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Schiavolin L, Lakhloufi D, Botquin G, Deneubourg G, Bruyns C, Steinmetz J, Henrot C, Delforge V, Smeesters PR, Botteaux A. Efficient and rapid one-step method to generate gene deletions in Streptococcus pyogenes. Microbiol Spectr 2024; 12:e0118524. [PMID: 39162539 PMCID: PMC11448258 DOI: 10.1128/spectrum.01185-24] [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: 05/13/2024] [Accepted: 06/29/2024] [Indexed: 08/21/2024] Open
Abstract
Streptococcus pyogenes or Group A Streptococcus (GAS) remains a significant infectious problem around the world, particularly in low- and middle-income settings. Moreover, a recent invasive GAS infection (iGAS) upsurge has been observed in high-income settings. However, to date, no vaccine is available. Finding a good vaccine antigen and understanding the role of virulence factors in GAS infections have been hampered, in part, by technical difficulties to transform the many different strains and generate knockout mutants. Using colE1-type plasmid as a suicide vector, we have set up a method allowing the generation of non-polar mutants of GAS in 3 days. IMPORTANCE Group A Streptococcus (GAS) is a major human pathogen, causing diseases ranging from mild and superficial infections of the skin and pharyngeal epithelium to severe systemic and invasive diseases. Since June 2022, several European countries, the US, and Australia are facing an upsurge of invasive life-threatening GAS infections. Finding a good vaccine antigen and understanding the role of virulence factors in GAS infections have been hampered, in part, by technical difficulties to transform the many different GAS strains and generate knockout mutants. Moreover, these tools must be adapted to a large range of different strains, since GAS are divided into more than 260 emm-types (M-type). We have set up a method allowing the generation of non-polar mutants of GAS in 3 days and in diverse backgrounds, which contrasts with previously published protocols.
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Affiliation(s)
- Lionel Schiavolin
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Dalila Lakhloufi
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Gwenaelle Botquin
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Geoffrey Deneubourg
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Corentin Bruyns
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Jenny Steinmetz
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Charlotte Henrot
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Valérie Delforge
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
| | - Pierre R. Smeesters
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
| | - Anne Botteaux
- Molecular Bacteriology, European Plotkin Institute for Vaccinology (EPIV), Université libre de Bruxelles, Brussels, Belgium
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Mårli MT, Oppegaard O, Porcellato D, Straume D, Kjos M. Genetic modification of Streptococcus dysgalactiae by natural transformation. mSphere 2024; 9:e0021424. [PMID: 38904369 PMCID: PMC11288034 DOI: 10.1128/msphere.00214-24] [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: 03/18/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Streptococcus dysgalactiae is an emerging human and animal pathogen. Functional studies of genes involved in virulence of S. dysgalactiae and other pyogenic group streptococci are often hampered by limited genetic tractability. It is known that pyogenic streptococci carry genes required for competence for natural transformation; however, in contrast to other streptococcal subgroups, there is limited evidence for gene transfer by natural transformation in these bacteria. In this study, we systematically assessed the genomes of 179 S. dysgalactiae strains of both human and animal origins (subsp. equisimilis and dysgalactiae, respectively) for the presence of genes required for natural transformation. While a considerable fraction of the strains contained inactive genes, the majority (64.2%) of the strains had an intact gene set. In selected strains, we examined the dynamics of competence activation after addition of competence-inducing pheromones using transcriptional reporter assays and exploratory RNA-seq. Based on these findings, we were able to establish a protocol allowing us to utilize natural transformation to construct deletion mutants by allelic exchange in several S. dysgalactiae strains of both subspecies. As part of the work, we deleted putative lactose utilization genes to study their role in growth on lactose. The data presented here provide new knowledge on the potential of horizonal gene transfer by natural transformation in S. dysgalactiae and, importantly, demonstrates the possibility to exploit natural transformation for genetic engineering in these bacteria. IMPORTANCE Numerous Streptococcus spp. exchange genes horizontally through natural transformation, which also facilitates efficient genetic engineering in these organisms. However, for the pyogenic group of streptococci, including the emerging pathogen Streptococcus dysgalactiae, there is limited experimental evidence for natural transformation. In this study, we demonstrate that natural transformation in vitro indeed is possible in S. dysgalactiae strains under optimal conditions. We utilized this method to perform gene deletion through allelic exchange in several strains, thereby paving the way for more efficient gene engineering methods in pyogenic streptococci.
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Affiliation(s)
- Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oddvar Oppegaard
- Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Alves J, Rand JD, Johnston ABE, Bowen C, Lynskey NN. Methylome-dependent transformation of emm1 group A streptococci. mBio 2023; 14:e0079823. [PMID: 37427929 PMCID: PMC10470502 DOI: 10.1128/mbio.00798-23] [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: 04/06/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Genetic intractability presents a fundamental barrier to the manipulation of bacteria, hindering advancements in microbiological research. Group A Streptococcus (GAS), a lethal human pathogen currently associated with an unprecedented surge of infections worldwide, exhibits poor genetic tractability attributed to the activity of a conserved type 1 restriction modification system (RMS). RMS detect and cleave specific target sequences in foreign DNA that are protected in host DNA by sequence-specific methylation. Overcoming this "restriction barrier" thus presents a major technical challenge. Here, we demonstrate for the first time that different RMS variants expressed by GAS give rise to genotype-specific and methylome-dependent variation in transformation efficiency. Furthermore, we show that the magnitude of impact of methylation on transformation efficiency elicited by RMS variant TRDAG, encoded by all sequenced strains of the dominant and upsurge-associated emm1 genotype, is 100-fold greater than for all other TRD tested and is responsible for the poor transformation efficiency associated with this lineage. In dissecting the underlying mechanism, we developed an improved GAS transformation protocol, whereby the restriction barrier is overcome by the addition of the phage anti-restriction protein Ocr. This protocol is highly effective for TRDAG strains including clinical isolates representing all emm1 lineages and will expedite critical research interrogating the genetics of emm1 GAS, negating the need to work in an RMS-negative background. These findings provide a striking example of the impact of RMS target sequence variation on bacterial transformation and the importance of defining lineage-specific mechanisms of genetic recalcitrance. IMPORTANCE Understanding the mechanisms by which bacterial pathogens are able to cause disease is essential to enable the targeted development of novel therapeutics. A key experimental approach to facilitate this research is the generation of bacterial mutants, through either specific gene deletions or sequence manipulation. This process relies on the ability to transform bacteria with exogenous DNA designed to generate the desired sequence changes. Bacteria have naturally developed protective mechanisms to detect and destroy invading DNA, and these systems severely impede the genetic manipulation of many important pathogens, including the lethal human pathogen group A Streptococcus (GAS). Many GAS lineages exist, of which emm1 is dominant among clinical isolates. Based on new experimental evidence, we identify the mechanism by which transformation is impaired in the emm1 lineage and establish an improved and highly efficient transformation protocol to expedite the generation of mutants.
