25 results on '"Pinault, Lucile"'
Search Results
2. Emergence and outcomes of the SARS-CoV-2 ‘Marseille-4’ variant
- Author
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Fournier, Pierre-Edouard, Colson, Philippe, Levasseur, Anthony, Devaux, Christian A., Gautret, Philippe, Bedotto, Marielle, Delerce, Jeremy, Brechard, Ludivine, Pinault, Lucile, Lagier, Jean-Christophe, Fenollar, Florence, and Raoult, Didier
- Published
- 2021
- Full Text
- View/download PDF
3. A metallo-β-lactamase enzyme for internal detoxification of the antibiotic thienamycin
- Author
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Diene, Seydina M., Pinault, Lucile, Baron, Sophie Alexandra, Azza, Saïd, Armstrong, Nicholas, Hadjadj, Linda, Chabrière, Eric, Rolain, Jean-Marc, Pontarotti, Pierre, and Raoult, Didier
- Published
- 2021
- Full Text
- View/download PDF
4. A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses
- Author
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Colson, Philippe, Pinault, Lucile, Azza, Said, Armstrong, Nicholas, Chabriere, Eric, La Scola, Bernard, Pontarotti, Pierre, and Raoult, Didier
- Published
- 2020
- Full Text
- View/download PDF
5. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms
- Author
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Diene, Seydina M., primary, Pontarotti, Pierre, additional, Azza, Saïd, additional, Armstrong, Nicholas, additional, Pinault, Lucile, additional, Chabrière, Eric, additional, Colson, Philippe, additional, Rolain, Jean-Marc, additional, and Raoult, Didier, additional
- Published
- 2023
- Full Text
- View/download PDF
6. Identification and Characterization of an HtrA Sheddase Produced by Coxiella burnetii
- Author
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Osman, Ikram Omar, primary, Caputo, Aurelia, additional, Pinault, Lucile, additional, Mege, Jean-Louis, additional, Levasseur, Anthony, additional, and Devaux, Christian A., additional
- Published
- 2023
- Full Text
- View/download PDF
7. Human metallo-β-lactamase enzymes degrade penicillin
- Author
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Diene, Seydina M., Pinault, Lucile, Keshri, Vivek, Armstrong, Nicholas, Khelaifia, Saber, Chabrière, Eric, Caetano-Anolles, Gustavo, Colson, Philippe, La Scola, Bernard, Rolain, Jean-Marc, Pontarotti, Pierre, and Raoult, Didier
- Published
- 2019
- Full Text
- View/download PDF
8. clbP Gene, a Potential New Member of the β-Lactamase Family
- Author
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Azour, Adel, primary, Al-Bayssari, Charbel, additional, Pinault, Lucile, additional, Azza, Saïd, additional, Rolain, Jean-Marc, additional, and Diene, Seydina M., additional
- Published
- 2022
- Full Text
- View/download PDF
9. New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome
- Author
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Maatouk, Mohamad, Ibrahim, Ahmad, Pinault, Lucile, Armstrong, Nicholas, Azza, Said, Rolain, Jean-Marc, Bittar, Fadi, Raoult, Didier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010)
- Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,antibiotic resistance ,multifunction hydrolase enzymes ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,candidate phyla radiation ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,RNase ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,beta-lactamase ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology - Abstract
International audience; The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.
- Published
- 2022
10. Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution
- Author
-
Devaux, Christian, Pinault, Lucile, Delerce, Jérémy, Raoult, Didier, Levasseur, Anthony, Frutos, Roger, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre National de la Recherche Scientifique (CNRS), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
- Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,SARS-CoV-2 ,viruses ,fungi ,COVID-19 ,ACE2 ,COVID-19 vaccines ,Review ,Microbiology ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,NRP-1 ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,variant viruses ,mink coronavirus - Abstract
International audience; The rapid spread of SARS-CoV-2 variants has quickly spanned doubts and the fear about their ability escape vaccine protection. Some of these variants initially identified in caged were also found in humans. The claim that these variants exhibited lower susceptibility to antibody neutralization led to the slaughter of 17 million minks in Denmark. SARS-CoV-2 prevalence tests led to the discovery of infected farmed minks worldwide. In this study, we revisit the issue of the circulation of SARS-CoV-2 variants in minks as a model of sarbecovirus interspecies evolution by: (1) comparing human and mink angiotensin I converting enzyme 2 (ACE2) and neuropilin 1 (NRP-1) receptors; (2) comparing SARS-CoV-2 sequences from humans and minks; (3) analyzing the impact of mutations on the 3D structure of the spike protein; and (4) predicting linear epitope targets for immune response. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. However, they are unlikely to lose most of the major epitopes predicted to be targets for neutralizing antibodies. We discuss the consequences of these results for the rational use of SARS-CoV-2 vaccines.
