1
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Xie O, Davies MR, Tong SYC. Streptococcus dysgalactiae subsp. equisimilis infection and its intersection with Streptococcus pyogenes. Clin Microbiol Rev 2024:e0017523. [PMID: 38856686 DOI: 10.1128/cmr.00175-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
SUMMARYStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen, Streptococcus pyogenes. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and S. pyogenes, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with S. pyogenes. In doing so, we highlight the importance of understanding the overlap of SDSE and S. pyogenes to inform surveillance and disease control strategies.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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2
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Tang D, Gueto-Tettay C, Hjortswang E, Ströbaek J, Ekström S, Happonen L, Malmström L, Malmström J. Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O. Anal Chem 2024; 96:9060-9068. [PMID: 38701337 PMCID: PMC11154737 DOI: 10.1021/acs.analchem.4c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
An important element of antibody-guided vaccine design is the use of neutralizing or opsonic monoclonal antibodies to define protective epitopes in their native three-dimensional conformation. Here, we demonstrate a multimodal mass spectrometry-based strategy for in-depth characterization of antigen-antibody complexes to enable the identification of protective epitopes using the cytolytic exotoxin Streptolysin O (SLO) from Streptococcus pyogenes as a showcase. We first discovered a monoclonal antibody with an undisclosed sequence capable of neutralizing SLO-mediated cytolysis. The amino acid sequence of both the antibody light and the heavy chain was determined using mass-spectrometry-based de novo sequencing, followed by chemical cross-linking mass spectrometry to generate distance constraints between the antibody fragment antigen-binding region and SLO. Subsequent integrative computational modeling revealed a discontinuous epitope located in domain 3 of SLO that was experimentally validated by hydrogen-deuterium exchange mass spectrometry and reverse engineering of the targeted epitope. The results show that the antibody inhibits SLO-mediated cytolysis by binding to a discontinuous epitope in domain 3, likely preventing oligomerization and subsequent secondary structure transitions critical for pore-formation. The epitope is highly conserved across >98% of the characterized S. pyogenes isolates, making it an attractive target for antibody-based therapy and vaccine design against severe streptococcal infections.
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Affiliation(s)
- Di Tang
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
| | - Carlos Gueto-Tettay
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
| | - Elisabeth Hjortswang
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
| | - Joel Ströbaek
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
| | - Simon Ekström
- SciLifeLab,
Integrated Structural Biology Platform, Structural Proteomics Unit
Sweden, Lund University, Klinikgatan 32, 222
42 Lund, Sweden
| | - Lotta Happonen
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
| | - Lars Malmström
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
| | - Johan Malmström
- Division
of Infection Medicine, Department of Clinical Sciences, Faculty of
Medicine, Lund University, Klinikgatan 32, 222 42 Lund, Sweden
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3
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Bessen DE, Beall BW, Hayes A, Huang W, DiChiara JM, Velusamy S, Tettelin H, Jolley KA, Fallon JT, Chochua S, Alobaidallah MSA, Higgs C, Barnett TC, Steemson JT, Proft T, Davies MR. Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A Streptococcus population. mBio 2024; 15:e0069324. [PMID: 38587426 PMCID: PMC11078000 DOI: 10.1128/mbio.00693-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as "pilin types." Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies.IMPORTANCEPrecision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends.
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Affiliation(s)
- Debra E. Bessen
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
| | - Bernard W. Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
- Eagle Global Scientific, LLC, Atlanta, Georgia, USA
| | - Andrew Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Weihua Huang
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
- Department of Pathology, Brody School of Medicine, Eastern Carolina University, Greenville, North Carolina, USA
| | - Jeanne M. DiChiara
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
| | - Srinivasan Velusamy
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Keith A. Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - John T. Fallon
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
- Department of Pathology, Brody School of Medicine, Eastern Carolina University, Greenville, North Carolina, USA
| | - Sopio Chochua
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Mosaed S. A. Alobaidallah
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
| | - Charlie Higgs
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy C. Barnett
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Australia
| | - John T. Steemson
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas Proft
- School of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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4
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Indraratna AD, Mytton S, Ricafrente A, Millar D, Gorman J, Azzopardi KI, Frost HR, Osowicki J, Steer AC, Skropeta D, Sanderson-Smith ML. A highly sensitive 3base™ assay for detecting Streptococcus pyogenes in saliva during controlled human pharyngitis. Talanta 2024; 276:126221. [PMID: 38776768 DOI: 10.1016/j.talanta.2024.126221] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
Streptococcus pyogenes (Group A Streptococcus; GAS) is a Gram-positive bacterium responsible for substantial human mortality and morbidity. Conventional diagnosis of GAS pharyngitis relies on throat swab culture, a low-throughput, slow, and relatively invasive 'gold standard'. While molecular approaches are becoming increasingly utilized, the potential of saliva as a diagnostic fluid for GAS infection remains largely unexplored. Here, we present a novel, high-throughput, sensitive, and robust speB qPCR assay that reliably detects GAS in saliva using innovative 3base™ technology (Genetic Signatures Limited, Sydney, Australia). The assay has been validated on baseline, acute, and convalescent saliva samples generated from the Controlled Human Infection for Vaccination Against Streptococcus (CHIVAS-M75) trial, in which healthy adult participants were challenged with emm75 GAS. In these well-defined samples, our high-throughput assay outperforms throat culture and conventional qPCR in saliva respectively, affirming the utility of the 3base™ platform, demonstrating the feasibility of saliva as a diagnostic biofluid, and paving the way for the development of novel non-invasive approaches for the detection of GAS and other oropharyngeal pathogens.
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Affiliation(s)
- Anuk D Indraratna
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia
| | - Sacha Mytton
- Genetic Signatures Limited, 7 Eliza Street, Newtown, New South Wales, 2042, Australia
| | - Alison Ricafrente
- Genetic Signatures Limited, 7 Eliza Street, Newtown, New South Wales, 2042, Australia
| | - Doug Millar
- Genetic Signatures Limited, 7 Eliza Street, Newtown, New South Wales, 2042, Australia
| | - Jody Gorman
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia
| | - Kristy I Azzopardi
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Hannah R Frost
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Joshua Osowicki
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia; Department of Paediatrics, University of Melbourne, Grattan Street, Melbourne, Victoria, 3010, Australia; Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital Melbourne, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Andrew C Steer
- Tropical Diseases, Murdoch Children's Research Institute, 50 Flemington Road, Melbourne, Victoria, 3052, Australia; Department of Paediatrics, University of Melbourne, Grattan Street, Melbourne, Victoria, 3010, Australia; Infectious Diseases Unit, Department of General Medicine, The Royal Children's Hospital Melbourne, 50 Flemington Road, Melbourne, Victoria, 3052, Australia
| | - Danielle Skropeta
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia
| | - Martina L Sanderson-Smith
- Molecular Horizons, School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, New South Wales, 2522, Australia.
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5
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Xie O, Zachreson C, Tonkin-Hill G, Price DJ, Lacey JA, Morris JM, McDonald MI, Bowen AC, Giffard PM, Currie BJ, Carapetis JR, Holt DC, Bentley SD, Davies MR, Tong SYC. Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange. Nat Commun 2024; 15:3477. [PMID: 38658529 PMCID: PMC11043366 DOI: 10.1038/s41467-024-47816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Cameron Zachreson
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
| | | | - David J Price
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacqueline M Morris
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Malcolm I McDonald
- Division of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Asha C Bowen
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Philip M Giffard
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Faculty of Health, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Jonathan R Carapetis
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Deborah C Holt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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6
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Xie O, Morris JM, Hayes AJ, Towers RJ, Jespersen MG, Lees JA, Ben Zakour NL, Berking O, Baines SL, Carter GP, Tonkin-Hill G, Schrieber L, McIntyre L, Lacey JA, James TB, Sriprakash KS, Beatson SA, Hasegawa T, Giffard P, Steer AC, Batzloff MR, Beall BW, Pinho MD, Ramirez M, Bessen DE, Dougan G, Bentley SD, Walker MJ, Currie BJ, Tong SYC, McMillan DJ, Davies MR. Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nat Commun 2024; 15:2286. [PMID: 38480728 PMCID: PMC10937727 DOI: 10.1038/s41467-024-46530-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
| | - Jacqueline M Morris
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rebecca J Towers
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, Cambridgeshire, UK
| | - Nouri L Ben Zakour
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Olga Berking
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen P Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Layla Schrieber
- Faculty of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Taylah B James
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kadaba S Sriprakash
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Science & Technology, University of New England, Armidale, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Tadao Hasegawa
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Phil Giffard
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Andrew C Steer
- Tropical Diseases, Murdoch Children's Research Institute, Parkville, Australia
| | - Michael R Batzloff
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute for Glycomics, Griffith University, Southport, Australia
| | - Bernard W Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marcos D Pinho
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mario Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Debra E Bessen
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Gordon Dougan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David J McMillan
- School of Science, Technology and Engineering, and Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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7
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Carducci M, Whitcombe A, Rovetini L, Massai L, Keeley AJ, de Silva TI, Bennett J, Berlanda Scorza F, Iturriza M, Moreland NJ, Moriel DG, Rossi O. Development and characterization of a hemolysis inhibition assay to determine functionality of anti-Streptolysin O antibodies in human sera. J Immunol Methods 2024; 526:113618. [PMID: 38237697 PMCID: PMC10921352 DOI: 10.1016/j.jim.2024.113618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024]
Abstract
The high burden of disease and the long-lasting sequelae following Streptococcus pyogenes (Strep A) infections make the development of an effective vaccine a global health priority. Streptolysin O (SLO), is a key toxin in the complex pathogenesis of Strep A infection. Antibodies are elicited against SLO after natural exposure and represent a key target for vaccine-induced immunity. Here we present the setup and characterization of a hemolysis assay to measure functionality of anti-SLO antibodies in human sera. Assay specificity, precision, linearity, reproducibility, and repeatability were determined. The assay was demonstrated to be highly sensitive, specific, reproducible, linear and performed well in assessing functionality of anti-SLO antibodies induced by exposed individuals. Moreover, different sources of critical reagents, in particular red- blood cells, have been compared and had minimal impact on assay performance. The assay presented here has throughput suitable for evaluating sera in vaccine clinical trials and sero-epidemiological studies to gain further insights into the functionality of infection- and vaccine-induced antibodies.
