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Boukthir S, Moullec S, Cariou ME, Meygret A, Morcet J, Faili A, Kayal S. A prospective survey of Streptococcus pyogenes infections in French Brittany from 2009 to 2017: Comprehensive dynamic of new emergent emm genotypes. PLoS One 2020; 15:e0244063. [PMID: 33332468 PMCID: PMC7746304 DOI: 10.1371/journal.pone.0244063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Streptococcus pyogenes or group A Streptococcus (GAS) causes diseases ranging from uncomplicated pharyngitis to life-threatening infections. It has complex epidemiology driven by the diversity, the temporal and geographical fluctuations of the circulating strains. Despite the global burden of GAS diseases, there is currently no available vaccination strategy against GAS infections. This study, based on a longitudinal population survey, aimed to understand the dynamic of GAS emm types and to give leads to better recognition of underlying mechanisms for the emergence of successful clones. From 2009 to 2017, we conducted a systematic culture-based diagnosis of GAS infections in a French Brittany population with a prospective recovery of clinical data. The epidemiological analysis was performed using emm typing combined with the structural and functional cluster-typing system for all the recovered strains. Risk factors for the invasiveness, identified by univariate analysis, were computed in a multiple logistic regression analysis, and the only independent risk factor remaining in the model was the age (OR for the entire range [CI95%] = 6.35 [3.63, 11.10]; p<0.0001). Among the 61 different emm types identified, the most prevalent were emm28 (16%), emm89 (15%), emm1 (14%), and emm4 (8%), which accounted for more than 50% of circulating strains. During the study period, five genotypes identified as emm44, 66, 75, 83, 87 emerged successively and belonged to clusters D4, E2, E3, and E6 that were different from those gathering “Prevalent” emm types (clusters A-C3 to 5, E1 and E4). We previously reported significant genetic modifications for emm44, 66, 83 and 75 types resulting possibly from a short adaptive evolution. Herein we additionally observed that the emergence of a new genotype could occur in a susceptible population having specific risk factors or probably lacking a naturally-acquired cluster-specific immune cross-protection. Among emergent emm types, emm75 and emm87 tend to become prevalent with a stable annual incidence and the risk of a clonal expansion have to be considered.
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Affiliation(s)
- Sarrah Boukthir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France
- Inserm, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | - Séverine Moullec
- Inserm, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | | | - Alexandra Meygret
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | - Jeff Morcet
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France
- Inserm, CIC 1414, Rennes, France
| | - Ahmad Faili
- Inserm, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Pharmacie, Rennes, France
| | - Samer Kayal
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France
- Inserm, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
- * E-mail:
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Turner CE, Holden MTG, Blane B, Horner C, Peacock SJ, Sriskandan S. The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression. mBio 2019; 10:e02521-19. [PMID: 31822586 PMCID: PMC6904876 DOI: 10.1128/mbio.02521-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Gene transfer and homologous recombination in Streptococcus pyogenes has the potential to trigger the emergence of pandemic lineages, as exemplified by lineages of emm1 and emm89 that emerged in the 1980s and 2000s, respectively. Although near-identical replacement gene transfer events in the nga (NADase) and slo (streptolysin O) loci conferring high expression of these toxins underpinned the success of these lineages, extension to other emm genotype lineages is unreported. The emergent emm89 lineage was characterized by five regions of homologous recombination additional to nga-slo, including complete loss of the hyaluronic acid capsule synthesis locus hasABC, a genetic trait replicated in two other leading emm types and recapitulated by other emm types by inactivating mutations. We hypothesized that other leading genotypes may have undergone similar recombination events. We analyzed a longitudinal data set of genomes from 344 clinical invasive disease isolates representative of locations across England, dating from 2001 to 2011, and an international collection of S. pyogenes genomes representing 54 different genotypes and found frequent evidence of recombination events at the nga-slo locus predicted to confer higher toxin genotype. We identified multiple associations between recombination at this locus and inactivating mutations within hasAB, suggesting convergent evolutionary pathways in successful genotypes. This included common genotypes emm28 and emm87. The combination of no or low capsule and high expression of nga and slo may underpin the success of many emergent S. pyogenes lineages of different genotypes, triggering new pandemics, and could change the way S. pyogenes causes disease.IMPORTANCEStreptococcus pyogenes is a genetically diverse pathogen, with over 200 different genotypes defined by emm typing, but only a minority of these genotypes are responsible for the majority of human infection in high-income countries. Two prevalent genotypes associated with disease rose to international dominance following recombination of a toxin locus that conferred increased expression. Here, we found that recombination of this locus and promoter has occurred in other diverse genotypes, events that may allow these genotypes to expand in the population. We identified an association between the loss of hyaluronic acid capsule synthesis and high toxin expression, which we propose may be associated with an adaptive advantage. As S. pyogenes pathogenesis depends both on capsule and toxin production, new variants with altered expression may result in abrupt changes in the molecular epidemiology of this pathogen in the human population over time.