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Affiliation(s)
- Joana Alves
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Joshua D. Rand
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Alix B. E. Johnston
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Connor Bowen
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
| | - Nicola N. Lynskey
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, United Kingdom
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Boukthir S, Gaudu P, Faili A, Kayal S. pBFK, a new thermosensitive shuttle vector for Streptococcus pyogenes gene deletion by homologous recombination. Heliyon 2023; 9:e16720. [PMID: 37346331 PMCID: PMC10279790 DOI: 10.1016/j.heliyon.2023.e16720] [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: 09/04/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
Streptococcus pyogenes, or Group A Streptococcus (GAS), is a major human pathogen for which genetic manipulation remains an ongoing challenge. We created a new temperature-sensitive plasmid pBFK expressing spectinomycin resistance adapted to homologous recombination procedure to perform a complete gene deletion in GAS. Herein the mutagenesis strategy with pBFK was performed in a highly virulent GAS emm3 genotype.
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Affiliation(s)
- S. Boukthir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France
- Inserm, CIC 1414, Rennes, France
| | - P. Gaudu
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - A. Faili
- Inserm, CIC 1414, Rennes, France
- OSS- Oncogenesis, Stress, Signaling, INSERM 1242, Rennes, France
- Université de Rennes, Faculté de Pharmacie, Rennes, France
| | - S. Kayal
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière, Rennes, France
- Inserm, CIC 1414, Rennes, France
- OSS- Oncogenesis, Stress, Signaling, INSERM 1242, Rennes, France
- Université de Rennes, Faculté de Médecine, Rennes, France
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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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Abstract
The nasopharynx and the skin are the major oxygen-rich anatomical sites for colonization by the human pathogen Streptococcus pyogenes (group A Streptococcus [GAS]). To establish infection, GAS must survive oxidative stress generated during aerobic metabolism and the release of reactive oxygen species (ROS) by host innate immune cells. Glutathione is the major host antioxidant molecule, while GAS is glutathione auxotrophic. Here, we report the molecular characterization of the ABC transporter substrate binding protein GshT in the GAS glutathione salvage pathway. We demonstrate that glutathione uptake is critical for aerobic growth of GAS and that impaired import of glutathione induces oxidative stress that triggers enhanced production of the reducing equivalent NADPH. Our results highlight the interrelationship between glutathione assimilation, carbohydrate metabolism, virulence factor production, and innate immune evasion. Together, these findings suggest an adaptive strategy employed by extracellular bacterial pathogens to exploit host glutathione stores for their own benefit.
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Brouwer S, Barnett TC, Ly D, Kasper KJ, De Oliveira DMP, Rivera-Hernandez T, Cork AJ, McIntyre L, Jespersen MG, Richter J, Schulz BL, Dougan G, Nizet V, Yuen KY, You Y, McCormick JK, Sanderson-Smith ML, Davies MR, Walker MJ. Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes. Nat Commun 2020; 11:5018. [PMID: 33024089 PMCID: PMC7538557 DOI: 10.1038/s41467-020-18700-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 09/01/2020] [Indexed: 02/03/2023] Open
Abstract
The re-emergence of scarlet fever poses a new global public health threat. The capacity of North-East Asian serotype M12 (emm12) Streptococcus pyogenes (group A Streptococcus, GAS) to cause scarlet fever has been linked epidemiologically to the presence of novel prophages, including prophage ΦHKU.vir encoding the secreted superantigens SSA and SpeC and the DNase Spd1. Here, we report the molecular characterization of ΦHKU.vir-encoded exotoxins. We demonstrate that streptolysin O (SLO)-induced glutathione efflux from host cellular stores is a previously unappreciated GAS virulence mechanism that promotes SSA release and activity, representing the first description of a thiol-activated bacterial superantigen. Spd1 is required for resistance to neutrophil killing. Investigating single, double and triple isogenic knockout mutants of the ΦHKU.vir-encoded exotoxins, we find that SpeC and Spd1 act synergistically to facilitate nasopharyngeal colonization in a mouse model. These results offer insight into the pathogenesis of scarlet fever-causing GAS mediated by prophage ΦHKU.vir exotoxins.
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Affiliation(s)
- Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Timothy C Barnett
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Diane Ly
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Katherine J Kasper
- Department of Microbiology and Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Tania Rivera-Hernandez
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Johanna Richter
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Benjamin L Schulz
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Victor Nizet
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, Hong Kong, China
| | - Yuanhai You
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - John K McCormick
- Department of Microbiology and Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
| | - Martina L Sanderson-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Mark R Davies
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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