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Affiliation(s)
- Martina Carducci
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy
| | - Alana Whitcombe
- School of Medical Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Luca Rovetini
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy
| | - Luisa Massai
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy
| | - Alexander J Keeley
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK; Vaccines and Immunity Theme, Medical Research Unit the Gambia at the London School of Hygiene and Tropical Medicine, Fajara, the Gambia; Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Unit the Gambia at the London School of Hygiene and Tropical Medicine, Fajara, the Gambia; Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Julie Bennett
- School of Medical Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand; Department of Public Health, University of Otago, Wellington, New Zealand
| | - Francesco Berlanda Scorza
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy
| | - Miren Iturriza
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy
| | - Nicole J Moreland
- School of Medical Sciences and Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Danilo G Moriel
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy
| | - Omar Rossi
- GSK Vaccines Institute for Global Health (GVGH), GSK Global Health Vaccines R&D, via Fiorentina 1, 53100 Siena, Italy.
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8
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Lai CY, Xie JX, Lai MC, Wu ZY, Lin JS, Huang YT, Chi CY, Chiang-Ni C, Walker MJ, Chang YC. Conserved molecular chaperone PrsA stimulates protective immunity against group A Streptococcus. NPJ Vaccines 2024; 9:46. [PMID: 38409165 PMCID: PMC10897429 DOI: 10.1038/s41541-024-00839-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
Group A Streptococcus (GAS) is a significant human pathogen that poses a global health concern. However, the development of a GAS vaccine has been challenging due to the multitude of diverse M-types and the risk of triggering cross-reactive immune responses. Our previous research has identified a critical role of PrsA1 and PrsA2, surface post-translational molecular chaperone proteins, in maintaining GAS proteome homeostasis and virulence traits. In this study, we aimed to further explore the potential of PrsA1 and PrsA2 as vaccine candidates for preventing GAS infection. We found that PrsA1 and PrsA2 are highly conserved among GAS isolates, demonstrating minimal amino acid variation. Antibodies specifically targeting PrsA1/A2 showed no cross-reactivity with human heart proteins and effectively enhanced neutrophil opsonophagocytic killing of various GAS serotypes. Additionally, passive transfer of PrsA1/A2-specific antibodies conferred protective immunity in infected mice. Compared to alum, immunization with CFA-adjuvanted PrsA1/A2 induced higher levels of Th1-associated IgG isotypes and complement activation and provided approximately 70% protection against invasive GAS challenge. These findings highlight the potential of PrsA1 and PrsA2 as universal vaccine candidates for the development of an effective GAS vaccine.
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Affiliation(s)
- Chien-Yu Lai
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Jia-Xun Xie
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Meng-Chih Lai
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Zhao-Yi Wu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Jr-Shiuan Lin
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Yu-Tsung Huang
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chia-Yu Chi
- National Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Miaoli, 300, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - Mark J Walker
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Yung-Chi Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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9
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Ganio K, Nasreen M, Yang Z, Maunders EA, Luo Z, Hossain SI, Ngu DHY, Ellis D, Gu J, Neville SL, Wilksch J, Gunn AP, Whittall JJ, Kobe B, Deplazes E, Kappler U, McDevitt CA. Hfe Permease and Haemophilus influenzae Manganese Homeostasis. ACS Infect Dis 2024; 10:436-452. [PMID: 38240689 PMCID: PMC10863617 DOI: 10.1021/acsinfecdis.3c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
Haemophilus influenzae is a commensal of the human upper respiratory tract that can infect diverse host niches due, at least in part, to its ability to withstand both endogenous and host-mediated oxidative stresses. Here, we show that hfeA, a gene previously linked to iron import, is essential for H. influenzae manganese recruitment via the HfeBCD transporter. Structural analyses show that metal binding in HfeA uses a unique mechanism that involves substantial rotation of the C-terminal lobe of the protein. Disruption of hfeA reduced H. influenzae manganese acquisition and was associated with decreased growth under aerobic conditions, impaired manganese-superoxide dismutase activity, reduced survival in macrophages, and changes in biofilm production in the presence of superoxide. Collectively, this work shows that HfeA contributes to H. influenzae manganese acquisition and virulence attributes. High conservation of the hfeABCD permease in Haemophilus species suggests that it may serve similar roles in other pathogenic Pasteurellaceae.
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Affiliation(s)
- Katherine Ganio
- Department
of Microbiology and Immunology, the Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Marufa Nasreen
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
| | - Zihao Yang
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
| | - Eve A. Maunders
- Department
of Microbiology and Immunology, the Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Zhenyao Luo
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
- Institute
for Molecular Bioscience, The University
of Queensland, St Lucia, Queensland 4072, Australia
| | - Sheikh Imamul Hossain
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
| | - Dalton H. Y. Ngu
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
- Institute
for Molecular Bioscience, The University
of Queensland, St Lucia, Queensland 4072, Australia
| | - Daniel Ellis
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jin Gu
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
| | - Stephanie L. Neville
- Department
of Microbiology and Immunology, the Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Jonathan Wilksch
- Department
of Microbiology and Immunology, the Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Adam P. Gunn
- Department
of Microbiology and Immunology, the Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Jonathan J. Whittall
- School of
Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Boštjan Kobe
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
- Institute
for Molecular Bioscience, The University
of Queensland, St Lucia, Queensland 4072, Australia
| | - Evelyne Deplazes
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- School
of Life Sciences, University of Technology
Sydney, Ultimo, New South Wales 2007, Australia
| | - Ulrike Kappler
- School
of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, The
University of Queensland, St Lucia, Queensland 4072, Australia
| | - Christopher A. McDevitt
- Department
of Microbiology and Immunology, the Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
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10
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Guerra S, LaRock C. Group A Streptococcus interactions with the host across time and space. Curr Opin Microbiol 2024; 77:102420. [PMID: 38219421 PMCID: PMC10922997 DOI: 10.1016/j.mib.2023.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
Group A Streptococcus (GAS) has a fantastically wide tissue tropism in humans, manifesting as different diseases depending on the strain's virulence factor repertoire and the tissue involved. Activation of immune cells and pro-inflammatory signaling has historically been considered an exclusively host-protective response that a pathogen would seek to avoid. However, recent advances in human and animal models suggest that in some tissues, GAS will activate and manipulate specific pro-inflammatory pathways to promote growth, nutrient acquisition, persistence, recurrent infection, competition with other microbial species, dissemination, and transmission. This review discusses molecular interactions between the host and pathogen to summarize how infection varies across tissue and stages of inflammation. A need for inflammation for GAS survival during common, mild infections may drive selection for mechanisms that cause pathological and excess inflammation severe diseases such as toxic shock syndrome, necrotizing fasciitis, and rheumatic heart disease.
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Affiliation(s)
- Stephanie Guerra
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Christopher LaRock
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA; Antimicrobial Resistance Center, Emory University, Atlanta, GA 30322, USA.
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11
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Smeesters PR, de Crombrugghe G, Tsoi SK, Leclercq C, Baker C, Osowicki J, Verhoeven C, Botteaux A, Steer AC. Global Streptococcus pyogenes strain diversity, disease associations, and implications for vaccine development: a systematic review. THE LANCET. MICROBE 2024; 5:e181-e193. [PMID: 38070538 DOI: 10.1016/s2666-5247(23)00318-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 02/12/2024]
Abstract
The high strain diversity of Streptococcus pyogenes serves as a major obstacle to vaccine development against this leading global pathogen. We did a systematic review of studies in PubMed, MEDLINE, and Embase that reported the global distribution of S pyogenes emm-types and emm-clusters from Jan 1, 1990, to Feb 23, 2023. 212 datasets were included from 55 countries, encompassing 74 468 bacterial isolates belonging to 211 emm-types. Globally, an inverse correlation was observed between strain diversity and the UNDP Human Development Index (HDI; r=-0·72; p<0·0001), which remained consistent upon subanalysis by global region and site of infection. Greater strain diversity was associated with a lower HDI, suggesting the role of social determinants in diseases caused by S pyogenes. We used a population-weighted analysis to adjust for the disproportionate number of epidemiological studies from high-income countries and identified 15 key representative isolates as vaccine targets. Strong strain type associations were observed between the site of infection (invasive, skin, and throat) and several streptococcal lineages. In conclusion, the development of a truly global vaccine to reduce the immense burden of diseases caused by S pyogenes should consider the multidimensional diversity of the pathogen, including its social and environmental context, and not merely its geographical distribution.
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Affiliation(s)
- Pierre R Smeesters
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium; Molecular Bacteriology Laboratory, European Plotkin Institute for Vaccinology, Université Libre de Bruxelles, Brussels, Belgium; Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
| | - Gabrielle de Crombrugghe
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium; Molecular Bacteriology Laboratory, European Plotkin Institute for Vaccinology, Université Libre de Bruxelles, Brussels, Belgium
| | - Shu Ki Tsoi
- Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Infectious Diseases Unit, Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Céline Leclercq
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
| | - Ciara Baker
- Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Joshua Osowicki
- Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Infectious Diseases Unit, Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
| | - Caroline Verhoeven
- Laboratoire d'enseignement des Mathématiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, European Plotkin Institute for Vaccinology, Université Libre de Bruxelles, Brussels, Belgium
| | - Andrew C Steer
- Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Infectious Diseases Unit, Royal Children's Hospital Melbourne, Melbourne, VIC, Australia
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12
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Proctor EJ, Frost HR, Satapathy S, Botquin G, Urbaniec J, Gorman J, De Oliveira DMP, McArthur J, Davies MR, Botteaux A, Smeesters P, Sanderson-Smith M. Molecular characterization of the interaction between human IgG and the M-related proteins from Streptococcus pyogenes. J Biol Chem 2024; 300:105623. [PMID: 38176650 PMCID: PMC10844976 DOI: 10.1016/j.jbc.2023.105623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Group A Streptococcal M-related proteins (Mrps) are dimeric α-helical-coiled-coil cell membrane-bound surface proteins. During infection, Mrp recruit the fragment crystallizable region of human immunoglobulin G via their A-repeat regions to the bacterial surface, conferring upon the bacteria enhanced phagocytosis resistance and augmented growth in human blood. However, Mrps show a high degree of sequence diversity, and it is currently not known whether this diversity affects the Mrp-IgG interaction. Herein, we report that diverse Mrps all bind human IgG subclasses with nanomolar affinity, with differences in affinity which ranged from 3.7 to 11.1 nM for mixed IgG. Using surface plasmon resonance, we confirmed Mrps display preferential IgG-subclass binding. All Mrps were found to have a significantly weaker affinity for IgG3 (p < 0.05) compared to all other IgG subclasses. Furthermore, plasma pulldown assays analyzed via Western blotting revealed that all Mrp were able to bind IgG in the presence of other serum proteins at both 25 °C and 37 °C. Finally, we report that dimeric Mrps bind to IgG with a 1:1 stoichiometry, enhancing our understanding of this important host-pathogen interaction.
