Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

[1]  V. Nizet,et al.  An Experimental Group A Streptococcus Vaccine That Reduces Pharyngitis and Tonsillitis in a Nonhuman Primate Model , 2019, mBio.

[2]  Jukka Corander,et al.  Fast and flexible bacterial genomic epidemiology with PopPUNK , 2018, bioRxiv.

[3]  Alexandre Souvorov,et al.  SKESA: strategic k-mer extension for scrupulous assemblies , 2018, Genome Biology.

[4]  K. Holt,et al.  Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae , 2018, bioRxiv.

[5]  J. Corander,et al.  Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli , 2018, bioRxiv.

[6]  Jukka Corander,et al.  pyseer: a comprehensive tool for microbial pangenome-wide association studies , 2018, bioRxiv.

[7]  V. Nizet,et al.  Virulence Role of the GlcNAc Side Chain of the Lancefield Cell Wall Carbohydrate Antigen in Non-M1-Serotype Group A Streptococcus , 2018, mBio.

[8]  M. Davies,et al.  Scarlet Fever Epidemic in China Caused by Streptococcus pyogenes Serotype M12: Epidemiologic and Molecular Analysis , 2018, EBioMedicine.

[9]  M. Gutmann,et al.  Frequency-dependent selection in vaccine-associated pneumococcal population dynamics , 2017, Nature Ecology & Evolution.

[10]  R. Lynfield,et al.  Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015 , 2017, mBio.

[11]  Andrea Beaton,et al.  Global, Regional, and National Burden of Rheumatic Heart Disease, 1990–2015 , 2017, The New England journal of medicine.

[12]  C. Buchrieser,et al.  Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila , 2017, PLoS genetics.

[13]  J. Coelho,et al.  Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing , 2017, PeerJ.

[14]  Daniel H. Huson,et al.  Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus , 2017, Nature.

[15]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[16]  R. Guy,et al.  Genome analysis following a national increase in Scarlet Fever in England 2014 , 2017, BMC Genomics.

[17]  Jukka Corander,et al.  Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations , 2016, bioRxiv.

[18]  M. Venkataswamy,et al.  Oral immunization of mice with recombinant rabies vaccine strain (ERAG3G) induces complete protection , 2015, Clinical and Experimental Vaccine Research.

[19]  G. Khazen,et al.  Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections , 2016, PloS one.

[20]  B. Shapiro,et al.  Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps , 2016, Scientific Reports.

[21]  Khalil Abudahab,et al.  Microreact: visualizing and sharing data for genomic epidemiology and phylogeography , 2016, Microbial genomics.

[22]  Cheryl P. Andam,et al.  Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule , 2016, mBio.

[23]  Julian Parkhill,et al.  Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.

[24]  David S. Wishart,et al.  PHASTER: a better, faster version of the PHAST phage search tool , 2016, Nucleic Acids Res..

[25]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[26]  Manisha Pandey,et al.  Combinatorial Synthetic Peptide Vaccine Strategy Protects against Hypervirulent CovR/S Mutant Streptococci , 2016, The Journal of Immunology.

[27]  Jukka Corander,et al.  Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes , 2016, Nature Communications.

[28]  Mark R. Davies,et al.  Invasive Group A Streptococcus Infection among Children, Rural Kenya , 2016, Emerging infectious diseases.

[29]  Michael D. Jones,et al.  Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom , 2015, mBio.

[30]  P. Brzoska,et al.  Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus , 2015, PloS one.

[31]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[32]  Andrew J. Page,et al.  Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.

[33]  Jacqueline A. Keane,et al.  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.

[34]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[35]  G. Dougan,et al.  Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance , 2014, Nature Genetics.

[36]  Michael W Parker,et al.  A systematic and functional classification of Streptococcus pyogenes that serves as a new tool for molecular typing and vaccine development. , 2014, The Journal of infectious diseases.

[37]  M. Sternberg,et al.  SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features , 2014, Journal of molecular biology.

[38]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[39]  V. Nizet,et al.  The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design. , 2014, Cell host & microbe.

[40]  A. Nerlich,et al.  Distribution of small native plasmids in Streptococcus pyogenes in India. , 2014, International journal of medical microbiology : IJMM.

[41]  M. Quail,et al.  Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination , 2014, mBio.

[42]  S. W. Long,et al.  Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences , 2014, Proceedings of the National Academy of Sciences.

[43]  Timothy C. Barnett,et al.  Disease Manifestations and Pathogenic Mechanisms of Group A Streptococcus , 2014, Clinical Microbiology Reviews.

[44]  N. Fittipaldi,et al.  Deriving Group A Streptococcus Typing Information from Short-Read Whole-Genome Sequencing Data , 2014, Journal of Clinical Microbiology.

[45]  M. Parker,et al.  Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration. , 2014, Journal of molecular biology.

[46]  Jukka Corander,et al.  Dense genomic sampling identifies highways of pneumococcal recombination , 2014, Nature Genetics.

[47]  M. Lipsitch,et al.  Population genomics of post-vaccine changes in pneumococcal epidemiology , 2013, Nature Genetics.

