Now showing items 21-38 of 38

    • Interim results of an ecological experiment — Conjugate vaccination against the pneumococcus and serotype replacement 

      Hausdorff, William P; Hanage, William P (Taylor & Francis, 2016)
      Streptococcus pneumoniae has more than 95 serotypes, each of which presumably can cause sepsis, meningitis, pneumonia, and acute otitis media. Pneumococcal conjugate vaccines (PCV) targeted against a limited number of ...
    • No coexistence for free: Neutral null models for multistrain pathogens 

      Lipsitch, Marc; Colijn, Caroline; Cohen, Ted; Hanage, William P.; Fraser, Christophe (Elsevier BV, 2009)
      In most pathogens, multiple strains are maintained within host populations. Quantifying the mechanisms underlying strain coexistence would aid public health planning and improve understanding of disease dynamics. We argue ...
    • Origin and Proliferation of Multiple-Drug Resistance in Bacterial Pathogens 

      Chang, Hsiao-Han; Cohen, Ted; Grad, Yonatan Hagai; Hanage, William P.; O, Thomas F.; Lipsitch, Marc (American Society for Microbiology, 2015)
      SUMMARY: Many studies report the high prevalence of multiply drug-resistant (MDR) strains. Because MDR infections are often significantly harder and more expensive to treat, they represent a growing public health threat. ...
    • Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus 

      Castillo-Ramírez, Santiago; Corander, Jukka; Marttinen, Pekka; Aldeljawi, Mona; Hanage, William P; Westh, Henrik; Boye, Kit; Gulay, Zeynep; Bentley, Stephen D; Parkhill, Julian; Holden, Matthew T; Feil, Edward J (BioMed Central, 2013)
      Background: Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic ...
    • A Pluralistic Account of Homology: Adapting the Models to the Data 

      Haggerty, Leanne S.; Jachiet, Pierre-Alain; Hanage, William P.; Fitzpatrick, David A.; Lopez, Philippe; O’Connell, Mary J.; Pisani, Davide; Wilkinson, Mark; Bapteste, Eric; McInerney, James O. (Oxford University Press, 2013)
      Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on ...
    • Pneumococcal Population Dynamics in the Conjugate Vaccine Era 

      Mitchell, Patrick Kevin (2016-05-05)
      The introduction of pneumococcal conjugate vaccines (PCVs) in the early years of the 21st century have led to significant changes in pneumococcal epidemiology. Using transmission modeling and genomics based approaches, ...
    • Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae 

      Croucher, Nicholas J.; Finkelstein, Jonathan A.; Pelton, Stephen I.; Parkhill, Julian; Bentley, Stephen D.; Lipsitch, Marc; Hanage, William P. (Nature Publishing Group, 2015)
      Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency ...
    • 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 ...
    • Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule 

      Chaguza, Chrispin; Andam, Cheryl P.; Harris, Simon R.; Cornick, Jennifer E.; Yang, Marie; Bricio-Moreno, Laura; Kamng’ona, Arox W.; Parkhill, Julian; French, Neil; Heyderman, Robert S.; Kadioglu, Aras; Everett, Dean B.; Bentley, Stephen D.; Hanage, William P. (American Society for Microbiology, 2016)
      ABSTRACT Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other ...
    • Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium 

      Willems, Rob J. L.; Top, Janetta; van Schaik, Willem; Leavis, Helen; Bonten, Marc; Sirén, Jukka; Hanage, William P.; Corander, Jukka (American Society of Microbiology, 2012)
      Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of ...
    • 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 ...
    • Understanding pneumococcal serotype 1 biology through population genomic analysis 

      Chaguza, Chrispin; Cornick, Jennifer E.; Harris, Simon R.; Andam, Cheryl P.; Bricio-Moreno, Laura; Yang, Marie; Yalcin, Feyruz; Ousmane, Sani; Govindpersad, Shanil; Senghore, Madikay; Ebruke, Chinelo; Du Plessis, Mignon; Kiran, Anmol M.; Pluschke, Gerd; Sigauque, Betuel; McGee, Lesley; Klugman, Keith P.; Turner, Paul; Corander, Jukka; Parkhill, Julian; Collard, Jean-Marc; Antonio, Martin; von Gottberg, Anne; Heyderman, Robert S.; French, Neil; Kadioglu, Aras; Hanage, William P.; Everett, Dean B.; Bentley, Stephen D. (BioMed Central, 2016)
      Background: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype ...
    • 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 ...
    • Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates 

      Salter, S. J.; Hinds, J.; Gould, K. A.; Lambertsen, L.; Hanage, William P.; Antonio, M.; Turner, P.; Hermans, P. W. M.; Bootsma, H. J.; O'Brien, K. L.; Bentley, S. D. (Society for General Microbiology, 2012)
      The capsule polysaccharide locus (cps) is the site of the capsule biosynthesis gene cluster in encapsulated Streptococcus pneumoniae. A set of pneumococcal samples and non-pneumococcal streptococci from Denmark, the Gambia, ...
    • Weak Epistasis May Drive Adaptation in Recombining Bacteria 

      Arnold, Brian John; Gutmann, Michael U.; Grad, Yonatan Hagai; Sheppard, Samuel K.; Corander, Jukka; Lipsitch, Marc; Hanage, William P. (Genetics Society of America, 2018)
      The impact of epistasis on the evolution of multi-locus traits depends on recombination. While sexually reproducing eukaryotes recombine so frequently that epistasis between polymorphisms is not considered to play a large ...
    • What is the Mechanism for Persistent Coexistence of Drug-susceptible and Drug-resistant Strains of Streptococcus pneumoniae? 

      Colijn, Caroline; Cohen, Ted; Fraser, Christophe; Hanage, William P.; Goldstein, Edward; Givon-Lavi, Noga; Dagan, Ron; Lipsitch, Marc (The Royal Society, 2009)
      The rise of antimicrobial resistance in many pathogens presents a major challenge to the treatment and control of infectious diseases. Furthermore, the observation that drug-resistant strains have risen to substantial ...
    • Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data 

      Worby, Colin J.; Lipsitch, Marc; Hanage, William P. (Public Library of Science, 2014)
      The prospect of using whole genome sequence data to investigate bacterial disease outbreaks has been keenly anticipated in many quarters, and the large-scale collection and sequencing of isolates from cases is becoming ...