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Affiliation(s)
- Emma-Jayne Proctor
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Hannah R Frost
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Sandeep Satapathy
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gwenaëlle Botquin
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Joanna Urbaniec
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Jody Gorman
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - David M P De Oliveira
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, QLD, Australia
| | - Jason McArthur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Pierre Smeesters
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Martina Sanderson-Smith
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.
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13
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Maunders EA, Giles MW, Ganio K, Cunningham BA, Bennett-Wood V, Cole GB, Ng D, Lai CC, Neville SL, Moraes TF, McDevitt CA, Tan A. Zinc acquisition and its contribution to Klebsiella pneumoniae virulence. Front Cell Infect Microbiol 2024; 13:1322973. [PMID: 38249299 PMCID: PMC10797113 DOI: 10.3389/fcimb.2023.1322973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024] Open
Abstract
Klebsiella pneumoniae is a World Health Organization priority pathogen and a significant clinical concern for infections of the respiratory and urinary tracts due to widespread and increasing resistance to antimicrobials. In the absence of a vaccine, there is an urgent need to identify novel targets for therapeutic development. Bacterial pathogens, including K. pneumoniae, require the d-block metal ion zinc as an essential micronutrient, which serves as a cofactor for ~6% of the proteome. During infection, zinc acquisition necessitates the use of high affinity uptake systems to overcome niche-specific zinc limitation and host-mediated nutritional immunity. Here, we report the identification of ZnuCBA and ZniCBA, two ATP-binding cassette permeases that are highly conserved in Klebsiella species and contribute to K. pneumoniae AJ218 zinc homeostasis, and the high-resolution structure of the zinc-recruiting solute-binding protein ZniA. The Znu and Zni permeases appear functionally redundant with abrogation of both systems required to reduce K. pneumoniae zinc accumulation. Disruption of both systems also exerted pleiotropic effects on the homeostasis of other d-block elements. Zinc limitation perturbed K. pneumoniae cell morphology and compromised resistance to stressors, such as salt and oxidative stress. The mutant strain lacking both systems showed significantly impaired virulence in acute lung infection models, highlighting the necessity of zinc acquisition in the virulence and pathogenicity of K. pneumoniae.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew W. Giles
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Bliss A. Cunningham
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Gregory B. Cole
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christine C. Lai
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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14
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Lacey JA, Bennett J, James TB, Hines BS, Chen T, Lee D, Sika-Paotonu D, Anderson A, Harwood M, Tong SY, Baker MG, Williamson DA, Moreland NJ. A worldwide population of Streptococcus pyogenes strains circulating among school-aged children in Auckland, New Zealand: a genomic epidemiology analysis. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 42:100964. [PMID: 38035130 PMCID: PMC10684382 DOI: 10.1016/j.lanwpc.2023.100964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 12/02/2023]
Abstract
Background Acute rheumatic fever (ARF) is a serious post-infectious sequala of Group A Streptococcus (GAS, Streptococcus pyogenes). In New Zealand (NZ) ARF is a major cause of health inequity. This study describes the genomic analysis of GAS isolates associated with childhood skin and throat infections in Auckland NZ. Methods Isolates (n = 469) collected between March 2018 and October 2019 from the throats and skin of children (5-14 years) underwent whole genomic sequencing. Equal representation across three ethnic groups was ensured through sample quotas with isolates obtained from Indigenous Māori (n = 157, 33%), NZ European/Other (n = 149, 32%) and Pacific Peoples children (n = 163, 35%). Using in silico techniques isolates were classified, assessed for diversity, and examined for distribution differences between groups. Comparisons were also made with GAS strains identified globally. Findings Genomic analysis revealed a diverse population consisting of 65 distinct sequence clusters. These sequence clusters spanned 49 emm-types, with 11 emm-types comprised of several, distinct sequence clusters. There is evidence of multiple global introductions of different lineages into the population, as well as local clonal expansion. The M1UK lineage comprised 35% of all emm1 isolates. Interpretation The GAS population was characterized by a high diversity of strains, resembling patterns observed in low- and middle-income countries. However, strains associated with outbreaks and antimicrobial resistance commonly found in high-income countries were also observed. This unique combination poses challenges for vaccine development, disease management and control. Funding The work was supported by the Health Research Council of New Zealand (HRC), award number 16/005.
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Affiliation(s)
- Jake A. Lacey
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Julie Bennett
- The Department of Public Health, University of Otago, Wellington, New Zealand
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Taylah B. James
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin S. Hines
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Tiffany Chen
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Darren Lee
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Anneka Anderson
- Te Kupenga Hauora Māori, The University of Auckland, New Zealand
| | - Matire Harwood
- Department of General Practice and Primary Healthcare, The University of Auckland, Auckland, New Zealand
| | - Steven Y.C. Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael G. Baker
- The Department of Public Health, University of Otago, Wellington, New Zealand
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Deborah A. Williamson
- Department of Infectious Diseases at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicole J. Moreland
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
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15
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Unoarumhi Y, Davis ML, Rowe LA, Mathis S, Li Z, Chochua S, Li Y, McGee L, Metcalf BJ, Lee JS, Beall B. A novel invasive Streptococcus pyogenes variant sublineage derived through recombinational replacement of the emm12 genomic region. Sci Rep 2023; 13:21510. [PMID: 38057343 PMCID: PMC10700362 DOI: 10.1038/s41598-023-48035-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Group A streptococcal strains potentially acquire new M protein gene types through genetic recombination (emm switching). To detect such variants, we screened 12,596 invasive GAS genomes for strains of differing emm types that shared the same multilocus sequence type (ST). Through this screening we detected a variant consisting of 16 serum opacity factor (SOF)-positive, emm pattern E, emm82 isolates that were ST36, previously only associated with SOF-negative, emm pattern A, emm12. The 16 emm82/ST36 isolates were closely interrelated (pairwise SNP distance of 0-43), and shared the same emm82-containing recombinational fragment. emm82/ST36 isolates carried the sof12 structural gene, however the sof12 indel characteristic of emm12 strains was corrected to confer the SOF-positive phenotype. Five independent emm82/ST36 invasive case isolates comprised two sets of genetically indistinguishable strains. The emm82/ST36 isolates were primarily macrolide resistant (12/16 isolates), displayed at least 4 different core genomic arrangements, and carried 11 different combinations of virulence and resistance determinants. Phylogenetic analysis revealed that emm82/ST36 was within a minor (non-clade 1) portion of ST36 that featured almost all ST36 antibiotic resistance. This work documents emergence of a rapidly diversifying variant that is the first confirmed example of an emm pattern A strain switched to a pattern E strain.
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Affiliation(s)
- Yvette Unoarumhi
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Morgan L Davis
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Lori A Rowe
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Saundra Mathis
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Zhongya Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Sopio Chochua
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Yuan Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Benjamin J Metcalf
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Justin S Lee
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA.
- Eagle GLobal Scientific, LLC, Atlanta, GA, USA.
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16
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Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Mutational spectra are associated with bacterial niche. Nat Commun 2023; 14:7091. [PMID: 37925514 PMCID: PMC10625568 DOI: 10.1038/s41467-023-42916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to detect both disruption of DNA repair processes and exposure to niche-specific mutagens. Here we reconstruct mutational spectra for 84 clades from 31 diverse bacterial species and find distinct mutational patterns. We extract signatures driven by specific DNA repair defects using hypermutator lineages, and further deconvolute the spectra into multiple signatures operating within different clades. We show that these signatures are explained by both bacterial phylogeny and replication niche. By comparing mutational spectra of clades from different environmental and biological locations, we identify niche-associated mutational signatures, and then employ these signatures to infer the predominant replication niches for several clades where this was previously obscure. Our results show that mutational spectra may be associated with sites of bacterial replication when mutagen exposures differ, and can be used in these cases to infer transmission routes for established and emergent human bacterial pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gemma G R Murray
- Parasites and Microbes Programme, Wellcome Sanger Institute; Wellcome Genome Campus, Cambridge, UK
| | - Roger C Lévesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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17
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Troese MJ, Burlet E, Cunningham MW, Alvarez K, Bentley R, Thomas N, Carwell S, Morefield GL. Group A Streptococcus Vaccine Targeting the Erythrogenic Toxins SpeA and SpeB Is Safe and Immunogenic in Rabbits and Does Not Induce Antibodies Associated with Autoimmunity. Vaccines (Basel) 2023; 11:1504. [PMID: 37766180 PMCID: PMC10534881 DOI: 10.3390/vaccines11091504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Group A streptococcus (GAS) is a global pathogen associated with significant morbidity and mortality for which there is currently no licensed vaccine. Vaccine development has been slow, mostly due to safety concerns regarding streptococcal antigens associated with autoimmunity and related complications. For a GAS vaccine to be safe, it must be ensured that the antigens used in the vaccine do not elicit an antibody response that can cross-react with host tissues. In this study, we evaluated the safety of our GAS vaccine candidate called VaxiStrep in New Zealand White rabbits. VaxiStrep is a recombinant fusion protein comprised of streptococcal pyrogenic exotoxin A (SpeA) and exotoxin B (SpeB), also known as erythrogenic toxins, adsorbed to an aluminum adjuvant. The vaccine elicited a robust immune response against the two toxins in the rabbits without any adverse events or toxicity. No signs of autoimmune pathology were detected in the rabbits' brains, hearts, and kidneys via immunohistochemistry, and serum antibodies did not cross-react with cardiac or neuronal tissue proteins associated with rheumatic heart disease or Sydenham chorea (SC). This study further confirms that VaxiStrep does not elicit autoantibodies and is safe to be tested in a first-in-human trial.
