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Evolutionary Genetics of Streptococcus pneumoniae
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Evolutionary Genetics of Streptococcus pneumoniae

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (31 July 2019) | Viewed by 18509

Special Issue Editors

Dr. Eric Miller

E-Mail Website
Guest Editor
Haverford College, Haverford, PA, USA
Interests: streptococcus; recombination; bacteriocins; quorum sensing; evolution; competence; antagonistic interactions; pathogenicity
Dr. Lauren Cowley

E-Mail Website
Co-Guest Editor
Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
Interests: genomics; Streptococcus pneumonia; GWAS; recombination; evolution; public health; antibiotic resistance

Special Issue Information

Dear Colleagues,

Understanding the biology of the pathogen Streptococcus pneumoniae will allow for improved public health policies for a disease that kills up to 1 million children each year globally. We must also understand how this biology changes through time to help prevent pneumococcal infections and deaths; how does S. pneumoniae evolve? Additionally, we can gain insight into general trends of genomic evolution in bacteria using pneumococcus as a genomic model organism due its particular set of characteristics: its natural competence and high rates of recombination; the large number of diverse, sequenced genomes, especially through The Global Pneumococcal Sequencing Project; and the defined selection pressures acting on pneumococcal populations in the form of antimicrobial resistance and vaccine-serotype replacement.

We are calling for articles for a Special Issue on the Evolutionary Genetics of S. pneumoniae that will both look towards the future (encompassing original research articles and short-communications on the biology and dynamics of pnuemococcal genetics and genomics) and examine the current state of the field through review articles. We are interested in articles examining any aspect of pneumococcus evolution, such as temporal changes, differences between populations, or evidence of adaption. Explorations of the evolution of microbial community dynamics, competence, antagonistic interactions (such as bacteriocins), antimicrobial resistance, and serotype replacement would all be considered for in this issue, provided they have explicit connections to genome evolution. Additionally, we welcome explorations into the mechanics of genome evolution, such as the role of repetitive units, plasmids, pathogenicity islands, and ICEs (integrative and conjugative elements) in how S. pneumoniae evolves.

Dr. Eric Miller
Dr. Lauren Cowley
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genomics
  • Evolutionary biology
  • Genome diversity and evolution
  • Adaptation
  • Serotype switching and replacement
  • Antimicrobial resistance
  • Competence
  • Recombination

Published Papers (4 papers)

