Population genomics of post-vaccine changes in pneumococcal epidemiology
Nicholas J. Croucher,Jonathan A. Finkelstein,Jonathan A. Finkelstein,Stephen I. Pelton,Patrick K. Mitchell,Grace M. Lee,Grace M. Lee,Julian Parkhill,Stephen D. Bentley,Stephen D. Bentley,William P. Hanage,Marc Lipsitch +11 more
Reads0
Chats0
TLDR
Comparison of closely related isolates showed the role of transformation in facilitating capsule switching to non-vaccine serotypes and the emergence of drug resistance in the impact of the 7-valent pneumococcal conjugate vaccine, but recombination was found to occur at significantly different rates across the species.Abstract:
Whole genome sequencing of 616 asymptomatically carried pneumococci was used to study the impact of the 7-valent pneumococcal conjugate vaccine. Comparison of closely related isolates revealed the role of transformation in facilitating capsule switching to non-vaccine serotypes and the emergence of drug resistance. However, such recombination was found to occur at significantly different rates across the species, and the evolution of the population was primarily driven by changes in the frequency of distinct genotypes extant pre-vaccine. These alterations resulted in little overall effect on accessory genome composition at the population level, contrasting with the fall in pneumococcal disease rates after the vaccine’s introduction.read more
Citations
More filters
Journal ArticleDOI
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker,Thomas Abeel,Terrance Shea,Margaret Priest,Amr Abouelliel,Sharadha Sakthikumar,Christina A. Cuomo,Qiandong Zeng,Jennifer R. Wortman,Sarah Young,Ashlee M. Earl +10 more
TL;DR: Pilon is a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions, which is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains.
Journal ArticleDOI
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
Nicholas J. Croucher,Andrew J. Page,Thomas R. Connor,Aidan Delaney,Jacqueline A. Keane,Stephen D. Bentley,Julian Parkhill,Simon R. Harris +7 more
TL;DR: Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity.
Journal ArticleDOI
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
TL;DR: The Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains is presented, demonstrating that the approach exhibits unrivaled speed while maintaining the accuracy of existing methods.
Journal ArticleDOI
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health
Kathryn E. Holt,Heiman F. L. Wertheim,Ruth N. Zadoks,Stephen Baker,Chris A. Whitehouse,David A. B. Dance,Adam Jenney,Thomas R. Connor,Li Yang Hsu,Juliëtte A. Severin,Sylvain Brisse,Hanwei Cao,Jonathan J. Wilksch,Claire L. Gorrie,Mark B. Schultz,David J. Edwards,Kinh Van Nguyen,Trung Vu Nguyen,Trinh Tuyet Dao,Martijn Mensink,Vien Le Minh,Nguyen Thi Khanh Nhu,Constance Schultsz,Kuntaman Kuntaman,Paul N. Newton,Paul N. Newton,Catrin E. Moore,Catrin E. Moore,Richard A. Strugnell,Nicholas R. Thomson,Nicholas R. Thomson +30 more
TL;DR: The DNA sequence of K. pneumoniae isolates from around the world is determined and it is shown that there is a wide spectrum of diversity, including variation within shared sequences and gain and loss of whole genes, and there is an unrecognized association between the possession of specific gene profiles associated with virulence and antibiotic resistance.
Journal ArticleDOI
ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Xavier Didelot,Daniel J. Wilson +1 more
TL;DR: This work uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction and finds evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582.
References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Journal ArticleDOI
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
TL;DR: The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7 is presented, which implements a family of Markov chain Monte Carlo algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses.
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Related Papers (5)
Rapid Pneumococcal Evolution in Response to Clinical Interventions
Nicholas J. Croucher,Simon R. Harris,Christophe Fraser,Michael A. Quail,John Burton,Mark van der Linden,Lesley McGee,Anne von Gottberg,Jae-Hoon Song,Kwan Soo Ko,Bruno Pichon,Stephen Baker,Christopher M. Parry,Lotte Lambertsen,Dea Shahinas,Dylan R. Pillai,Timothy J. Mitchell,Gordon Dougan,Alexander Tomasz,Keith P. Klugman,Keith P. Klugman,Keith P. Klugman,Julian Parkhill,William P. Hanage,William P. Hanage,Stephen D. Bentley +25 more