- Published
- 2021
11. Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus?
- Author
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Aherfi, Sarah, primary, Brahim Belhaouari, Djamal, additional, Pinault, Lucile, additional, Baudoin, Jean-Pierre, additional, Decloquement, Philippe, additional, Abrahao, Jonatas, additional, Colson, Philippe, additional, Levasseur, Anthony, additional, Lamb, David C., additional, Chabriere, Eric, additional, Raoult, Didier, additional, and La Scola, Bernard, additional
- Published
- 2021
- Full Text
- View/download PDF
12. Could β-Lactam Antibiotics Block Humoral Immunity?
- Author
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Melenotte, Cléa, primary, Pontarotti, Pierre, additional, Pinault, Lucile, additional, Mège, Jean-Louis, additional, Devaux, Christian, additional, and Raoult, Didier, additional
- Published
- 2021
- Full Text
- View/download PDF
13. Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage
- Author
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Colson, Philippe, primary, Levasseur, Anthony, additional, Delerce, Jeremy, additional, Pinault, Lucile, additional, Dudouet, Pierre, additional, Devaux, Christian, additional, Fournier, Pierre-Edouard, additional, La Scola, Bernard, additional, Lagier, Jean-Christophe, additional, and Raoult, Didier, additional
- Published
- 2021
- Full Text
- View/download PDF
14. Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2?
- Author
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Devaux, Christian A., Pinault, Lucile, Osman, Ikram Omar, Raoult, Didier, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
China ,coronavirus ,ACE2 ,Replication Origin ,Polymorphism, Single Nucleotide ,Host Specificity ,in silico analyses ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Chiroptera ,Animals ,Humans ,Genetic Predisposition to Disease ,Pangolins ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Pandemics ,Original Research ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Receptors, Angiotensin ,SARS-CoV-2 ,Ophiophagus hannah ,Public Health, Environmental and Occupational Health ,COVID-19 ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Public Health - Abstract
International audience; A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile ( Ophiophagus hannah ) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin ( Manis javanica ) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.
- Published
- 2021
15. Emergence of Bat-Related Betacoronaviruses: Hazard and Risks
- Author
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Frutos, Roger, primary, Serra-Cobo, Jordi, additional, Pinault, Lucile, additional, Lopez Roig, Marc, additional, and Devaux, Christian A., additional
- Published
- 2021
- Full Text
- View/download PDF
16. Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea
- Author
-
Diene, Seydina M., primary, Pinault, Lucile, additional, Armstrong, Nicholas, additional, Azza, Said, additional, Keshri, Vivek, additional, Khelaifia, Saber, additional, Chabrière, Eric, additional, Caetano-Anolles, Gustavo, additional, Rolain, Jean-Marc, additional, Pontarotti, Pierre, additional, and Raoult, Didier, additional
- Published
- 2020
- Full Text
- View/download PDF
17. Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases
- Author
-
Keshri, Vivek, primary, Chabrière, Eric, additional, Pinault, Lucile, additional, Colson, Philippe, additional, Diene, Seydina M, additional, Rolain, Jean-Marc, additional, Raoult, Didier, additional, and Pontarotti, Pierre, additional
- Published
- 2020
- Full Text
- View/download PDF
18. Paradoxical β-lactamase activity of archaeal encoding enzymes
- Author
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Diene, Seydina M., Pinault, Lucile, Armstrong, Nicholas, Keshri, Vivek, Khelaifia, Saber, Chabrière, Eric, Caetano-Anolles, Gustavo, Rolain, Jean-Marc, Pontarotti, Pierre, and Raoult, Didier
- Abstract
β-lactams targeting the bacterial cell wall are not efficient on archaea. Using phylogenetic analysis and common ancestor sequences for bacterial β-lactamases, we found serendipitously class B and class C-like β-lactamase genes in most archaea genomes. The class B β-lactamase appears to be highly conserved in archaea and to has been transferred in the bacterial genus Elizabethkingia . The experimentaly expressed class B enzyme from Methanosarcina barkeri was able to digest penicillin G and was inhibited by a β-lactamase inhibitor (i.e. sulbactam). The class C-like β-lactamase was more closely related to DD-peptidase enzymes than know bacterial class C β-lactamases. The use of these very conserved genes in this domain cannot be explored as a defense system against β-lactams but may be used to feed β-lactams as a source of carbon as shown in bacteria.
