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Bekliz M, Adea K, Puhach O, Perez-Rodriguez F, Marques Melancia S, Baggio S, Corvaglia AR, Jacquerioz F, Alvarez C, Essaidi-Laziosi M, Escadafal C, Kaiser L, Eckerle I. Analytical Sensitivity of Eight Different SARS-CoV-2 Antigen-Detecting Rapid Tests for Omicron-BA.1 Variant. Microbiol Spectr 2022; 10:e0085322. [PMID: 35938792 PMCID: PMC9430749 DOI: 10.1128/spectrum.00853-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/14/2022] [Indexed: 11/24/2022] Open
Abstract
The emergence of each novel SARS-CoV-2 variant of concern (VOC) requires investigation of its potential impact on the performance of diagnostic tests in use, including antigen-detecting rapid diagnostic tests (Ag-RDTs). Although anecdotal reports have been circulating that the newly emerged Omicron-BA.1 variant is in principle detectable by Ag-RDTs, few data on sensitivity are available. We have performed (i) analytical sensitivity testing with cultured virus in eight Ag-RDTs and (ii) retrospective testing in duplicates with clinical samples from vaccinated individuals with Omicron-BA.1 (n = 59) or Delta (n = 54) breakthrough infection on seven Ag-RDTs. Overall, in our analytical study we have found heterogenicity between Ag-RDTs for detecting Omicron-BA.1. When using cultured virus, we observed a trend toward lower endpoint sensitivity for Omicron-BA.1 detection than for earlier circulating SARS-CoV-2 and the other VOCs. In our retrospective study, the detection of Delta and Omicron-BA.1 was assessed in a comparable set of stored clinical samples using seven Ag-RDTs. Four hundred ninety-seven of all 826 tests (60.17%) performed on Omicron-BA.1 samples were positive, compared to 489/756 (64.68%) for Delta samples. In the analytical study, the sensitivity for both Omicron-BA.1 and Delta between the Ag-RDTs was variable. All seven Ag-RDTs showed comparable sensitivities to detect Omicron-BA.1 and Delta in the retrospective study. IMPORTANCE Sensitivity for detecting Omicron-BA.1 shows high heterogenicity between Ag-RDTs, necessitating a careful consideration when using these tests to guide infection prevention measures. Analytical and retrospective testing is a proxy and timely solution to generate rapid performance data, but it is not a replacement for clinical evaluations, which are urgently needed. Biological and technical reasons for detection failure by some Ag-RDTs need to be further investigated.
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Affiliation(s)
- Meriem Bekliz
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Kenneth Adea
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olha Puhach
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francisco Perez-Rodriguez
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Stéfane Marques Melancia
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Stephanie Baggio
- Division of Prison Health, Geneva University Hospitals & University of Geneva, Geneva, Switzerland
| | - Anna-Rita Corvaglia
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Frederique Jacquerioz
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
- Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland
- Primary Care Division, Geneva University Hospitals, Geneva, Switzerland
| | - Catia Alvarez
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Manel Essaidi-Laziosi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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Laumay F, Benchetrit H, Corvaglia AR, van der Mee-Marquet N, François P. The Staphylococcus aureus CC398 Lineage: An Evolution Driven by the Acquisition of Prophages and Other Mobile Genetic Elements. Genes (Basel) 2021; 12:genes12111752. [PMID: 34828356 PMCID: PMC8623586 DOI: 10.3390/genes12111752] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/31/2022] Open
Abstract
Among clinically relevant lineages of Staphylococcus aureus, the lineage or clonal complex 398 (CC398) is of particular interest. Strains from this lineage were only described as livestock colonizers until 2007. Progressively, cases of infection were reported in humans in contact with farm animals, and now, CC398 isolates are increasingly identified as the cause of severe infections even in patients without any contact with animals. These observations suggest that CC398 isolates have spread not only in the community but also in the hospital setting. In addition, several recent studies have reported that CC398 strains are evolving towards increased virulence and antibiotic resistance. Identification of the origin and emergence of this clonal complex could probably benefit future large-scale studies that aim to detect sources of contamination and infection. Current evidence indicates that the evolution of CC398 strains towards these phenotypes has been driven by the acquisition of prophages and other mobile genetic elements. In this short review, we summarize the main knowledge of this major lineage of S. aureus that has become predominant in the human clinic worldwide within a single decade.