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Research

12 pages, 3031 KiB  
Article
Evolution of Streptococcus pneumoniae Serotype 3 in England and Wales: A Major Vaccine Evader
by Natalie Groves, Carmen L. Sheppard, David Litt, Samuel Rose, Ana Silva, Nina Njoku, Sofia Rodrigues, Zahin Amin-Chowdhury, Nicholas Andrews, Shamez Ladhani and Norman K. Fry
Genes 2019, 10(11), 845; https://doi.org/10.3390/genes10110845 - 25 Oct 2019
Cited by 43 | Viewed by 5503
Abstract
Despite its inclusion in pneumococcal conjugate vaccine 13 (PCV13), Streptococcus pneumoniae serotype 3 remains a major cause of invasive pneumococcal disease in England and Wales. Previous studies have indicated that there are distinct lineages within serotype 3 clonal complex 180 and the clade [...] Read more.
Despite its inclusion in pneumococcal conjugate vaccine 13 (PCV13), Streptococcus pneumoniae serotype 3 remains a major cause of invasive pneumococcal disease in England and Wales. Previous studies have indicated that there are distinct lineages within serotype 3 clonal complex 180 and the clade distributions have shifted in recent years with the emergence of clade II. We undertook whole genome sequencing and genomic analysis of 616 serotype 3 isolates from England and Wales between 2003 and 2018, including invasive and carriage isolates. Our investigations showed that clade II has expanded since 2014 and now represents 50% of serotype 3 invasive pneumococcal disease (IPD) isolates in England and Wales. Genomic analysis of antibiotic resistance and protein antigen genes showed that distinct profiles are present within the clades which could account for the recent emergence of this clade. This investigation highlights the importance and utility of routine whole genome sequencing and its ability to identify new and emerging variation at the single nucleotide level which informs surveillance and will impact future vaccine development. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Streptococcus pneumoniae)
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21 pages, 3004 KiB  
Article
Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae
by Min Jung Kwun, Marco R. Oggioni, Stephen D. Bentley, Christophe Fraser and Nicholas J. Croucher
Genes 2019, 10(9), 707; https://doi.org/10.3390/genes10090707 - 13 Sep 2019
Cited by 3 | Viewed by 3288
Abstract
A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the [...] Read more.
A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Streptococcus pneumoniae)
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17 pages, 2046 KiB  
Article
The Genomics of Streptococcus pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13
by Carmen L. Sheppard, Natalie Groves, Nicholas Andrews, David J. Litt, Norman K. Fry, Jo Southern and Elizabeth Miller
Genes 2019, 10(9), 687; https://doi.org/10.3390/genes10090687 - 06 Sep 2019
Cited by 14 | Viewed by 3884
Abstract
We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N = 346), 2010 (N = 127), 2013 (N = 153), 2016 (N = 187) and [...] Read more.
We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N = 346), 2010 (N = 127), 2013 (N = 153), 2016 (N = 187) and 2018 (N = 64) in UK households which covers the period pre-PCV7 to post-PCV13 implementation. The genomic lineages seen in the population were determined using multi-locus sequence typing (MLST) and PopPUNK (Population Partitioning Using Nucleotide K-mers) which was used for local and global comparisons. A Roary core genome alignment of all the carriage genomes was used to investigate phylogenetic relationships between the lineages. The results showed an influx of previously undetected sequence types after vaccination associated with non-vaccine serotypes. A small number of lineages persisted throughout, associated with both non-vaccine and vaccine types (such as ST199), or that could be an example of serotype switching from vaccine to non-vaccine types (ST177). Serotype 3 persisted throughout the study years, represented by ST180 and Global Pneumococcal Sequencing Cluster (GPSC) 12; the local PopPUNK analysis and core genome maximum likelihood phylogeny separated them into two clades, one of which is only seen in later study years. The genomic data showed that serotype replacement in the carriage studies was mostly due to a change in genotype as well as serotype, but that some important genetic lineages, previously associated with vaccine types, persisted. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Streptococcus pneumoniae)
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15 pages, 3304 KiB  
Article
Three New Integration Vectors and Fluorescent Proteins for Use in the Opportunistic Human Pathogen Streptococcus pneumoniae
by Lance E. Keller, Anne-Stéphanie Rueff, Jun Kurushima and Jan-Willem Veening
Genes 2019, 10(5), 394; https://doi.org/10.3390/genes10050394 - 22 May 2019
Cited by 20 | Viewed by 5387
Abstract
Here, we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogen Streptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform (PEP), employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple [...] Read more.
Here, we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogen Streptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform (PEP), employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple cloning sites allowing for fast and interchangeable cloning. PEP plasmids replicate in Escherichia coli and harbor integration sites that have homology in a large set of pneumococcal strains, including recent clinical isolates. In addition, several options of antibiotic resistance markers are available, even allowing for selection in multidrug resistant clinical isolates. The transformation efficiency of these PEP vectors as well as their ability to be expressed simultaneously was tested. Two of the three PEP vectors share homology of the integration regions with over half of the S. pneumoniae genomes examined. Transformation efficiency varied among PEP vectors based on the length of the homology regions, but all were highly transformable and can be integrated simultaneously in strain D39V. Vectors used for pneumococcal cloning are an important tool for researchers for a wide range of uses. The PEP vectors described are of particular use because they have been designed to allow for easy transfer of genes between vectors as well as integrating into transcriptionally silent areas of the chromosome. In addition, we demonstrate the successful production of several new spectrally distinct fluorescent proteins (mTurquoise2, mNeonGreen and mScarlet-I) from the PEP vectors. The PEP vectors and newly described fluorescent proteins will expand the genetic toolbox for pneumococcal researchers and aid future discoveries. Full article
(This article belongs to the Special Issue Evolutionary Genetics of Streptococcus pneumoniae)
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