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Ayotte Y, Bernet E, Bilodeau F, Cimino M, Gagnon D, Lebughe M, Mistretta M, Ogadinma P, Ouali SL, Sow AA, Chatel-Chaix L, Descoteaux A, Manina G, Richard D, Veyrier F, LaPlante SR. Fragment-Based Phenotypic Lead Discovery To Identify New Drug Seeds That Target Infectious Diseases. ACS Chem Biol 2021; 16:2158-2163. [PMID: 34699722 DOI: 10.1021/acschembio.1c00657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based lead discovery has emerged over the last decades as one of the most powerful techniques for identifying starting chemical matter to target specific proteins or nucleic acids in vitro. However, the use of such low-molecular-weight fragment molecules in cell-based phenotypic assays has been historically avoided because of concerns that bioassays would be insufficiently sensitive to detect the limited potency expected for such small molecules and that the high concentrations required would likely implicate undesirable artifacts. Herein, we applied phenotype cell-based screens using a curated fragment library to identify inhibitors against a range of pathogens including Leishmania, Plasmodium falciparum, Neisseria, Mycobacterium, and flaviviruses. This proof-of-concept shows that fragment-based phenotypic lead discovery (FPLD) can serve as a promising complementary approach for tackling infectious diseases and other drug-discovery programs.
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Affiliation(s)
- Yann Ayotte
- Institut national de la recherche scientifique - Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Eve Bernet
- Bacterial Symbionts Evolution, Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - François Bilodeau
- NMX Research and Solutions, Inc., 500 Boulevard Cartier Ouest, Laval, Quebec H7V 5B7, Canada
| | - Mena Cimino
- Microbial Individuality and Infection Group, Cell Biology and Infection Department, Institut Pasteur, 25-28 Rue du Docteur Roux 75015, Paris, France
| | - Dominic Gagnon
- Centre de recherche du CHU de Québec-Université Laval, Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Marthe Lebughe
- Bacterial Symbionts Evolution, Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Maxime Mistretta
- Microbial Individuality and Infection Group, Cell Biology and Infection Department, Institut Pasteur, 25-28 Rue du Docteur Roux 75015, Paris, France
| | - Paul Ogadinma
- NMX Research and Solutions, Inc., 500 Boulevard Cartier Ouest, Laval, Quebec H7V 5B7, Canada
| | - Sarah-Lisa Ouali
- Institut national de la recherche scientifique - Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Aïssatou Aïcha Sow
- Institut national de la recherche scientifique - Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Laurent Chatel-Chaix
- Institut national de la recherche scientifique - Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Albert Descoteaux
- Institut national de la recherche scientifique - Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Giulia Manina
- Microbial Individuality and Infection Group, Cell Biology and Infection Department, Institut Pasteur, 25-28 Rue du Docteur Roux 75015, Paris, France
| | - Dave Richard
- Centre de recherche du CHU de Québec-Université Laval, Département de Microbiologie-Infectiologie et d’Immunologie, Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Frédéric Veyrier
- Bacterial Symbionts Evolution, Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Steven R. LaPlante
- Institut national de la recherche scientifique - Armand-Frappier Santé Biotechnologie Research Centre, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
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Alabi A, Kazimoto T, Lebughe M, Vubil D, Phaku P, Mandomando I, Kern WV, Abdulla S, Mellmann A, Peitzmann L, Bischoff M, Peters G, Herrmann M, Grobusch MP, Schaumburg F, Rieg S. Management of superficial and deep-seated Staphylococcus aureus skin and soft tissue infections in sub-Saharan Africa: a post hoc analysis of the StaphNet cohort. Infection 2018; 46:395-404. [PMID: 29667040 DOI: 10.1007/s15010-018-1140-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
Abstract
PURPOSE The incidence of Staphylococcus aureus skin and soft tissue infection (SSTI) is high in sub-Saharan Africa. This is fueled by a high prevalence of Panton-Valentine leukocidin (PVL), which can be associated with necrotizing disease. The aim was to describe the clinical presentation and the treatment of SSTI in the African setting and to identify challenges in the management. METHODS Patients (n = 319) were recruited in DR Congo (n = 56, 17.6%), Gabon (n = 89, 27.9%), Mozambique (n = 79, 24.8%) and Tanzania (n = 95, 29.8%) during the prospective observational StaphNet cohort study (2010-2015). A physician recorded the clinical management in standardized questionnaires and stratified the entity of SSTI into superficial (sSSTI) or deep-seated (dSSTI). Selected virulence factors (PVL, β hemolysin) and multilocus sequence types (MLST) were extracted from whole genome sequencing data. RESULTS There were 220/319 (69%) sSSTI and 99/319 (31%) dSSTI. Compared to sSSTI, patients with dSSTI were more often hospitalized (13.2 vs. 23.5%, p = 0.03), HIV-positive (7.6 vs. 15.9%, p = 0.11), and required more often incision and drainage (I&D, 45.5 vs. 76.5%, p = 0.04). The proportion of an adequate antimicrobial therapy increased marginally from day 1 (empirical therapy) to day 3 (definite therapy), for sSSTI (70.7 to 72.4%) and dSSTI (55.4 to 58.9%). PVL was a risk factor for I&D (OR = 1.7, p = 0.02) and associated with MLST clonal complex CC121 (OR = 2.7, p < 0.001). CONCLUSION Appropriate antimicrobial agents and surgical services to perform I&D were available for the majority of patients. Results from susceptibility testing should be considered more efficiently in the selection of antimicrobial therapy.
