Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome

(2018) Taj Azarian et al.   PLoS Pathogens

Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage

(2017) Sonja Lehtinen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Naturally Acquired Human Immunity to Pneumococcus Is Dependent on Antibody to Protein Antigens

(2017) Robert Wilson et al.   PLoS Pathogens

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

(2017) Jukka Corander et al.   Nature Ecology & Evolution

Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States

(2016) B.J. Metcalf et al.   CLINICAL MICROBIOLOGY AND INFECTION

Capsular Polysaccharide (CPS) Release by Serotype 3 Pneumococcal Strains Reduces the Protective Effect of Anti-Type 3 CPS Antibodies

(2015) Eun Hwa Choi et al.   Clinical and Vaccine Immunology

Effect of use of 13-valent pneumococcal conjugate vaccine in children on invasive pneumococcal disease in children and adults in the USA: analysis of multisite, population-based surveillance

(2015) Matthew R Moore et al.   LANCET INFECTIOUS DISEASES

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae

(2015) Eleanor R. Watkins et al.   PLoS Pathogens

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Serotype-specific effectiveness and correlates of protection for the 13-valent pneumococcal conjugate vaccine: a postlicensure indirect cohort study

(2014) Nick J Andrews et al.   LANCET INFECTIOUS DISEASES

Nasopharyngeal Carriage and Transmission of Streptococcus pneumoniae in American Indian Households after a Decade of Pneumococcal Conjugate Vaccine Use

(2014) Jonathan F. Mosser et al.   PLoS One

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

(2014) Rafal Mostowy et al.   PLoS Genetics

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Modified Opsonization, Phagocytosis, and Killing Assays To Measure Potentially Protective Antibodies against Pneumococcal Surface Protein A

(2013) Calvin C. Daniels et al.   Clinical and Vaccine Immunology

Comparative Immunogenicity and Efficacy of 13-Valent and 7-Valent Pneumococcal Conjugate Vaccines in Reducing Nasopharyngeal Colonization: A Randomized Double-Blind Trial

(2013) Ron Dagan et al.   CLINICAL INFECTIOUS DISEASES

Serum antibody responses to pneumococcal colonization in the first 2 years of life: results from an SE Asian longitudinal cohort study

(2013) P. Turner et al.   CLINICAL MICROBIOLOGY AND INFECTION

Surface Charge of Streptococcus pneumoniae Predicts Serotype Distribution

(2013) Yuan Li et al.   INFECTION AND IMMUNITY

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Early Trends for Invasive Pneumococcal Infections in Children After the Introduction of the 13-valent Pneumococcal Conjugate Vaccine

(2013) Sheldon L. Kaplan et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Multiple antigen-presenting system (MAPS) to induce comprehensive B- and T-cell immunity

(2013) F. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

(2013) Nicholas J. Croucher et al.   PLoS Genetics

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Niche and Neutral Effects of Acquired Immunity Permit Coexistence of Pneumococcal Serotypes

(2012) S. Cobey et al.   SCIENCE

A High-Resolution View of Genome-Wide Pneumococcal Transformation

(2012) Nicholas J. Croucher et al.   PLoS Pathogens

Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate

(2011) Romina Camilli et al.   BMC MICROBIOLOGY

Outpatient Antibiotic Prescribing and Nonsusceptible Streptococcus pneumoniae in the United States, 1996-2003

(2011) L. A. Hicks et al.   CLINICAL INFECTIOUS DISEASES

Serotype replacement in disease after pneumococcal vaccination

(2011) Daniel M Weinberger et al.   LANCET

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete

(2010) William P. Hanage et al.   Epidemics

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

High prevalence of multidrug-resistant Pneumococcal molecular epidemiology network clones among Streptococcus pneumoniae isolates from adult patients with community-acquired pneumonia in Japan

(2009) S. Imai et al.   CLINICAL MICROBIOLOGY AND INFECTION

Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

(2009) P. Romero et al.   JOURNAL OF BACTERIOLOGY

An Unusual Pneumococcal Sequence Type Is the Predominant Cause of Serotype 3 Invasive Disease in South Africa

(2009) Kedibone M. Mothibeli et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus

(2009) W. P. Hanage et al.   SCIENCE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Molecular characteristics of serotype 3 Streptococcus pneumoniae isolates among community-acquired pneumonia patients in Japan

(2008) Rie Isozumi et al.   JOURNAL OF INFECTION AND CHEMOTHERAPY

High Rates of Molecular Evolution in Hantaviruses

(2008) C. Ramsden et al.   MOLECULAR BIOLOGY AND EVOLUTION