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Affiliation(s)
- Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland; (F.L.); (A.-R.C.)
- Institut des Agents Infectieux, Centre de Biologie du Nord, Hospices Civils de Lyon, F-69003 Lyon, France
| | - Hugo Benchetrit
- UFR de Chimie et de Biologie, Faculté des Sciences, Université Grenoble Alpes, 38000 Grenoble, France;
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland; (F.L.); (A.-R.C.)
- Geneva Centre for Emerging Viral Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | | | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland; (F.L.); (A.-R.C.)
- Correspondence:
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Laumay F, Corvaglia AR, Diene SM, Girard M, Oechslin F, van der Mee-Marquet N, Entenza JM, François P. Temperate Prophages Increase Bacterial Adhesin Expression and Virulence in an Experimental Model of Endocarditis Due to Staphylococcus aureus From the CC398 Lineage. Front Microbiol 2019; 10:742. [PMID: 31105650 PMCID: PMC6492496 DOI: 10.3389/fmicb.2019.00742] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/25/2019] [Indexed: 01/13/2023] Open
Abstract
Until 2007, Staphylococcus aureus from clonal complex 398 (CC398) was exclusively associated with livestock species and companion animals. Recently, several studies described the emergence of S. aureus CC398 as etiologies of severe infections in humans living in an animal-free environment. Recent sequencing efforts showed that the mobile genetic elements found in CC398 isolates were specific for each population and enabled differentiation of strains responsible for asymptomatic colonization from strains involved in bloodstream infections. We mobilized prophages from a human CC398 isolate and introduced them into two naïve ancestral isolates devoid of prophages that exclusively colonize animals. These lysogenized ancestral CC398 isolates acquired features related to virulence, such as an increased capacity to adhere to human extracellular matrix proteins and the ability to invade and survive within non-phagocytic cells. Pathogenicity of several clinical isolates from the CC398 lineage as well as ancestral and in vitro lysogenized ancestral counterparts was assessed in a model of infectious endocarditis in rats. Natural and artificial lysogens were not only more invasive than their prophage-free parent but also showed an increased capacity to multiply within aortic vegetations. This study identified prophages as mediators of bacterial virulence in a model of infectious endocarditis, probably through promotion of interaction with extracellular matrix components. Further studies are needed to identify mechanisms leading to promotion of intrinsic virulence.
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Affiliation(s)
- Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Seydina M Diene
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine et de Pharmacie, Aix-Marseille University, Marseille, France
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - José Manuel Entenza
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
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Mikheyeva IV, Thomas JM, Kolar SL, Corvaglia AR, Gaϊa N, Leo S, Francois P, Liu GY, Rawat M, Cheung AL. YpdA, a putative bacillithiol disulfide reductase, contributes to cellular redox homeostasis and virulence in Staphylococcus aureus. Mol Microbiol 2019; 111:1039-1056. [PMID: 30636083 DOI: 10.1111/mmi.14207] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2018] [Indexed: 11/28/2022]
Abstract
The intracellular redox environment of Staphylococcus aureus is mainly buffered by bacillithiol (BSH), a low molecular weight thiol. The identity of enzymes responsible for the recycling of oxidized bacillithiol disulfide (BSSB) to the reduced form (BSH) remains elusive. We examined YpdA, a putative bacillithiol reductase, for its role in maintaining intracellular redox homeostasis. The ypdA mutant showed increased levels of BSSB and a lower bacillithiol redox ratio vs. the isogenic parent, indicating a higher level of oxidative stress within the bacterial cytosol. We showed that YpdA consumed NAD(P)H; and YpdA protein levels were augmented in response to stress. Wild type strains overexpressing YpdA showed increased tolerance to oxidants and electrophilic agents. Importantly, YpdA overexpression in the parental strain caused an increase in BSH levels accompanied by a decrease in BSSB concentration in the presence of stress, resulting in an increase in bacillithiol redox ratio vs. the vector control. Additionally, the ypdA mutant exhibited decreased survival in human neutrophils (PMNs) as compared with the parent, while YpdA overexpression protected the resulting strain from oxidative stress in vitro and from killing by human neutrophils ex vivo. Taken together, these data present a new role for YpdA in S. aureus physiology and virulence through the bacillithiol system.