[48]  M. Pirmohamed,et al.  Emergence and global spread of epidemic healthcare-associated Clostridium difficile , 2012, Nature Genetics.

[49]  C. Gillen,et al.  Group a streptococcal vaccine candidates: potential for the development of a human vaccine. , 2013, Current topics in microbiology and immunology.

[50]  V. Nizet,et al.  Conserved anchorless surface proteins as group A streptococcal vaccine candidates , 2012, Journal of Molecular Medicine.

[51]  J. Musser,et al.  Multi High-Throughput Approach for Highly Selective Identification of Vaccine Candidates: the Group A Streptococcus Case , 2012, Molecular & Cellular Proteomics.

[52]  J. Corander,et al.  Detection of recombination events in bacterial genomes from large population samples , 2011, Nucleic acids research.

[53]  T. Penfound,et al.  New 30-valent M protein-based vaccine evokes cross-opsonic antibodies against non-vaccine serotypes of group A streptococci. , 2011, Vaccine.

[54]  Ying Gao,et al.  Bioinformatics Applications Note Sequence Analysis Cd-hit Suite: a Web Server for Clustering and Comparing Biological Sequences , 2022 .

[55]  J. Carapetis,et al.  Global emm type distribution of group A streptococci: systematic review and implications for vaccine development. , 2009, The Lancet. Infectious diseases.

[56]  J. Tagg,et al.  Streptococcal bacteriocins and the case for Streptococcus salivarius as model oral probiotics. , 2009, Future microbiology.

[57]  P. O’Toole,et al.  Model for substrate interactions in C5a peptidase from Streptococcus pyogenes: A 1.9 A crystal structure of the active form of ScpA. , 2009, Journal of molecular biology.

[58]  X. Didelot,et al.  A comparison of homologous recombination rates in bacteria and archaea , 2009, The ISME Journal.

[59]  R. Lynfield,et al.  Plasmid-Borne erm(T) from Invasive, Macrolide-Resistant Streptococcus pyogenes Strains , 2008, Antimicrobial Agents and Chemotherapy.

[60]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[61]  F. González-Candelas,et al.  Population structure and recombination in environmental isolates of Legionella pneumophila. , 2007, Environmental Microbiology.

[62]  M. Juliano,et al.  Towards a Vaccine Against Rheumatic Fever , 2006, Clinical & developmental immunology.

[63]  J. Zabriskie,et al.  Group A streptococcus (GAS) carbohydrate as an immunogen for protection against GAS infection. , 2006, The Journal of infectious diseases.

[64]  J. Carapetis,et al.  The global burden of group A streptococcal diseases. , 2005, The Lancet. Infectious diseases.

[65]  J. Langley,et al.  Safety and immunogenicity of 26-valent group a streptococcus vaccine in healthy adult volunteers. , 2005, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[66]  J. Musser,et al.  Evolutionary origin and emergence of a highly successful clone of serotype M1 group a Streptococcus involved multiple horizontal gene transfer events. , 2005, The Journal of infectious diseases.

[67]  W. Hanage,et al.  Using Multilocus Sequence Data To Define the Pneumococcus , 2005, Journal of bacteriology.

[68]  Sylvain Brisse,et al.  Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates , 2005, Journal of Clinical Microbiology.

[69]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[70]  James D. Campbell,et al.  Safety and immunogenicity of a recombinant multivalent group a streptococcal vaccine in healthy adults: phase 1 trial. , 2004, JAMA.

[71]  Adeline R. Whitney,et al.  Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[72]  M. Davies,et al.  Protection against group A streptococcus by immunization with J8-diphtheria toxoid: contribution of J8- and diphtheria toxoid-specific antibodies to protection. , 2003, The Journal of infectious diseases.

[73]  Brian G. Spratt,et al.  Multilocus Sequence Typing of Streptococcus pyogenes and the Relationships between emm Type and Clone , 2001, Infection and Immunity.

[74]  D. Jackson,et al.  New multi-determinant strategy for a group A streptococcal vaccine designed for the Australian Aboriginal population , 2000, Nature Medicine.

[75]  Nicholas P. J. Day,et al.  Multilocus Sequence Typing for Characterization of Methicillin-Resistant and Methicillin-Susceptible Clones ofStaphylococcus aureus , 2000, Journal of Clinical Microbiology.

[76]  P. Cleary,et al.  Intranasal immunization with C5a peptidase prevents nasopharyngeal colonization of mice by the group A Streptococcus , 1997, Infection and immunity.

[77]  S. Subbarao,et al.  Identification of isp, a locus encoding an immunogenic secreted protein conserved among group A streptococci , 1996, Infection and immunity.

[78]  R. Facklam,et al.  Sequencing emm-specific PCR products for routine and accurate typing of group A streptococci , 1996, Journal of clinical microbiology.

[79]  K. Timmis,et al.  The fibronectin binding domain of the Sfb protein adhesin of Streptococcus pyogenes occurs in many group A streptococci and does not cross-react with heart myosin. , 1994, Microbial pathogenesis.