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
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TLDR
How genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales is detailed.Abstract:
Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 (Spain23F-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphisms arising through horizontal sequence transfer. More than 700 recombinations were detected, with genes encoding major antigens frequently affected. Among these were 10 capsule-switching events, one of which accompanied a population shift as vaccine-escape serotype 19A isolates emerged in the USA after the introduction of the conjugate polysaccharide vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and macrolides was observed to occur on multiple occasions. This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales.read more
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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
Biological Roles of Glycans
TL;DR: It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences, as they are no different from other major macromolecular building blocks of life, simply more rapidly evolving and complex.
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
Polyamine transporter potABCD is required for virulence of encapsulated but not nonencapsulated Streptococcus pneumoniae
TL;DR: The pot operon is important for the regulation of protein expression and biofilm formation in both encapsulated and NCC1 nonencapsulated Streptococcus pneumoniae, however, in contrast to encapsulated pneumococcal strains, polyamine acquisition via the PotABCD is not required for MNZ67 murine colonization, persistence in the lungs, or full virulence in a model of OM.
Journal ArticleDOI
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
TL;DR: Artemis is presented as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation.
References
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Journal ArticleDOI
Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates
Katherine L. O'Brien,Lara J. Wolfson,James P. Watt,Emily Henkle,Maria Deloria-Knoll,Natalie McCall,Ellen Lee,Kim Mulholland,Orin S. Levine,Thomas Cherian +9 more
TL;DR: The burden of pneumococcal pneumonia is measured by applying the proportion of pneumonia cases caused by S pneumoniae derived from efficacy estimates from vaccine trials to WHO country-specific estimates of all-cause pneumonia cases and deaths, using disease incidence and case-fatality data from a systematic literature review.
Journal ArticleDOI
Evolution of MRSA During Hospital Transmission and Intercontinental Spread
Simon R. Harris,Edward J. Feil,Matthew T. G. Holden,Michael A. Quail,Emma K. Nickerson,Emma K. Nickerson,Narisara Chantratita,Susana Gardete,Susana Gardete,Ana Tavares,Nicholas P. J. Day,Nicholas P. J. Day,Jodi A. Lindsay,Jonathan D. Edgeworth,Jonathan D. Edgeworth,Hermínia de Lencastre,Hermínia de Lencastre,Julian Parkhill,Sharon J. Peacock,Sharon J. Peacock,Stephen D. Bentley +20 more
TL;DR: A high-throughput genomics approach is used to show that isolates of methicillin-resistant Staphylococcus aureus are precisely differentiated into a global geographic structure and suggest that intercontinental transmission has occurred for nearly four decades.
Journal ArticleDOI
Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes.
Stephen D. Bentley,David M. Aanensen,Angeliki Mavroidi,David L. Saunders,Ester Rabbinowitsch,Matthew Collins,Kathy Donohoe,David Harris,Lee Murphy,Michael A. Quail,Gabby Samuel,Ian C. Skovsted,Margit S. Kaltoft,Bart Barrell,Peter R. Reeves,Julian Parkhill,Brian G. Spratt +16 more
TL;DR: This work provides the sequences of the capsular biosynthetic genes of all 90 serotypes of Streptococcus pneumoniae and relate these to the known polysaccharide structures and patterns of immunological reactivity of typing sera, thereby providing the most complete understanding of the genetics and origins of bacterial poly Saccharide diversity.
Journal ArticleDOI
Nomenclature of Major Antimicrobial-Resistant Clones of Streptococcus pneumoniae Defined by the Pneumococcal Molecular Epidemiology Network
L. McGee,Linda K. McDougal,J. Zhou,Brian G. Spratt,Fred C. Tenover,R C George,Regine Hakenbeck,Waleria Hryniewicz,J. C. Lefévre,Alexander Tomasz,Keith P. Klugman +10 more
TL;DR: The nomenclature for 16 pneumococcal clones that have contributed to the increase in antimicrobial resistance worldwide and can serve as a prototype for the collaboration of scientists in identifying clones of important human pathogens and as a model for the development of other networks.
Journal ArticleDOI
Population snapshot of emergent Streptococcus pneumoniae serotype 19A in the United States, 2005.
Matthew R. Moore,Robert E. Gertz,Robyn L. Woodbury,Genevieve A Barkocy-Gallagher,William Schaffner,Catherine Lexau,Kenneth A. Gershman,Arthur Reingold,Monica M. Farley,Lee H. Harrison,James L. Hadler,Nancy M. Bennett,Ann Thomas,Lesley McGee,Tamara Pilishvili,Angela B. Brueggemann,Cynthia G. Whitney,James H. Jorgensen,Bernard Beall +18 more
TL;DR: PCV7 ineffectiveness against serotype 19A, antibiotic resistance, clonal expansion and emergence, and capsular switching have contributed to the genetic diversity of 19A and to its emergence as the predominant invasive pneumococcal serotype in the United States.
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