Now showing items 1-11 of 11

    • Detection of Recombination Events in Bacterial Genomes from Large Population Samples 

      Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas Jason; Connor, Thomas R.; Harris, Simon R.; Bentley, Stephen D.; Corander, Jukka (Oxford University Press, 2012)
      Analysis of important human pathogen populations is currently under transition toward whole-genome sequencing of growing numbers of samples collected on a global scale. Since recombination in bacteria is often an important ...
    • Distinct Effects on Diversifying Selection by Two Mechanisms of Immunity Against Streptococcus pneumoniae 

      Li, Yuan; Gierahn, Todd; Thompson, Claudette M.; Trzciński, Krzysztof; Ford, Christopher Burton; Croucher, Nicholas Jason; Gouveia, Paulo; Flechtner, Jessica B.; Malley, Richard; Lipsitch, Marc (Public Library of Science, 2012)
      Antigenic variation to evade host immunity has long been assumed to be a driving force of diversifying selection in pathogens. Colonization by Streptococcus pneumoniae, which is central to the organism's transmission and ...
    • Diversification of bacterial genome content through distinct mechanisms over different timescales 

      Croucher, Nicholas J.; Coupland, Paul G.; Stevenson, Abbie E.; Callendrello, Alanna; Bentley, Stephen D.; Hanage, William P. (Nature Pub. Group, 2014)
      Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled ...
    • Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection 

      Croucher, Nicholas J.; Mitchell, Andrea M.; Gould, Katherine A.; Inverarity, Donald; Barquist, Lars; Feltwell, Theresa; Fookes, Maria C.; Harris, Simon R.; Dordel, Janina; Salter, Susannah J.; Browall, Sarah; Zemlickova, Helena; Parkhill, Julian; Normark, Staffan; Henriques-Normark, Birgitta; Hinds, Jason; Mitchell, Tim J.; Bentley, Stephen D. (Public Library of Science, 2013)
      Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences ...
    • Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape 

      Croucher, Nicholas J.; Chewapreecha, Claire; Hanage, William P.; Harris, Simon R.; McGee, Lesley; van der Linden, Mark; Song, Jae-Hoon; Ko, Kwan Soo; de Lencastre, Herminia; Turner, Claudia; Yang, Fan; Sá-Leão, Raquel; Beall, Bernard; Klugman, Keith P.; Parkhill, Julian; Turner, Paul; Bentley, Stephen D. (Oxford University Press, 2014)
      The multidrug-resistant Streptococcus pneumoniae Taiwan19F-14, or PMEN14, clone was first observed with a 19F serotype, which is targeted by the heptavalent polysaccharide conjugate vaccine (PCV7). However, “vaccine escape” ...
    • Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity 

      Li, Yuan; Croucher, Nicholas J; Thompson, Claudette M; Trzciński, Krzysztof; Hanage, William P; Lipsitch, Marc (BioMed Central, 2015)
      Background: Understanding genetic determinants of a microbial phenotype generally involves creating and comparing isogenic strains differing at the locus of interest, but the naturally existing genomic and phenotypic ...
    • Population genomics of post-vaccine changes in pneumococcal epidemiology 

      Croucher, Nicholas J.; Finkelstein, Jonathan A.; Pelton, Stephen I.; Mitchell, Patrick K.; Lee, Grace M.; Parkhill, Julian; Bentley, Stephen D.; Hanage, William P.; Lipsitch, Marc (2013)
      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 ...
    • Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins 

      Croucher, Nicholas J.; Page, Andrew J.; Connor, Thomas R.; Delaney, Aidan J.; Keane, Jacqueline A.; Bentley, Stephen D.; Parkhill, Julian; Harris, Simon R. (Oxford University Press, 2015)
      The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple ...
    • Selective and Genetic Constraints on Pneumococcal Serotype Switching 

      Croucher, Nicholas J.; Kagedan, Lisa; Thompson, Claudette M.; Parkhill, Julian; Bentley, Stephen D.; Finkelstein, Jonathan A.; Lipsitch, Marc; Hanage, William P. (Public Library of Science, 2015)
      Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules (serotypes), which can be classified into “serogroups” based on cross-reactivity with certain ...
    • Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced 

      Chang, Qiuzhi; Stevenson, Abbie E; Croucher, Nicholas J; Lee, Grace M; Pelton, Stephen I; Lipsitch, Marc; Finkelstein, Jonathan A; Hanage, William P (BioMed Central, 2015)
      Background: The success of 7-valent pneumococcal conjugate vaccination (PCV-7) introduced to the US childhood immunization schedule in 2000 was partially offset by increases in invasive pneumococcal disease (IPD) and ...
    • Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone 

      Croucher, Nicholas J; Hanage, William P; Harris, Simon R; McGee, Lesley; van der Linden, Mark; de Lencastre, Herminia; Sá-Leão, Raquel; Song, Jae-Hoon; Ko, Kwan Soo; Beall, Bernard; Klugman, Keith P; Parkhill, Julian; Tomasz, Alexander; Kristinsson, Karl G; Bentley, Stephen D (BioMed Central, 2014)
      Background: Pneumococcal β-lactam resistance was first detected in Iceland in the late 1980s, and subsequently peaked at almost 25% of clinical isolates in the mid-1990s largely due to the spread of the internationally-d ...