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Affiliation(s)
| | | | - Madeleine W. Cunningham
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathy Alvarez
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Rebecca Bentley
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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18
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Su X, Stadler RV, Xu F, Wu J. Malaria Genomics, Vaccine Development, and Microbiome. Pathogens 2023; 12:1061. [PMID: 37624021 PMCID: PMC10459703 DOI: 10.3390/pathogens12081061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Recent advances in malaria genetics and genomics have transformed many aspects of malaria research in areas of molecular evolution, epidemiology, transmission, host-parasite interaction, drug resistance, pathogenicity, and vaccine development. Here, in addition to introducing some background information on malaria parasite biology, parasite genetics/genomics, and genotyping methods, we discuss some applications of genetic and genomic approaches in vaccine development and in studying interactions with microbiota. Genetic and genomic data can be used to search for novel vaccine targets, design an effective vaccine strategy, identify protective antigens in a whole-organism vaccine, and evaluate the efficacy of a vaccine. Microbiota has been shown to influence disease outcomes and vaccine efficacy; studying the effects of microbiota in pathogenicity and immunity may provide information for disease control. Malaria genetics and genomics will continue to contribute greatly to many fields of malaria research.
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Affiliation(s)
- Xinzhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (R.V.S.); (F.X.); (J.W.)
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19
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Lacey JA, Marcato AJ, Chisholm RH, Campbell PT, Zachreson C, Price DJ, James TB, Morris JM, Gorrie CL, McDonald MI, Bowen AC, Giffard PM, Holt DC, Currie BJ, Carapetis JR, Andrews RM, Davies MR, Geard N, McVernon J, Tong SYC. Evaluating the role of asymptomatic throat carriage of Streptococcus pyogenes in impetigo transmission in remote Aboriginal communities in Northern Territory, Australia: a retrospective genomic analysis. THE LANCET. MICROBE 2023; 4:e524-e533. [PMID: 37211022 DOI: 10.1016/s2666-5247(23)00068-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Streptococcus pyogenes, or group A Streptococcus (GAS), infections contribute to a high burden of disease in Aboriginal Australians, causing skin infections and immune sequelae such as rheumatic heart disease. Controlling skin infections in these populations has proven difficult, with transmission dynamics being poorly understood. We aimed to identify the relative contributions of impetigo and asymptomatic throat carriage to GAS transmission. METHODS In this genomic analysis, we retrospectively applied whole genome sequencing to GAS isolates that were collected as part of an impetigo surveillance longitudinal household survey conducted in three remote Aboriginal communities in the Northern Territory of Australia between Aug 6, 2003, and June 22, 2005. We included GAS isolates from all throats and impetigo lesions of people living in two of the previously studied communities. We classified isolates into genomic lineages based on pairwise shared core genomes of more than 99% with five or fewer single nucleotide polymorphisms. We used a household network analysis of epidemiologically and genomically linked lineages to quantify the transmission of GAS within and between households. FINDINGS We included 320 GAS isolates in our analysis: 203 (63%) from asymptomatic throat swabs and 117 (37%) from impetigo lesions. Among 64 genomic lineages (encompassing 39 emm types) we identified 264 transmission links (involving 93% of isolates), for which the probable source was asymptomatic throat carriage in 166 (63%) and impetigo lesions in 98 (37%). Links originating from impetigo cases were more frequent between households than within households. Households were infected with GAS for a mean of 57 days (SD 39 days), and once cleared, reinfected 62 days (SD 40 days) later. Increased household size and community presence of GAS and scabies were associated with slower clearance of GAS. INTERPRETATION In communities with high prevalence of endemic GAS-associated skin infection, asymptomatic throat carriage is a GAS reservoir. Public health interventions such as vaccination or community infection control programmes aimed at interrupting transmission of GAS might need to include consideration of asymptomatic throat carriage. FUNDING Australian National Health and Medical Research Council.
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Affiliation(s)
- Jake A Lacey
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC Australia
| | - Adrian J Marcato
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia
| | - Rebecca H Chisholm
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia; Department of Mathematical and Physical Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Patricia T Campbell
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia
| | - Cameron Zachreson
- School of Computing and Information systems, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, VIC Australia
| | - David J Price
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC Australia
| | - Taylah B James
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC Australia
| | - Jacqueline M Morris
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC Australia
| | - Malcolm I McDonald
- Division of Tropical Health and Medicine, James Cook University, Nguma-bada Campus, Cairns, QLD, Australia
| | - Asha C Bowen
- Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Philip M Giffard
- Global and Tropical Healthy Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; School of Medicine, Faculty of Health, Charles Darwin University, Darwin, NT, Australia
| | - Deborah C Holt
- Global and Tropical Healthy Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; School of Medicine, Faculty of Health, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Healthy Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Jonathan R Carapetis
- Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Ross M Andrews
- Global and Tropical Healthy Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC Australia
| | - Nicholas Geard
- School of Computing and Information systems, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, VIC Australia
| | - Jodie McVernon
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, University of Melbourne, Melbourne, VIC Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Melbourne, at the Peter Doherty Institute for Infection and Immunity VIC, Australia; Global and Tropical Healthy Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
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20
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Brouwer S, Rivera-Hernandez T, Curren BF, Harbison-Price N, De Oliveira DMP, Jespersen MG, Davies MR, Walker MJ. Pathogenesis, epidemiology and control of Group A Streptococcus infection. Nat Rev Microbiol 2023; 21:431-447. [PMID: 36894668 PMCID: PMC9998027 DOI: 10.1038/s41579-023-00865-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2023] [Indexed: 03/11/2023]
Abstract
Streptococcus pyogenes (Group A Streptococcus; GAS) is exquisitely adapted to the human host, resulting in asymptomatic infection, pharyngitis, pyoderma, scarlet fever or invasive diseases, with potential for triggering post-infection immune sequelae. GAS deploys a range of virulence determinants to allow colonization, dissemination within the host and transmission, disrupting both innate and adaptive immune responses to infection. Fluctuating global GAS epidemiology is characterized by the emergence of new GAS clones, often associated with the acquisition of new virulence or antimicrobial determinants that are better adapted to the infection niche or averting host immunity. The recent identification of clinical GAS isolates with reduced penicillin sensitivity and increasing macrolide resistance threatens both frontline and penicillin-adjunctive antibiotic treatment. The World Health Organization (WHO) has developed a GAS research and technology road map and has outlined preferred vaccine characteristics, stimulating renewed interest in the development of safe and effective GAS vaccines.
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Affiliation(s)
- Stephan Brouwer
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Bodie F Curren
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nichaela Harbison-Price
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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21
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Kaci A, Jonassen CM, Skrede S, Sivertsen A, Steinbakk M, Oppegaard O. Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018. Front Microbiol 2023; 14:1171913. [PMID: 37485526 PMCID: PMC10361778 DOI: 10.3389/fmicb.2023.1171913] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/31/2023] [Indexed: 07/25/2023] Open
Abstract
Background Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized. Methods We carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE. Results The phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling. Conclusion Recombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages. The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics.
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Affiliation(s)
- Alba Kaci
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
| | - Christine M. Jonassen
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Steinar Skrede
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Audun Sivertsen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | | | - Martin Steinbakk
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
| | - Oddvar Oppegaard
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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22
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Yu D, Guo D, Zheng Y, Yang Y. A review of penicillin binding protein and group A Streptococcus with reduced-β-lactam susceptibility. Front Cell Infect Microbiol 2023; 13:1117160. [PMID: 37065204 PMCID: PMC10102528 DOI: 10.3389/fcimb.2023.1117160] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
With the widespread use of antibiotics, antimicrobial resistance (AMR) has become a global problem that endangers public health. Despite the global high prevalence of group A Streptococcus (GAS) infections and the global widespread use of β-lactams, β-lactams remain the first-line treatment option for GAS infection. β-hemolytic streptococci maintain a persistent susceptibility to β-lactams, which is an extremely special phenomenon in the genus Streptococci, while the exact current mechanism is not known. In recent years, several studies have found that the gene encoding penicillin binding protein 2X (pbp2x) is associated with GAS with reduced-β-lactam susceptibility. The purpose of this review is to summarize the current published data on GAS penicillin binding proteins and β-lactam susceptibility, to explore the relationship between them, and to be alert to the emergence of GAS with reduced susceptibility to β-lactams.
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Affiliation(s)
- Dingle Yu
- Shenzhen Children’s Hospital, Shenzhen, China
| | - Danchun Guo
- Shenzhen Children’s Hospital, Shenzhen, China
| | - Yuejie Zheng
- Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Yuejie Zheng, ; Yonghong Yang,
| | - Yonghong Yang
- Shenzhen Children’s Hospital, Shenzhen, China
- Microbiology Laboratory, National Center for Children’s Health, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- *Correspondence: Yuejie Zheng, ; Yonghong Yang,
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23
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Burns K, Dorfmueller HC, Wren BW, Mawas F, Shaw HA. Progress towards a glycoconjugate vaccine against Group A Streptococcus. NPJ Vaccines 2023; 8:48. [PMID: 36977677 PMCID: PMC10043865 DOI: 10.1038/s41541-023-00639-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
The Group A Carbohydrate (GAC) is a defining feature of Group A Streptococcus (Strep A) or Streptococcus pyogenes. It is a conserved and simple polysaccharide, comprising a rhamnose backbone and GlcNAc side chains, further decorated with glycerol phosphate on approximately 40% GlcNAc residues. Its conservation, surface exposure and antigenicity have made it an interesting focus on Strep A vaccine design. Glycoconjugates containing this conserved carbohydrate should be a key approach towards the successful mission to build a universal Strep A vaccine candidate. In this review, a brief introduction to GAC, the main carbohydrate component of Strep A bacteria, and a variety of published carrier proteins and conjugation technologies are discussed. Components and technologies should be chosen carefully for building affordable Strep A vaccine candidates, particularly for low- and middle-income countries (LMICs). Towards this, novel technologies are discussed, such as the prospective use of bioconjugation with PglB for rhamnose polymer conjugation and generalised modules for membrane antigens (GMMA), particularly as low-cost solutions to vaccine production. Rational design of "double-hit" conjugates encompassing species specific glycan and protein components would be beneficial and production of a conserved vaccine to target Strep A colonisation without invoking an autoimmune response would be ideal.