- Published
- 2019
- Full Text
- View/download PDF
19. Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization–Time of Flight Spectrum Database
- Author
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Pinault, Lucile, Chabrière, Eric, Raoult, Didier, Fenollar, Florence, Carroll, Karen, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)
- Subjects
Microbiology (medical) ,Databases, Factual ,Urine ,Urinalysis ,computer.software_genre ,medicine.disease_cause ,Enterococcus faecalis ,03 medical and health sciences ,0302 clinical medicine ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,Predictive Value of Tests ,Staphylococcus epidermidis ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,medicine ,Humans ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Prospective Studies ,030212 general & internal medicine ,ComputingMilieux_MISCELLANEOUS ,0303 health sciences ,Staphylococcus saprophyticus ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Bacteria ,biology ,Database ,030306 microbiology ,business.industry ,Pseudomonas aeruginosa ,Bacteriology ,biology.organism_classification ,Antimicrobial ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Bacterial Typing Techniques ,3. Good health ,Staphylococcus aureus ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Urinary Tract Infections ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,business ,computer ,Enterococcus faecium - Abstract
Urinary tract infections are among the most common reasons for antimicrobial treatment, and early diagnosis could have a significant impact by enabling rapid administration of the adapted antibiotic and preventing complications. The current delay between sample receipt and pathogen identification is about 24 to 48 h, which could be significantly shortened by use of an accurate direct method. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is already used for the identification of pathogens in clinical laboratories and constitutes a promising tool for direct diagnosis. A simple preparation protocol was established for the processing of urine samples prior to MS analysis. MALDI-TOF spectra collected directly from 1,000 infected urine samples were used to create a specific reference database (named Urinf). A prospective study was then carried out to evaluate the Urinf database and compare the results obtained with the standard database provided by Bruker on the Biotyper Real Time Classification software. Seven hundred eighty urine specimens were processed and analyzed according to our method. Among them, almost 90% of 500 infected monobacterial samples could be correctly diagnosed with the Urinf database, compared to 50% using the standard database. The identification of Enterobacteriaceae, Staphylococcus aureus, Staphylococcus saprophyticus, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium was greatly improved but not for Staphylococcus epidermidis. The creation of a database adapted to a particular type of clinical sample has great potential to increase both the rate and rapidity of pathogen identification. Sensitivity still remains to be improved for bacterial species that exhibit few specific peaks on mass spectra.
- Published
- 2019
20. Evaluation of a robust engineered enzyme towards organophosphorus insecticide bioremediation using planarians as biosensors
- Author
-
Poirier, Laetitia, primary, Pinault, Lucile, additional, Armstrong, Nicholas, additional, Ghigo, Eric, additional, Daudé, David, additional, and Chabrière, Eric, additional
- Published
- 2019
- Full Text
- View/download PDF
21. Zafirlukast Inhibits Complexation of Lsr2 with DNA and Growth of Mycobacterium tuberculosis
- Author
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Pinault, Lucile, primary, Han, Jeong-Sun, additional, Kang, Choong-Min, additional, Franco, Jimmy, additional, and Ronning, Donald R., additional
- Published
- 2013
- Full Text
- View/download PDF
22. New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome.
- Author
-
Maatouk M, Ibrahim A, Pinault L, Armstrong N, Azza S, Rolain JM, Bittar F, and Raoult D
- Subjects
- Bacteria genetics, Bacteria metabolism, Humans, RNA, Ribosomal, 16S genetics, beta-Lactams, beta-Lactamase Inhibitors, beta-Lactamases genetics, beta-Lactamases metabolism
- Abstract
The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.
