4.7 Article

Phylogenomic insights into evolutionary trajectories of multidrug resistant S. pneumoniae CC271 over a period of 14 years in China

Related references

Note: Only part of the references are listed.
Article Immunology

Effect of pneumococcal conjugate vaccine availability on Streptococcus pneumoniae infections and genetic recombination in Zhejiang, China from 2009 to 2019

Xueqing Wu et al.

Summary: This study evaluated the impact of interrupted PCV availability on pneumococcal pneumonia and genetic variation of Streptococcus pneumoniae. The findings showed that interrupted PCV availability affected the prevalence of pneumococcal disease and pneumococcal genome variation.

EMERGING MICROBES & INFECTIONS (2022)

Article Infectious Diseases

Effect of pneumococcal conjugate vaccines and SARS-CoV-2 on antimicrobial resistance and the emergence of Streptococcus pneumoniae serotypes with reduced susceptibility in Spain, 2004-20: a national surveillance study

Julio Sempere et al.

Summary: The study reveals a decline in serotypes included in PCV7 and PCV13 after their introduction in Spain, but an increase in non-PCV13 serotypes (mainly 11A, 24F, and 23B) that are not susceptible to PCV13, posing a threat to antibiotic resistance. An increase in pneumococcal strains with reduced susceptibility to 13-lactams and erythromycin was observed in 2020, coinciding with the emergence of SARS-CoV-2.

LANCET MICROBE (2022)

Article Immunology

Molecular Characterization Based on Whole-Genome Sequencing of Streptococcus pneumoniae in Children Living in Southwest China During 2017-2019

Ziyi Yan et al.

Summary: This study investigated the prevalence and molecular characteristics of Streptococcus pneumoniae isolated from children in Southwest China from 2017 to 2019. The most common serotypes were identified as 19F, 19A, 6B, 6A, and 14, with a PCV13 coverage rate of 77.3%. High rates of resistance to erythromycin and clindamycin were observed. Different serotypes and clades varied in the carriage of virulence and resistance genes, with serotype 19F/ST271 showing higher antibiotic resistance and a higher likelihood of carrying pilus and other virulence genes.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2021)

Review Genetics & Heredity

Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics

Stephen D. Bentley et al.

Summary: Vaccines are powerful tools in infectious disease prevention, but often fail to eradicate pathogens completely, leading to the emergence of vaccine-evading strains. Genomics is being widely adopted as the optimal approach for pathogen surveillance, enabling early identification of high-risk strains and the potential to forecast their emergence for immediate intervention.

GENOME MEDICINE (2021)

Article Biochemical Research Methods

SciPy 1.0: fundamental algorithms for scientific computing in Python

Pauli Virtanen et al.

NATURE METHODS (2020)

Article Biochemistry & Molecular Biology

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Sebastian Duchene et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemical Research Methods

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Evolutionary Biology

bModelTest: Bayesian phylogenetic site model averaging and model comparison

Remco R. Bouckaert et al.

BMC EVOLUTIONARY BIOLOGY (2017)

Review Microbiology

Within-host evolution of bacterial pathogens

Xavier Didelot et al.

NATURE REVIEWS MICROBIOLOGY (2016)

Article Biochemical Research Methods

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page et al.

BIOINFORMATICS (2015)

Review Microbiology

The application of genomics to tracing bacterial pathogen transmission

Nicholas J. Croucher et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Nicholas J. Croucher et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Evolutionary Biology

Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

Nicholas J. Croucher et al.

GENOME BIOLOGY AND EVOLUTION (2014)

Article Biochemistry & Molecular Biology

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

Guy Baele et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Microbiology

Molecular mechanisms of β-lactam resistance in Streptococcus pneumoniae

Regine Hakenbeck et al.

FUTURE MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

Guy Baele et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Immunology

Shifting Genetic Structure of Invasive Serotype 19A Pneumococci in the United States

Bernard W. Beall et al.

JOURNAL OF INFECTIOUS DISEASES (2011)

Article Immunology

Carried Pneumococci in Massachusetts Children The Contribution of Clonal Expansion and Serotype Switching

William P. Hanage et al.

PEDIATRIC INFECTIOUS DISEASE JOURNAL (2011)

Article Biochemical Research Methods

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

Alexandre P. Francisco et al.

BMC BIOINFORMATICS (2009)

Article Biotechnology & Applied Microbiology

Genome-wide dissection of globally emergent multi-drug resistant serotype 19A Streptococcus pneumoniae

Dylan R. Pillai et al.

BMC GENOMICS (2009)

Article Immunology

Population snapshot of emergent streptococcus pneumoniae serotype 19A in the United States, 2005

Matthew R. Moore et al.

JOURNAL OF INFECTIOUS DISEASES (2008)

Article Biochemistry & Molecular Biology

Bayesian coalescent inference of past population dynamics from molecular sequences

AJ Drummond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Infectious Diseases

The successful clone:: the vector of dissemination of resistance in Streptococcus pneumoniae

KP Klugman

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2002)