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Affiliation(s)
- Keira Burns
- Vaccine Division, Scientific Research & Innovation Group, MHRA, Potters Bar, UK
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, Dow Street, Dundee, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Fatme Mawas
- Vaccine Division, Scientific Research & Innovation Group, MHRA, Potters Bar, UK
| | - Helen A Shaw
- Vaccine Division, Scientific Research & Innovation Group, MHRA, Potters Bar, UK.
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24
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Davies MR, Keller N, Brouwer S, Jespersen MG, Cork AJ, Hayes AJ, Pitt ME, De Oliveira DMP, Harbison-Price N, Bertolla OM, Mediati DG, Curren BF, Taiaroa G, Lacey JA, Smith HV, Fang NX, Coin LJM, Stevens K, Tong SYC, Sanderson-Smith M, Tree JJ, Irwin AD, Grimwood K, Howden BP, Jennison AV, Walker MJ. Detection of Streptococcus pyogenes M1 UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA. Nat Commun 2023; 14:1051. [PMID: 36828918 PMCID: PMC9951164 DOI: 10.1038/s41467-023-36717-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
A new variant of Streptococcus pyogenes serotype M1 (designated 'M1UK') has been reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase in invasive infections, and exhibiting enhanced expression of the superantigen SpeA. The progenitor S. pyogenes 'M1global' and M1UK clones can be differentiated by 27 SNPs and 4 indels, yet the mechanism for speA upregulation is unknown. Here we investigate the previously unappreciated expansion of M1UK in Australia, now isolated from the majority of serious infections caused by serotype M1 S. pyogenes. M1UK sub-lineages circulating in Australia also contain a novel toxin repertoire associated with epidemic scarlet fever causing S. pyogenes in Asia. A single SNP in the 5' transcriptional leader sequence of the transfer-messenger RNA gene ssrA drives enhanced SpeA superantigen expression as a result of ssrA terminator read-through in the M1UK lineage. This represents a previously unappreciated mechanism of toxin expression and urges enhanced international surveillance.
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Affiliation(s)
- Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia M Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bodie F Curren
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen V Smith
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Ning-Xia Fang
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martina Sanderson-Smith
- Illawarra Health and Medical Research Institute and Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia.,Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, QLD, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amy V Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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Genomic Characterization of Skin and Soft Tissue Streptococcus pyogenes Isolates from a Low-Income and a High-Income Setting. mSphere 2023; 8:e0046922. [PMID: 36507654 PMCID: PMC9942559 DOI: 10.1128/msphere.00469-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource-limited settings. The development of a vaccine against S. pyogenes is a global health priority to reduce the burden of postinfection rheumatic heart disease. To support this, molecular characterization of circulating S. pyogenes isolates is needed. We performed whole-genome analyses of S. pyogenes isolates from skin and soft tissue infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where there is a high burden of such infections. To act as a comparator to these LIC isolates, skin infection isolates from Sheffield, United Kingdom (a high-income country [HIC]), were also sequenced. The LIC isolates from The Gambia were genetically more diverse (46 emm types in 107 isolates) than the HIC isolates from Sheffield (23 emm types in 142 isolates), with only 7 overlapping emm types. Other molecular markers were shared, including a high prevalence of the skin infection-associated emm pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT-4. Fewer of the Gambian LIC isolates carried prophage-associated superantigens (64%) and DNases (26%) than did the Sheffield HIC isolates (99% and 95%, respectively). We also identified streptococcin genes unique to 36% of the Gambian LIC isolates and a higher prevalence (48%) of glucuronic acid utilization pathway genes in the Gambian LIC isolates than in the Sheffield HIC isolates (26%). Comparison to a wider collection of HIC and LIC isolate genomes supported our findings of differing emm diversity and prevalence of bacterial factors. Our study provides insight into the genetics of LIC isolates and how they compare to HIC isolates. IMPORTANCE The global burden of rheumatic heart disease (RHD) has triggered a World Health Organization response to drive forward development of a vaccine against the causative human pathogen Streptococcus pyogenes. This burden stems primarily from low- and middle-income settings where there are high levels of S. pyogenes skin and soft tissue infections, which can lead to RHD. Our study provides much needed whole-genome-based molecular characterization of isolates causing skin infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where infection and RHD rates are high. Although we identified a greater level of diversity in these LIC isolates than in isolates from Sheffield, United Kingdom (a high-income country), there were some shared features. There were also some features that differed by geographical region, warranting further investigation into their contribution to infection. Our study has also contributed data essential for the development of a vaccine that would target geographically relevant strains.
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Christine TD, Clothilde C, Mathieu B, Laurence A, Valentin K, Cédric M, Wing Rod A, Yves V, Francois S. FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform 2023; 5:lqad013. [PMID: 36814455 PMCID: PMC9940456 DOI: 10.1093/nargab/lqad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/21/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.
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Affiliation(s)
| | | | - Blaison Mathieu
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - Albar Laurence
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Klein Valentin
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - Mariac Cédric
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - A. Wing Rod
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Abstract
Recent efforts have re-invigorated the Streptococcus pyogenes (Group A Streptococcus) vaccine development field, though scientific, regulatory and commercial barriers persist, and the vaccine pipeline remains sparse. There is an ongoing need to accelerate all aspects of development to address the large global burden of disease caused by the pathogen. Building on over 100 years of S. pyogenes vaccine development, there are currently eight candidates on a product development track, including four M protein-based candidates and four candidates designed around non-M protein antigens. These candidates have demonstrated proof of concept for protection against S. pyogenes in preclinical models, one has demonstrated safety and immunogenicity in a Phase 1 trial and at least four others are poised to soon enter clinical trials. To maintain momentum, the Strep A Vaccine Global Consortium (SAVAC) was established to bring together experts to accelerate global S. pyogenes vaccine development. This article highlights the past, present and future of S. pyogenes vaccine development and emphasizes key priorities, and the role of SAVAC, in advancing the field.
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Boeddha NP, Atkins L, de Groot R, Driessen G, Hazelzet J, Zenz W, Carrol ED, Anderson ST, Martinon-Torres F, Agyeman PKA, Galassini R, Herberg J, Levin M, Schlapbach LJ, Emonts M. Group A streptococcal disease in paediatric inpatients: a European perspective. Eur J Pediatr 2023; 182:697-706. [PMID: 36449079 PMCID: PMC9709363 DOI: 10.1007/s00431-022-04718-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022]
Abstract
Group A streptococcal (GAS) disease shows increasing incidence worldwide. We characterised children admitted with GAS infection to European hospitals and studied risk factors for severity and disability. This is a prospective, multicentre, cohort study (embedded in EUCLIDS and the Swiss Pediatric Sepsis Study) including 320 children, aged 1 month to 18 years, admitted with GAS infection to 41 hospitals in 6 European countries from 2012 to 2016. Demographic, clinical, microbiological and outcome data were collected. A total of 195 (61%) patients had sepsis. Two hundred thirty-six (74%) patients had GAS detected from a normally sterile site. The most common infection sites were the lower respiratory tract (LRTI) (22%), skin and soft tissue (SSTI) (23%) and bone and joint (19%). Compared to patients not admitted to PICU, patients admitted to PICU more commonly had LRTI (39 vs 8%), infection without a focus (22 vs 8%) and intracranial infection (9 vs 3%); less commonly had SSTI and bone and joint infections (p < 0.001); and were younger (median 40 (IQR 21-83) vs 56 (IQR 36-85) months, p = 0.01). Six PICU patients (2%) died. Sequelae at discharge from hospital were largely limited to patients admitted to PICU (29 vs 3%, p < 0.001; 12% overall) and included neurodisability, amputation, skin grafts, hearing loss and need for surgery. More patients were recruited in winter and spring (p < 0.001). CONCLUSION In an era of observed marked reduction in vaccine-preventable infections, GAS infection requiring hospital admission is still associated with significant severe disease in younger children, and short- and long-term morbidity. Further advances are required in the prevention and early recognition of GAS disease. WHAT IS KNOWN • Despite temporal and geographical variability, there is an increase of incidence of infection with group A streptococci. However, data on the epidemiology of group A streptococcal infections in European children is limited. WHAT IS NEW • In a large, prospective cohort of children with community-acquired bacterial infection requiring hospitalisation in Europe, GAS was the most frequent pathogen, with 12% disability at discharge, and 2% mortality in patients with GAS infection. • In children with GAS sepsis, IVIG was used in only 4.6% of patients and clindamycin in 29% of patients.
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Affiliation(s)
- Navin P Boeddha
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
- Department of Pediatrics, Maasstad Hospital, Rotterdam, the Netherlands
| | - Lucy Atkins
- Paediatric Immunology, Infectious Diseases & Allergy Dept., Great North Children's Hospital, Newcastle Upon Tyne Hospitals NHS Foundation Trust, RVI, Clinical Resources Building, Queen Victoria Road, Newcastle Upon Tyne, NE1 4LP, UK
| | - Ronald de Groot
- Division of Pediatric Infectious Diseases and Immunology and Laboratory of Infectious Diseases, Department of Pediatrics, Radboud Institute of Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Gertjan Driessen
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
- Department of Paediatrics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jan Hazelzet
- Department of Public Health, Erasmus MC, Rotterdam, the Netherlands
| | - Werner Zenz
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Enitan D Carrol
- Institute of Infection, Veterinary and Ecological Sciences Global Health, University of Liverpool, Liverpool, UK
- Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | | | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases Section, Pediatrics Department, Santiago de Compostela, Spain
| | - Philipp K A Agyeman
- Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Rachel Galassini
- Section of Paediatrics Division of Infectious Disease, Imperial College of London, London, UK
| | - Jethro Herberg
- Section of Paediatrics Division of Infectious Disease, Imperial College of London, London, UK
| | - Michael Levin
- Section of Paediatrics Division of Infectious Disease, Imperial College of London, London, UK
| | - Luregn J Schlapbach
- Neonatal and Pediatric Intensive Care Unit, University Children`s Hospital Zürich and Children`s Research Center, Zurich, Switzerland
| | - Marieke Emonts
- Paediatric Immunology, Infectious Diseases & Allergy Dept., Great North Children's Hospital, Newcastle Upon Tyne Hospitals NHS Foundation Trust, RVI, Clinical Resources Building, Queen Victoria Road, Newcastle Upon Tyne, NE1 4LP, UK.