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Affiliation(s)
- Irina V Mikheyeva
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jason M Thomas
- Biology Department, California State University, Fresno, Fresno, CA 93740, USA
| | - Stacey L Kolar
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Nadia Gaϊa
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Stefano Leo
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - Patrice Francois
- Genomic Research Laboratory, Service of Infectious Diseases, University Hospital of Geneva, 1205 Geneva 4, Switzerland
| | - George Y Liu
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Rawat
- Biology Department, California State University, Fresno, Fresno, CA 93740, USA
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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van der Mee-Marquet N, Corvaglia AR, Valentin AS, Hernandez D, Bertrand X, Girard M, Kluytmans J, Donnio PY, Quentin R, François P. Analysis of prophages harbored by the human-adapted subpopulation of Staphylococcus aureus CC398. Infect Genet Evol 2013; 18:299-308. [PMID: 23770143 DOI: 10.1016/j.meegid.2013.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 05/30/2013] [Accepted: 06/09/2013] [Indexed: 01/27/2023]
Abstract
Staphylococcus aureus clonal complex 398 is a livestock-associated pathogen that poses a worldwide threat because of its ability to colonize and infect both humans and animals. We used high-resolution whole-genome microarrays, prophage profiling, immune evasion cluster characterization and whole-genome sequencing to investigate the roles of prophages in the emerging human-adapted subpopulation of CC398 that has been associated with invasive infections in humans living in animal-free environments. We characterized one phage and two prophages specifically harbored by CC398 isolates belonging to the emerging subpopulation. We introduced the phage into permissive prophage-free isolates. We investigated the effects of lysogeny on the host ability to resist further phage infection and transformation, to acquire the capacity to invade human cells, and to express virulence factors encoded by prophages. We report evidence of a defective ϕMR11-like helper prophage, named StauST398-5pro, specifically associated with the emerging non-LA CC398 subpopulation. StauST398-5pro confers substantial protection against horizontal genetic transfer to its host. It interacts with a human-associated β-converting prophage encoding immune-modulating proteins such that virulence genes are expressed during stress situations. Our findings provide insight into the role of phages in the expression of virulence and in the spread of genetic information among new host-adapted S. aureus isolates. We demonstrate that functional prophage elements can condition host specificity and confer new virulence traits on emerging intra-species clones of bacteria.
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Oun S, Redder P, Didier JP, François P, Corvaglia AR, Buttazzoni E, Giraud C, Girard M, Schrenzel J, Linder P. The CshA DEAD-box RNA helicase is important for quorum sensing control in Staphylococcus aureus. RNA Biol 2012; 10:157-65. [PMID: 23229022 PMCID: PMC3590232 DOI: 10.4161/rna.22899] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DEAD-box RNA helicases are present in almost all living organisms and participate in various processes of RNA metabolism. Bacterial proteins of this large family were shown to be required for translation initiation, ribosome biogenesis and RNA decay. The latter is primordial for rapid adaptation to changing environmental conditions. In particular, the RhlB RNA helicase from E. coli was shown to assist the bacterial degradosome machinery. Recently, the CshA DEAD-box proteins from Bacillus subtilis and Staphylococcus aureus were shown to interact with proteins that are believed to form the degradosome. S. aureus can cause life-threatening disease, with particular concern focusing on biofilm formation on catheters and prosthetic devices, since in this form the bacteria are almost impossible to eradicate both by the immune system and antibiotic treatment. This persistent state relies on the expression of surface encoded proteins that allow attachment to various surfaces, and contrasts with the dispersal mode of growth that relies on the secretion of proteins such as hemolysins and proteases. The switch between these two states is mainly mediated by the Staphylococcal cell density sensing system encoded by agr. We show that inactivation of the cshA DEAD-box gene results in dysregulation of biofilm formation and hemolysis through modulation of agr mRNA stability. Importantly, inactivation of the agrA gene in the cshA mutant background reverses the defect, indicating that cshA is genetically upstream of agr and that a delicate balance of agr mRNA abundance mediated through stability control by CshA is critical for proper expression of virulence factors.
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Affiliation(s)
- Stella Oun
- Department of Microbiology and Molecular Medicine, CMU, Medical Faculty, University of Geneva, Genève, Switzerland
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