The Genomics of Streptococcus Pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13

Fast and flexible bacterial genomic epidemiology with PopPUNK

(2019) John A. Lees et al.   GENOME RESEARCH

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

(2019) Rebecca A. Gladstone et al.   EBioMedicine

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

(2019) Stephanie W Lo et al.   LANCET INFECTIOUS DISEASES

Effectiveness of the seven-valent and thirteen-valent pneumococcal conjugate vaccines in England: The indirect cohort design, 2006–2018

(2019) Nick Andrews et al.   VACCINE

Rapid increase in non-vaccine serotypes causing invasive pneumococcal disease in England and Wales, 2000–17: a prospective national observational cohort study

(2018) Shamez N Ladhani et al.   LANCET INFECTIOUS DISEASES

Pneumococcal carriage in children and their household contacts six years after introduction of the 13-valent pneumococcal conjugate vaccine in England

(2018) Jo Southern et al.   PLoS One

Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes ofStreptococcus pneumoniae

(2018) Uri Obolski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of vaccines in fighting antimicrobial resistance (AMR)

(2018) Kathrin U. Jansen et al.   Human Vaccines & Immunotherapeutics

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

(2018) Taj Azarian et al.   PLoS Pathogens

Pneumococcal 23B Molecular Subtype Identified Using Whole Genome Sequencing

(2017) Georgia Kapatai et al.   Genome Biology and Evolution

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

(2017) John A Lees et al.   eLife

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

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

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

(2016) Marta Nascimento et al.   BIOINFORMATICS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Whole genome sequencing ofStreptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline

(2016) Georgia Kapatai et al.   PeerJ

MOST: a modified MLST typing tool based on short read sequencing

(2016) Rediat Tewolde et al.   PeerJ

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Effect of the 13-valent pneumococcal conjugate vaccine on invasive pneumococcal disease in England and Wales 4 years after its introduction: an observational cohort study

(2015) Pauline A Waight et al.   LANCET INFECTIOUS DISEASES

Five winters of pneumococcal serotype replacement in UK carriage following PCV introduction

(2015) Rebecca A. Gladstone et al.   VACCINE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Pneumococcal carriage in children and adults two years after introduction of the thirteen valent pneumococcal conjugate vaccine in England

(2014) Albert Jan van Hoek et al.   VACCINE

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A Longitudinal Study of Streptococcus pneumoniae Carriage in a Cohort of Infants and Their Mothers on the Thailand-Myanmar Border

(2012) Paul Turner et al.   PLoS One

Herd immunity and serotype replacement 4 years after seven-valent pneumococcal conjugate vaccination in England and Wales: an observational cohort study

(2011) Elizabeth Miller et al.   LANCET INFECTIOUS DISEASES

Effect of Pneumococcal Conjugate Vaccination on Serotype-Specific Carriage and Invasive Disease in England: A Cross-Sectional Study

(2011) Stefan Flasche et al.   PLOS MEDICINE