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
- NIHR Newcastle Biomedical Research Centre Based at Newcastle Upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle Upon Tyne, UK.
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Frost HR, Guglielmini J, Duchêne S, Lacey JA, Sanderson-Smith M, Steer AC, Walker MJ, Botteaux A, Davies MR, Smeesters PR. Promiscuous evolution of Group A Streptococcal M and M-like proteins. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001280. [PMID: 36748538 PMCID: PMC9993116 DOI: 10.1099/mic.0.001280] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Group A Streptococcus (GAS) M and M-like proteins are essential virulence factors and represent the primary epidemiological marker of this pathogen. Protein sequences encoding 1054 M, Mrp and Enn proteins, from 1668 GAS genomes, were analysed by SplitsTree4, partitioning around medoids and co-occurrence. The splits network and groups-based analysis of all M and M-like proteins revealed four large protein groupings, with multiple evolutionary histories as represented by multiple edges for most splits, leading to 'M-family-groups' (FG) of protein sequences: FG I, Mrp; FG II, M protein and Protein H; FG III, Enn; and FG IV, M protein. M and Enn proteins formed two groups with nine sub-groups and Mrp proteins formed four groups with ten sub-groups. Discrete co-occurrence of M and M-like proteins were identified suggesting that while dynamic, evolution may be constrained by a combination of functional and virulence attributes. At a granular level, four distinct family-groups of M, Enn and Mrp proteins are observable, with Mrp representing the most genetically distinct of the family-group of proteins. While M and Enn protein families generally group into three distinct family-groups, horizontal and vertical gene flow between distinct GAS strains is ongoing.
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Affiliation(s)
- Hannah R Frost
- Molecular Bacteriology Laboratory, Université libre de Bruxelles, Brussels, Belgium.,Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, Australia
| | - Julien Guglielmini
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Sebastian Duchêne
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jake A Lacey
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Martina Sanderson-Smith
- Illawarra Health and Medical Research Institute and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Andrew C Steer
- Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, Université libre de Bruxelles, Brussels, Belgium
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Pierre R Smeesters
- Molecular Bacteriology Laboratory, Université libre de Bruxelles, Brussels, Belgium.,Tropical Diseases Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
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30
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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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Host-Mediated Copper Stress Is Not Protective against Streptococcus pneumoniae D39 Infection. Microbiol Spectr 2022; 10:e0249522. [PMID: 36413018 PMCID: PMC9769658 DOI: 10.1128/spectrum.02495-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Metal ions are required by all organisms for the chemical processes that support life. However, in excess they can also exert toxicity within biological systems. During infection, bacterial pathogens such as Streptococcus pneumoniae are exposed to host-imposed metal intoxication, where the toxic properties of metals, such as copper, are exploited to aid in microbial clearance. However, previous studies investigating the antimicrobial efficacy of copper in vivo have reported variable findings. Here, we use a highly copper-sensitive strain of S. pneumoniae, lacking both copper efflux and intracellular copper buffering by glutathione, to investigate how copper stress is managed and where it is encountered during infection. We show that this strain exhibits highly dysregulated copper homeostasis, leading to the attenuation of growth and hyperaccumulation of copper in vitro. In a murine infection model, whole-tissue copper quantitation and elemental bioimaging of the murine lung revealed that infection with S. pneumoniae resulted in increased copper abundance in specific tissues, with the formation of spatially discrete copper hot spots throughout the lung. While the increased copper was able to reduce the viability of the highly copper-sensitive strain in a pneumonia model, copper levels in professional phagocytes and in a bacteremic model were insufficient to prosecute bacterial clearance. Collectively, this study reveals that host copper is redistributed to sites of infection and can impact bacterial viability in a hypersusceptible strain. However, in wild-type S. pneumoniae, the concerted actions of the copper homeostatic mechanisms are sufficient to facilitate continued viability and virulence of the pathogen. IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is one of the world's foremost bacterial pathogens. Treatment of both localized and systemic pneumococcal infection is becoming complicated by increasing rates of multidrug resistance globally. Copper is a potent antimicrobial agent used by the mammalian immune system in the defense against bacterial pathogens. However, unlike other bacterial species, this copper stress is unable to prosecute pneumococcal clearance. This study determines how the mammalian host inflicts copper stress on S. pneumoniae and the bacterial copper tolerance mechanisms that contribute to maintenance of viability and virulence in vitro and in vivo. This work has provided insight into the chemical biology of the host-pneumococcal interaction and identified a potential avenue for novel antimicrobial development.
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32
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Zang M, Ascari A, Adams FG, Alquethamy S, Eijkelkamp BA. Characterizing the role of phosphatidylglycerol-phosphate phosphatases in Acinetobacter baumannii cell envelope biogenesis and antibiotic resistance. Cell Surf 2022; 9:100092. [PMID: 36545493 PMCID: PMC9760654 DOI: 10.1016/j.tcsw.2022.100092] [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: 07/03/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
The dissemination of multi-drug resistant Acinetobacter baumannii threatens global healthcare systems and necessitates the development of novel therapeutic options. The Gram-negative bacterial cell envelope provides a first defensive barrier against antimicrobial assault. Essential components of this multi-layered complex are the phospholipid-rich membranes. Phosphatidylglycerol phosphate (PGP) phosphatases are responsible for a key step in the biosynthesis of a major phospholipid species, phosphatidylglycerol (PG), but these enzymes have also been implicated in the biogenesis of other cell envelope components. Our bioinformatics analyses identified two putative PGP candidates in the A. baumannii genome, PgpA and PgpB. Phospholipid analyses of isogenic pgpA mutants in two distinct A. baumannii strains revealed a shift in the desaturation levels of phosphatidylethanolamine (PE) phospholipid species, possibly due to the activation of the phospholipid desaturase DesA. We also investigated the impact of the inner membrane phosphatases on other cell envelope components, which revealed a role of PgpB in the maintenance of the A. baumannii peptidoglycan layer, and consequently carbapenem resistance. Collectively, this work provides novel insights into the roles of PGP phosphatases on the global lipidomic landscape of A. baumannii and their interconnectivity with the biogenesis of other cell envelope components. The non-essentiality of these candidates exemplifies metabolic versatility of A. baumannii, which is believed to be key to its success as global pathogen.
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Affiliation(s)
- Maoge Zang
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Alice Ascari
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia,Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Felise G. Adams
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Saleh Alquethamy
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Bart A. Eijkelkamp
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia,Corresponding author.
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ICU Management of Invasive β-Hemolytic Streptococcal Infections. Infect Dis Clin North Am 2022; 36:861-887. [DOI: 10.1016/j.idc.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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34
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Host-dependent resistance of Group A Streptococcus to sulfamethoxazole mediated by a horizontally-acquired reduced folate transporter. Nat Commun 2022; 13:6557. [PMID: 36450721 PMCID: PMC9712650 DOI: 10.1038/s41467-022-34243-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/19/2022] [Indexed: 12/03/2022] Open
Abstract
Described antimicrobial resistance mechanisms enable bacteria to avoid the direct effects of antibiotics and can be monitored by in vitro susceptibility testing and genetic methods. Here we describe a mechanism of sulfamethoxazole resistance that requires a host metabolite for activity. Using a combination of in vitro evolution and metabolic rescue experiments, we identify an energy-coupling factor (ECF) transporter S component gene (thfT) that enables Group A Streptococcus to acquire extracellular reduced folate compounds. ThfT likely expands the substrate specificity of an endogenous ECF transporter to acquire reduced folate compounds directly from the host, thereby bypassing the inhibition of folate biosynthesis by sulfamethoxazole. As such, ThfT is a functional equivalent of eukaryotic folate uptake pathways that confers very high levels of resistance to sulfamethoxazole, yet remains undetectable when Group A Streptococcus is grown in the absence of reduced folates. Our study highlights the need to understand how antibiotic susceptibility of pathogens might function during infections to identify additional mechanisms of resistance and reduce ineffective antibiotic use and treatment failures, which in turn further contribute to the spread of antimicrobial resistance genes amongst bacterial pathogens.
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35
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Chaguza C, Jamrozy D, Bijlsma MW, Kuijpers TW, van de Beek D, van der Ende A, Bentley SD. Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion. Nat Commun 2022; 13:4215. [PMID: 35864107 PMCID: PMC9304382 DOI: 10.1038/s41467-022-31858-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
Group B Streptococcus (GBS), or Streptococcus agalactiae, is a pathogen that causes preterm births, stillbirths, and acute invasive neonatal disease burden and mortality. Here, we investigate bacterial genetic signatures associated with disease onset time and meningeal tissue infection in acute invasive neonatal GBS disease. We carry out a genome-wide association study (GWAS) of 1,338 GBS isolates from newborns with acute invasive disease; the isolates had been collected annually, for 30 years, through a national bacterial surveillance program in the Netherlands. After controlling for the population structure, we identify genetic variation within noncoding and coding regions, particularly the capsule biosynthesis locus, statistically associated with neonatal GBS disease onset time and meningeal invasion. Our findings highlight the impact of integrating microbial population genomics and clinical pathogen surveillance, and demonstrate the effect of GBS genetics on disease pathogenesis in neonates and infants. Group B Streptococcus (GBS) causes neonatal disease and mortality worldwide. Here, the authors use genome-wide association analyses to identify bacterial genetic signatures associated with disease onset time and meningeal tissue infection in acute invasive neonatal GBS disease.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. .,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Merijn W Bijlsma
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Haematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Diederik van de Beek
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Amsterdam Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands. .,Netherlands Reference Laboratory for Bacterial Meningitis, Center of Infection and Immunity Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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36
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Current Techniques to Study Beneficial Plant-Microbe Interactions. Microorganisms 2022; 10:microorganisms10071380. [PMID: 35889099 PMCID: PMC9317800 DOI: 10.3390/microorganisms10071380] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.