- Published
- 2022
- Full Text
- View/download PDF
23. Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution.
- Author
-
Devaux CA, Pinault L, Delerce J, Raoult D, Levasseur A, and Frutos R
- Abstract
The rapid spread of SARS-CoV-2 variants has quickly spanned doubts and the fear about their ability escape vaccine protection. Some of these variants initially identified in caged were also found in humans. The claim that these variants exhibited lower susceptibility to antibody neutralization led to the slaughter of 17 million minks in Denmark. SARS-CoV-2 prevalence tests led to the discovery of infected farmed minks worldwide. In this study, we revisit the issue of the circulation of SARS-CoV-2 variants in minks as a model of sarbecovirus interspecies evolution by: (1) comparing human and mink angiotensin I converting enzyme 2 (ACE2) and neuropilin 1 (NRP-1) receptors; (2) comparing SARS-CoV-2 sequences from humans and minks; (3) analyzing the impact of mutations on the 3D structure of the spike protein; and (4) predicting linear epitope targets for immune response. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. However, they are unlikely to lose most of the major epitopes predicted to be targets for neutralizing antibodies. We discuss the consequences of these results for the rational use of SARS-CoV-2 vaccines., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Devaux, Pinault, Delerce, Raoult, Levasseur and Frutos.)
- Published
- 2021
- Full Text
- View/download PDF
24. Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2?
- Author
-
Devaux CA, Pinault L, Osman IO, and Raoult D
- Subjects
- Animals, China, Chiroptera virology, Genetic Predisposition to Disease, Humans, Ophiophagus hannah virology, Pandemics, Pangolins virology, Polymorphism, Single Nucleotide, COVID-19 immunology, COVID-19 pathology, Host Specificity genetics, Receptors, Angiotensin genetics, Replication Origin, SARS-CoV-2 genetics, SARS-CoV-2 pathogenicity
- Abstract
A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile ( Ophiophagus hannah ) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin ( Manis javanica ) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Devaux, Pinault, Osman and Raoult.)
- Published
- 2021
- Full Text
- View/download PDF
25. Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization-Time of Flight Spectrum Database.
- Author
-
Pinault L, Chabrière E, Raoult D, and Fenollar F
- Subjects
- Bacteria classification, Humans, Predictive Value of Tests, Prospective Studies, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Urinary Tract Infections microbiology, Bacteria isolation & purification, Bacterial Typing Techniques methods, Databases, Factual standards, Urinalysis methods, Urinary Tract Infections diagnosis
- Abstract
Urinary tract infections are among the most common reasons for antimicrobial treatment, and early diagnosis could have a significant impact by enabling rapid administration of the adapted antibiotic and preventing complications. The current delay between sample receipt and pathogen identification is about 24 to 48 h, which could be significantly shortened by use of an accurate direct method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is already used for the identification of pathogens in clinical laboratories and constitutes a promising tool for direct diagnosis. A simple preparation protocol was established for the processing of urine samples prior to MS analysis. MALDI-TOF spectra collected directly from 1,000 infected urine samples were used to create a specific reference database (named Urinf). A prospective study was then carried out to evaluate the Urinf database and compare the results obtained with the standard database provided by Bruker on the Biotyper Real Time Classification software. Seven hundred eighty urine specimens were processed and analyzed according to our method. Among them, almost 90% of 500 infected monobacterial samples could be correctly diagnosed with the Urinf database, compared to 50% using the standard database. The identification of Enterobacteriaceae , Staphylococcus aureus , Staphylococcus saprophyticus , Pseudomonas aeruginosa , Enterococcus faecalis , and Enterococcus faecium was greatly improved but not for Staphylococcus epidermidis The creation of a database adapted to a particular type of clinical sample has great potential to increase both the rate and rapidity of pathogen identification. Sensitivity still remains to be improved for bacterial species that exhibit few specific peaks on mass spectra., (Copyright © 2019 American Society for Microbiology.)
- Published
- 2019
- Full Text
- View/download PDF
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