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Affiliation(s)
- Abraham Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | | | - Marthe Lebughe
- Institut National de Recherche Bio-Médicale (INRB), Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Delfino Vubil
- Manhiça Health Research Center, Manhiça, Maputo, Mozambique
| | - Patrick Phaku
- Institut National de Recherche Bio-Médicale (INRB), Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Inacio Mandomando
- Manhiça Health Research Center, Manhiça, Maputo, Mozambique.,Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Winfried V Kern
- Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Salim Abdulla
- Ifakara Health Institute (IHI), Dar es Salaam, Tanzania
| | | | - Lena Peitzmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Martin P Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.,Division of Internal Medicine, Department of Infectious Diseases, Center of Tropical Medicine and Travel Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
| | - Siegbert Rieg
- Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
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Lebughe M, Phaku P, Niemann S, Mumba D, Peters G, Muyembe-Tamfum JJ, Mellmann A, Strauß L, Schaumburg F. The Impact of the Staphylococcus aureus Virulome on Infection in a Developing Country: A Cohort Study. Front Microbiol 2017; 8:1662. [PMID: 28900424 PMCID: PMC5581934 DOI: 10.3389/fmicb.2017.01662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022] Open
Abstract
We performed a cohort study to analyze the virulome of Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing and to assess its impact on the course of S. aureus infections. Community-associated S. aureus from nasal colonization (n = 100) and infection (n = 86) were prospectively collected. Phenotypic susceptibility testing and WGS was done for each isolate. WGS data were used to screen for 79 different virulence factors and for genotyping purposes (spa typing, multilocus sequence typing). The majority of the 79 virulence factors were equally distributed among isolates from colonization and infection. Panton-Valentine leukocidin (PVL) and the non-truncated hemolysin β were associated with skin and soft tissue infection (SSTI) and recurrence of disease but did not influence the course of infection (i.e., mortality, surgical intervention). For the first time, we show that not only PVL but also hemolysin β could contribute to the development of SSTI in PVL-endemic areas such as Africa.
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Affiliation(s)
- Marthe Lebughe
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Patrick Phaku
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Silke Niemann
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
| | - Dieudonné Mumba
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | | | - Lena Strauß
- Institute of Hygiene, University Hospital MünsterMünster, Germany
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
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Phaku P, Lebughe M, Strauß L, Peters G, Herrmann M, Mumba D, Mellmann A, Muyembe-Tamfum JJ, Schaumburg F. Unveiling the molecular basis of antimicrobial resistance in Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing. Clin Microbiol Infect 2016; 22:644.e1-5. [PMID: 27102139 DOI: 10.1016/j.cmi.2016.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/29/2016] [Accepted: 04/08/2016] [Indexed: 11/25/2022]
Abstract
Staphylococcus aureus from sub-Saharan Africa is frequently resistant to antimicrobial agents that are commonly used to treat invasive infections in resource-limited settings. The underlying mechanisms of resistance are largely unknown. We therefore performed whole genome sequencing (WGS) on S. aureus from the Democratic Republic of the Congo (DRC) to analyse the genetic determinants of antimicrobial resistance. One hundred S. aureus samples were collected from community-associated asymptomatic nasal carriers in the metropolitan area of Kinshasa, DRC, between 2013 and 2014. Phenotypic resistance against 15 antimicrobial agents was compared to the genotypic results that were extracted from WGS data using Mykrobe predictor and the SeqSphere(+) software that screened for 106 target genes associated with resistance. Isolates were phenotypically resistant against penicillin (97%, n=97), trimethoprim (72%, n=72) and tetracycline (54%, n=45). Thirty-three isolates (33%) were methicillin-resistant S. aureus (MRSA). Of these, nine isolates (27.3%) were oxacillin-susceptible MRSA (OS-MRSA) and belonged to ST8 (t1476). The Y195F mutation of FemA was associated with OS-MRSA (p 0.015). The majority of trimethoprim resistant isolates carried dfrG. Tetracycline resistance was associated with tet(K). The concordance between phenotypic susceptibility testing and both WGS analysis tools was similar and ranged between 96% and 100%. In conclusion, a high proportion of OS-MRSA in the DRC was linked to mutations of FemA. Genotypic and phenotypical antimicrobial susceptibility testing showed high concordance. This encourages the future use of WGS in routine antimicrobial susceptibility testing.
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Affiliation(s)
- P Phaku
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - M Lebughe
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - L Strauß
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - G Peters
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - M Herrmann
- Institute of Medical Microbiology and Hygiene, University Hospital of Saarland, Homburg, Germany
| | - D Mumba
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - A Mellmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - J-J Muyembe-Tamfum
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - F Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
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