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Metsky HC, Welch NL, Pillai PP, Haradhvala NJ, Rumker L, Mantena S, Zhang YB, Yang DK, Ackerman CM, Weller J, Blainey PC, Myhrvold C, Mitzenmacher M, Sabeti PC. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol 2022; 40:1123-1131. [PMID: 35241837 PMCID: PMC9287178 DOI: 10.1038/s41587-022-01213-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022]
Abstract
Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.
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Affiliation(s)
- Hayden C Metsky
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
| | - Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Virology Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biophysics Program, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | | | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Mitzenmacher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 24:100488. [PMID: 35769175 PMCID: PMC9234096 DOI: 10.1016/j.lanwpc.2022.100488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.
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Affiliation(s)
- Mark R. Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aaron P. Jenkins
- Centre for Ecosystem Management, Edith Cowan University, Western Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Adam Jenney
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jake A. Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vanessa K. Wong
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Aalisha Sahukhan
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Helen Thomson
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
| | - Andrew Page
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | | | - Eric Rafai
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A. Crump
- Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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Development and Characterisation of a Four-Plex Assay to Measure Streptococcus pyogenes Antigen-Specific IgG in Human Sera. Methods Protoc 2022; 5:mps5040055. [PMID: 35893581 PMCID: PMC9326740 DOI: 10.3390/mps5040055] [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: 05/29/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
The measurement of antibodies to vaccine antigens is crucial for research towards a safe and effective vaccine for Streptococcus pyogenes (Strep A). We describe the establishment and detailed characterisation of a four-plex assay to measure IgG to the Strep A vaccine antigens SpyCEP, Slo, SpyAD and GAC using the Luminex multiplex platform. A standard curve was established and characterized to allow the quantification of antigen-specific IgG. Assay specificity, precision, linearity, reproducibility and repeatability were determined via the measurement of antigen-specific IgG from pooled human serum. The assay is highly specific, reproducible and performs well across a large range of antibody concentrations against all four antigens. It is, therefore, suitable for future clinical trials in humans with a four-component vaccine, as well as for seroepidemiological studies to gain insights into naturally occurring immunity.
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40
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Maunders EA, Ngu DHY, Ganio K, Hossain SI, Lim BYJ, Leeming MG, Luo Z, Tan A, Deplazes E, Kobe B, McDevitt CA. The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis. Front Microbiol 2022; 13:903146. [PMID: 35685933 PMCID: PMC9171197 DOI: 10.3389/fmicb.2022.903146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/03/2022] Open
Abstract
Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bryan Y. J. Lim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Boštjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Boštjan Kobe,
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Christopher A. McDevitt,
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41
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Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes. J Clin Microbiol 2022; 60:e0031522. [DOI: 10.1128/jcm.00315-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Streptococcus pyogenes
is a major human pathogen with high genetic diversity, largely created by recombination and horizontal gene transfer, making it difficult to use single nucleotide polymorphism (SNP)-based genome-wide analyses for surveillance. Using a gene-by-gene approach on 208 complete genomes of
S. pyogenes
, a novel whole-genome multilocus sequence typing (wgMLST) schema was developed, comprising 3,044 target loci.
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42
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Barth DD, Mullane MJ, Sampson C, Chou C, Pickering J, Nicol MP, Davies MR, Carapetis J, Bowen AC. Missing Piece Study protocol: prospective surveillance to determine the epidemiology of group A streptococcal pharyngitis and impetigo in remote Western Australia. BMJ Open 2022; 12:e057296. [PMID: 35387825 PMCID: PMC8987764 DOI: 10.1136/bmjopen-2021-057296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Group A β-haemolytic Streptococcus (GAS), a Gram-positive bacterium, causes skin, mucosal and systemic infections. Repeated GAS infections can lead to autoimmune diseases acute rheumatic fever (ARF) and rheumatic heart disease (RHD). Aboriginal and Torres Strait Islander peoples in Australia have the highest rates of ARF and RHD in the world. Despite this, the contemporaneous prevalence and incidence of GAS pharyngitis and impetigo in remote Australia remains unknown. To address this, we have designed a prospective surveillance study of GAS pharyngitis and impetigo to collect coincident contemporary evidence to inform and enhance primary prevention strategies for ARF. METHODS AND ANALYSIS The Missing Piece Study aims to document the epidemiology of GAS pharyngitis and impetigo through collection of clinical, serological, microbiological and bacterial genomic data among remote-living Australian children. The study comprises two components: (1) screening of all children at school for GAS pharyngitis and impetigo up to three times a year and (2) weekly active surveillance visits to detect new cases of pharyngitis and impetigo. Environmental swabbing in remote schools will be included, to inform environmental health interventions. In addition, the application of new diagnostic technologies, microbiome analysis and bacterial genomic evaluations will enhance primary prevention strategies, having direct bearing on clinical care, vaccine development and surveillance for vaccine clinical trials. ETHICS AND DISSEMINATION Ethical approval has been obtained from the Western Australian Aboriginal Health Ethics Committee (Ref: 892) and Human Research Ethics Committee of the University of Western Australia (Ref: RA/4/20/5101). Study findings will be shared with community members, teachers and children at participating schools, together with academic and medical services. Sharing findings in an appropriate manner is important and will be done in a suitable way which includes plain language summaries and presentations. Finally, findings and updates will also be disseminated to collaborators, researchers and health planners through peer-reviewed journal publications.
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Affiliation(s)
- Dylan D Barth
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Marianne J Mullane
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Claudia Sampson
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Coco Chou
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Janessa Pickering
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Mark P Nicol
- Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jonathan Carapetis
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Asha C Bowen
- Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Nedlands, Western Australia, Australia
- Institute for Health Research, University of Notre Dame, Fremantle, Western Australia, Australia
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43
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Rafei R, Al Iaali R, Osman M, Dabboussi F, Hamze M. A global snapshot on the prevalent macrolide-resistant emm types of Group A Streptococcus worldwide, their phenotypes and their resistance marker genotypes during the last two decades: A systematic review. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105258. [PMID: 35219865 DOI: 10.1016/j.meegid.2022.105258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 12/29/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Watchful epidemiological surveillance of macrolide-resistant Group A Streptococcus (MRGAS) clones is important owing to the evolutionary and epidemiological dynamic of GAS. Meanwhile, data on the global distribution of MRGAS emm types according to macrolide resistance phenotypes and genotypes are scant and need to be updated. For this, the present systematic review analyses a global set of extensively characterized MRGAS isolates from patients of diverse ages and clinical presentations over approximately two decades (2000 to 2020) and recaps the peculiar epidemiological features of the dominant MRGAS clones. Based on the inclusion and exclusion criteria, 53 articles (3593 macrolide-resistant and 15,951 susceptible isolates) distributed over 23 countries were dissected with a predominance of high-income countries over low-income ones. Although macrolide resistance in GAS is highly variable in different countries, its within-GAS distribution seems not to be random. emm pattern E, 13 major emm types (emm12, 4, 28, 77, 75, 11, 22, 92, 58, 60, 94, 63, 114) and 4 emm clusters (A-C4, E1, E6, and E2) were significantly associated with macrolide resistance. emm patterns A-C and D, 14 major emm types (emm89, 3, 6, 2, 44, 82, 87, 118, 5, 49, 81, 59, 227, 78) and 3 well-defined emm clusters (A-C5, E3, and D4) were significantly associated with macrolide susceptibility. Scrutinizing the tendency of each MRGAS emm type to be significantly associated with specific macrolide resistance phenotype or genotype, interesting vignettes are also unveiled. The 30-valent vaccine covers ~95% of MRGAS isolates. The presented data urge the importance of comprehensive nationwide sustained surveillance of MRGAS circulating clones particularly in Low and Middle income countries where sampling bias is high and GAS epidemiology is obfuscated and needs to be demystified.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
| | - Rayane Al Iaali
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon; Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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44
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De Oliveira DMP, Keller B, Hayes AJ, Ong CLY, Harbison-Price N, El-Deeb IM, Li G, Keller N, Bohlmann L, Brouwer S, Turner AG, Cork AJ, Jones TR, Paterson DL, McEwan AG, Davies MR, McDevitt CA, von Itzstein M, Walker MJ. Neurodegenerative Disease Treatment Drug PBT2 Breaks Intrinsic Polymyxin Resistance in Gram-Positive Bacteria. Antibiotics (Basel) 2022; 11:antibiotics11040449. [PMID: 35453201 PMCID: PMC9027797 DOI: 10.3390/antibiotics11040449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 12/03/2022] Open
Abstract
Gram-positive bacteria do not produce lipopolysaccharide as a cell wall component. As such, the polymyxin class of antibiotics, which exert bactericidal activity against Gram-negative pathogens, are ineffective against Gram-positive bacteria. The safe-for-human-use hydroxyquinoline analog ionophore PBT2 has been previously shown to break polymyxin resistance in Gram-negative bacteria, independent of the lipopolysaccharide modification pathways that confer polymyxin resistance. Here, in combination with zinc, PBT2 was shown to break intrinsic polymyxin resistance in Streptococcus pyogenes (Group A Streptococcus; GAS), Staphylococcus aureus (including methicillin-resistant S. aureus), and vancomycin-resistant Enterococcus faecium. Using the globally disseminated M1T1 GAS strain 5448 as a proof of principle model, colistin in the presence of PBT2 + zinc was shown to be bactericidal in activity. Any resistance that did arise imposed a substantial fitness cost. PBT2 + zinc dysregulated GAS metal ion homeostasis, notably decreasing the cellular manganese content. Using a murine model of wound infection, PBT2 in combination with zinc and colistin proved an efficacious treatment against streptococcal skin infection. These findings provide a foundation from which to investigate the utility of PBT2 and next-generation polymyxin antibiotics for the treatment of Gram-positive bacterial infections.
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Affiliation(s)
- David M. P. De Oliveira
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Bernhard Keller
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; (A.J.H.); (M.R.D.); (C.A.M.)
| | - Cheryl-Lynn Y. Ong
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Ibrahim M. El-Deeb
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia; (I.M.E.-D.); (M.v.I.)
| | - Gen Li
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Nadia Keller
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Lisa Bohlmann
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Andrew G. Turner
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Amanda J. Cork
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Thomas R. Jones
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - David L. Paterson
- Australian Infectious Diseases Research Centre, UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4006, Australia;
| | - Alastair G. McEwan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
| | - Mark R. Davies
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; (A.J.H.); (M.R.D.); (C.A.M.)