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Affiliation(s)
- Claire E Turner
- Molecular Biology & Biotechnology, The Florey Institute, University of Sheffield, Sheffield, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Matthew T G Holden
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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Osowicki J, Azzopardi KI, McIntyre L, Rivera-Hernandez T, Ong CLY, Baker C, Gillen CM, Walker MJ, Smeesters PR, Davies MR, Steer AC. A Controlled Human Infection Model of Group A Streptococcus Pharyngitis: Which Strain and Why? mSphere 2019; 4:e00647-18. [PMID: 30760615 PMCID: PMC6374595 DOI: 10.1128/msphere.00647-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/16/2019] [Indexed: 01/23/2023] Open
Abstract
Group A Streptococcus (GAS) is a major cause of global infection-related morbidity and mortality. A modern controlled human infection model (CHIM) of GAS pharyngitis can accelerate vaccine development and pathogenesis research. A robust rationale for strain selection is central to meeting ethical, scientific, and regulatory requirements. Multifaceted characterization studies were done to compare a preferred candidate emm75 (M75) GAS strain to three other strains: an alternative candidate emm12 (M12) strain, an M1 strain used in 1970s pharyngitis CHIM studies (SS-496), and a representative (5448) of the globally disseminated M1T1 clone. A range of approaches were used to explore strain growth, adherence, invasion, delivery characteristics, short- and long-term viability, phylogeny, virulence factors, vaccine antigens, resistance to killing by human neutrophils, and lethality in a murine invasive model. The strains grew reliably in a medium without animal-derived components, were consistently transferred using a swab method simulating the CHIM protocol, remained viable at -80°C, and carried genes for most candidate vaccine antigens. Considering GAS molecular epidemiology, virulence factors, in vitro assays, and results from the murine model, the contemporary strains show a spectrum of virulence, with M75 appearing the least virulent and 5448 the most. The virulence profile of SS-496, used safely in 1970s CHIM studies, was similar to that of 5448 in the animal model and virulence gene carriage. The results of this multifaceted characterization confirm the M75 strain as an appropriate choice for initial deployment in the CHIM, with the aim of safely and successfully causing pharyngitis in healthy adult volunteers.IMPORTANCE GAS (Streptococcus pyogenes) is a leading global cause of infection-related morbidity and mortality. A modern CHIM of GAS pharyngitis could help to accelerate vaccine development and drive pathogenesis research. Challenge strain selection is critical to the safety and success of any CHIM and especially so for an organism such as GAS, with its wide strain diversity and potential to cause severe life-threatening acute infections (e.g., toxic shock syndrome and necrotizing fasciitis) and postinfectious complications (e.g., acute rheumatic fever, rheumatic heart disease, and acute poststreptococcal glomerulonephritis). In this paper, we outline the rationale for selecting an emm75 strain for initial use in a GAS pharyngitis CHIM in healthy adult volunteers, drawing on the findings of a broad characterization effort spanning molecular epidemiology, in vitro assays, whole-genome sequencing, and animal model studies.
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Affiliation(s)
- Joshua Osowicki
- Tropical Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia
| | - Kristy I Azzopardi
- Tropical Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tania Rivera-Hernandez
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Cheryl-Lynn Y Ong
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ciara Baker
- Tropical Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Christine M Gillen
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - Pierre R Smeesters
- Tropical Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Paediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Andrew C Steer
- Tropical Diseases, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia
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