine. Clonal complexes (cc) 32, 41/44 and 269, considered the best covered lineages, were further sub-typed according to Bexsero Antigen Sequence Type (BAST) scheme. We also genotyped by WGS 40 Nm of serogroup W (NmW) collected in the country between 2010 and 2016. NmW cc22 isolates appeared to be covered by the vaccine, which was not the case for cc11 isolates, whose incidence has recently increased in Switzerland and all over Europe. Our work underlines the benefit of using WGS for surveillance of vaccine antigen variant distribution in local Nm population and taking proper measures to prevent the spread of NmB.
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Affiliation(s)
- Stefano Leo
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Gisela C Getaz-Jimenez Velasco
- Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Gesuele Renzi
- Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Abdessalam Cherkaoui
- Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Eva Hong
- Invasive Bacterial Infection and National Reference Centre for Meningococci, Institut Pasteur, Paris, France
| | - Muhamed-Kheir Taha
- Invasive Bacterial Infection and National Reference Centre for Meningococci, Institut Pasteur, Paris, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, University Hospitals and University of Geneva, Geneva, Switzerland; Swiss National Reference Center for Meningococci (www.meningo.ch), Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland.
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