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; (A.J.H.); (M.R.D.); (C.A.M.)
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia; (I.M.E.-D.); (M.v.I.)
| | - Mark J. Walker
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (D.M.P.D.O.); (B.K.); (C.-L.Y.O.); (N.H.-P.); (G.L.); (N.K.); (L.B.); (S.B.); (A.G.T.); (A.J.C.); (A.G.M.)
- Correspondence: ; Tel.: +61-7-33461623
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Andrejko K, Whittles LK, Lewnard JA. Health-Economic Value of Vaccination Against Group A Streptococcus in the United States. Clin Infect Dis 2022; 74:983-992. [PMID: 34192307 DOI: 10.1093/cid/ciab597] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Vaccines are needed to reduce the burden of group A Streptococcus (GAS). We assessed the potential health-economic value of GAS vaccines achievable through prevention of invasive disease and acute upper respiratory infections in the United States. METHODS We estimated annual incidence of invasive GAS disease and associated costs incurred from hospitalization and management of long-term sequelae, as well as productivity losses resulting from acute illness, long-term disability, and mortality. We also estimated healthcare and productivity costs associated with GAS pharyngitis, sinusitis, and acute otitis media. We estimated costs averted by prevention of invasive disease and acute upper respiratory infections for vaccines with differing efficacy profiles; our base case considered vaccines meeting the World Health Organization Preferred Product Profile (WHO-PPP) with a 6-year average duration of protection. RESULTS Costs of invasive GAS disease and acute upper respiratory infections totaled $6.08 (95% confidence interval [CI], $5.33-$6.86) billion annually. Direct effects of vaccines meeting WHO-PPP characteristics and administered at ages 12 and 18 months would avert $609 (95% CI, $558-$663) million in costs annually, primarily by preventing noninvasive disease; with an additional dose at age 5 years, averted costs would total $869 (95% CI, $798-$945) million annually. Adult vaccination at age 65 years would avert $326 (95% CI, $271-$387) million in annual costs associated with invasive GAS disease. Indirect effects of vaccination programs reducing incidence of GAS diseases across all ages by 20% would avert roughly $1 billion in costs each year. CONCLUSIONS The economic burden of GAS is substantial. Our findings should inform prioritization of GAS vaccine development and evaluation.
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Affiliation(s)
- Kristin Andrejko
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Lilith K Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.,Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Modeling Methodology, School of Public Health, Imperial College London, London, United Kingdom
| | - Joseph A Lewnard
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, California, USA.,Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA.,Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, USA
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Ali A, Zeb I, Alouffi A, Zahid H, Almutairi MM, Ayed Alshammari F, Alrouji M, Termignoni C, Vaz IDS, Tanaka T. Host Immune Responses to Salivary Components - A Critical Facet of Tick-Host Interactions. Front Cell Infect Microbiol 2022; 12:809052. [PMID: 35372098 PMCID: PMC8966233 DOI: 10.3389/fcimb.2022.809052] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/04/2022] [Indexed: 12/15/2022] Open
Abstract
Tick sialome is comprised of a rich cocktail of bioactive molecules that function as a tool to disarm host immunity, assist blood-feeding, and play a vibrant role in pathogen transmission. The adaptation of the tick's blood-feeding behavior has lead to the evolution of bioactive molecules in its saliva to assist them to overwhelm hosts' defense mechanisms. During a blood meal, a tick secretes different salivary molecules including vasodilators, platelet aggregation inhibitors, anticoagulants, anti-inflammatory proteins, and inhibitors of complement activation; the salivary repertoire changes to meet various needs such as tick attachment, feeding, and modulation or impairment of the local dynamic and vigorous host responses. For instance, the tick's salivary immunomodulatory and cement proteins facilitate the tick's attachment to the host to enhance prolonged blood-feeding and to modulate the host's innate and adaptive immune responses. Recent advances implemented in the field of "omics" have substantially assisted our understanding of host immune modulation and immune inhibition against the molecular dynamics of tick salivary molecules in a crosstalk between the tick-host interface. A deep understanding of the tick salivary molecules, their substantial roles in multifactorial immunological cascades, variations in secretion, and host immune responses against these molecules is necessary to control these parasites. In this article, we reviewed updated knowledge about the molecular mechanisms underlying host responses to diverse elements in tick saliva throughout tick invasion, as well as host defense strategies. In conclusion, understanding the mechanisms involved in the complex interactions between the tick salivary components and host responses is essential to decipher the host defense mechanisms against the tick evasion strategies at tick-host interface which is promising in the development of effective anti-tick vaccines and drug therapeutics.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ismail Zeb
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hafsa Zahid
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fahdah Ayed Alshammari
- College of Sciences and Literature Microbiology, Nothern Border University, Rafha, Saudi Arabia
| | - Mohammed Alrouji
- College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Carlos Termignoni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
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Structural and biochemical characterization of Acinetobacter baumannii ZnuA. J Inorg Biochem 2022; 231:111787. [DOI: 10.1016/j.jinorgbio.2022.111787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/06/2022] [Indexed: 11/19/2022]
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Integrative Reverse Genetic Analysis Identifies Polymorphisms Contributing to Decreased Antimicrobial Agent Susceptibility in Streptococcus pyogenes. mBio 2022; 13:e0361821. [PMID: 35038921 PMCID: PMC8764543 DOI: 10.1128/mbio.03618-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Identification of genetic polymorphisms causing increased antibiotic resistance in bacterial pathogens traditionally has proceeded from observed phenotype to defined mutant genotype. The availability of large collections of microbial genome sequences that lack antibiotic susceptibility metadata provides an important resource and opportunity to obtain new information about increased antimicrobial resistance by a reverse genotype-to-phenotype bioinformatic and experimental workflow. We analyzed 26,465 genome sequences of Streptococcus pyogenes, a human pathogen causing 700 million infections annually. The population genomic data identified amino acid changes in penicillin-binding proteins 1A, 1B, 2A, and 2X with signatures of evolution under positive selection as potential candidates for causing decreased susceptibility to β-lactam antibiotics. Construction and analysis of isogenic mutant strains containing individual amino acid replacements in penicillin-binding protein 2X (PBP2X) confirmed that the identified residues produced decreased susceptibility to penicillin. We also discovered the first chimeric PBP2X in S. pyogenes and show that strains containing it have significantly decreased β-lactam susceptibility. The novel integrative reverse genotype-to-phenotype strategy presented is broadly applicable to other pathogens and likely will lead to new knowledge about antimicrobial agent resistance, a massive public health problem worldwide. IMPORTANCE The recent demonstration that naturally occurring amino acid substitutions in Streptococcus pyogenes PBP2X are sufficient to cause severalfold reduced susceptibility to multiple β-lactam antibiotics in vitro raises the concern that these therapeutic agents may become compromised. Substitutions in PBP2X are common first-step mutations that, with the incremental accumulation of additional adaptive mutations within the PBPs, can result in high-level resistance. Because β-lactam susceptibility testing is not routinely performed, the nature and extent of such substitutions within the PBPs of S. pyogenes are poorly characterized. To address this knowledge deficit, polymorphisms in the PBPs were identified among the most comprehensive cohort of S. pyogenes genome sequences investigated to date. The mutational processes and selective forces acting on the PBPs were assessed to identify specific substitutions likely to influence β-lactam susceptibility and to evaluate factors posited to be impediments to resistance emergence.
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Bengtsson RJ, Simpkin AJ, Pulford CV, Low R, Rasko DA, Rigden DJ, Hall N, Barry EM, Tennant SM, Baker KS. Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. Nat Microbiol 2022; 7:251-261. [PMID: 35102306 PMCID: PMC8813619 DOI: 10.1038/s41564-021-01054-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
AbstractShigella spp. are the leading bacterial cause of severe childhood diarrhoea in low- and middle-income countries (LMICs), are increasingly antimicrobial resistant and have no widely available licenced vaccine. We performed genomic analyses of 1,246 systematically collected shigellae sampled from seven countries in sub-Saharan Africa and South Asia as part of the Global Enteric Multicenter Study (GEMS) between 2007 and 2011, to inform control and identify factors that could limit the effectiveness of current approaches. Through contemporaneous comparison among major subgroups, we found that S. sonnei contributes ≥6-fold more disease than other Shigella species relative to its genomic diversity, and highlight existing diversity and adaptative capacity among S. flexneri that may generate vaccine escape variants in <6 months. Furthermore, we show convergent evolution of resistance against ciprofloxacin, the current WHO-recommended antimicrobial for the treatment of shigellosis, among Shigella isolates. This demonstrates the urgent need to integrate existing genomic diversity into vaccine and treatment plans for Shigella, providing a framework for the focused application of comparative genomics to guide vaccine development, and the optimization of control and prevention strategies for other pathogens relevant to public health policy considerations.
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Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis. Sci Rep 2022; 12:1515. [PMID: 35087075 PMCID: PMC8795270 DOI: 10.1038/s41598-022-04995-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/05/2022] [Indexed: 11/08/2022] Open
Abstract
Streptococcus consists of ecologically diverse species, some of which are important pathogens of humans and animals. We sought to quantify and compare the frequencies and characteristics of within-species recombination in the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes and Streptococcus suis. We used 1081, 1813 and 1204 publicly available genome sequences of each species, respectively. Based on their core genomes, S. agalactiae had the highest relative rate of recombination to mutation (11.5743) compared to S. pyogenes (1.03) and S. suis (0.57). The proportion of the species pan-genome that have had a history of recombination was 12.85%, 24.18% and 20.50% of the pan-genomes of each species, respectively. The composition of recombining genes varied among the three species, and some of the most frequently recombining genes are implicated in adhesion, colonization, oxidative stress response and biofilm formation. For each species, a total of 22.75%, 29.28% and 18.75% of the recombining genes were associated with prophages. The cargo genes of integrative conjugative elements and integrative and mobilizable elements contained genes associated with antimicrobial resistance and virulence. Homologous recombination and mobilizable pan-genomes enable the creation of novel combinations of genes and sequence variants, and the potential for high-risk clones to emerge.
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