Now showing items 1-20 of 38

    • Biomedical Ph.D. Students Enrolled in Two Elite Universities in the United Kingdom and the United States Report Adopting Multiple Learning Relationships 

      Kemp, Matthew W.; Lazarus, Benjamin M.; Perron, Gabriel G.; Hanage, William P.; Chapman, Elaine (Public Library of Science, 2014)
      Objective: The ability to form multiple learning relationships is a key element of the doctoral learning environment in the biomedical sciences. Of these relationships, that between student and supervisor has long been ...
    • Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen 

      Grad, Yonatan Hagai; Godfrey, Paul; Cerquiera, Gustavo C.; Mariani-Kurkdjian, Patricia; Gouali, Malika; Bingen, Edouard; Shea, Terrence P.; Haas, Brian J.; Griggs, Allison; Young, Sarah; Zeng, Qiandong; Lipsitch, Marc; Waldor, Matthew K; Weill, François-Xavier; Wortman, Jennifer R.; Hanage, William P. (American Society of Microbiology, 2013)
      The large outbreak of diarrhea and hemolytic uremic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli O104:H4 in Europe from May to July 2011 highlighted the potential of a rarely identified E. coli serogroup ...
    • Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes 

      Chewapreecha, Claire; Marttinen, Pekka; Croucher, Nicholas J.; Salter, Susannah J.; Harris, Simon R.; Mather, Alison E.; Hanage, William P.; Goldblatt, David; Nosten, Francois H.; Turner, Claudia; Turner, Paul; Bentley, Stephen D.; Parkhill, Julian (Public Library of Science, 2014)
      Traditional genetic association studies are very difficult in bacteria, as the generally limited recombination leads to large linked haplotype blocks, confounding the identification of causative variants. Beta-lactam ...
    • 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 ...
    • The Distribution of Pairwise Genetic Distances: A Tool for Investigating Disease Transmission 

      Worby, Colin J.; Chang, Hsiao-Han; Hanage, William P.; Lipsitch, Marc (Genetics Society of America, 2014)
      Whole-genome sequencing of pathogens has recently been used to investigate disease outbreaks and is likely to play a growing role in real-time epidemiological studies. Methods to analyze high-resolution genomic data in ...
    • Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening 

      Croucher, Nicholas J.; Campo, Joseph J.; Le, Timothy Q.; Liang, Xiaowu; Bentley, Stephen D.; Hanage, William P.; Lipsitch, Marc (Proceedings of the National Academy of Sciences, 2017)
      Characterizing the immune response to pneumococcal proteins is critical in understanding this bacterium's epidemiology and vaccinology. Probing a custom-designed proteome microarray with sera from 35 healthy US adults ...
    • 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 ...
    • Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era 

      Lee, Grace; Huang, Susan Jen; Rifas-Shiman, Sheryl Lynn; Hinrichsen, Virginia; Pelton, Stephen I; Kleinman, Kenneth Paul; Hanage, William P.; Lipsitch, Marc; McAdam, Alexander John; Finkelstein, Jonathan Arie (Springer Science + Business Media, 2009)
      BACKGROUND: The incidence of community-associated methicillin-resistant Staphylococcus aureus (MRSA) has risen dramatically in the U.S., particularly among children. Although Streptococcus pneumoniae colonization has been ...
    • Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003–2011 

      Goldstein, Edward; Greene, Sharon K; Olson, Donald R; Hanage, William P; Lipsitch, Marc (John Wiley & Sons, Ltd, 2015)
      Background: Hospitalization burden associated with influenza and respiratory syncytial virus (RSV) is uncertain due to ambiguity in the inference methodologies employed for its estimation. Objectives: Utilization of a new ...
    • 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” ...
    • Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti 

      Katz, Lee S.; Petkau, Aaron; Beaulaurier, John; Tyler, Shaun; Antonova, Elena S.; Turnsek, Maryann A.; Guo, Yan; Wang, Susana; Paxinos, Ellen E.; Orata, Fabini; Gladney, Lori M.; Stroika, Steven; Folster, Jason P.; Rowe, Lori; Freeman, Molly M.; Knox, Natalie; Frace, Mike; Boncy, Jacques; Graham, Morag; Hammer, Brian K.; Boucher, Yan; Bashir, Ali; Hanage, William P.; Van Domselaar, Gary; Tarr, Cheryl L. (American Society of Microbiology, 2013)
      ABSTRACT Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it ...
    • Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics 

      Perron, Gabriel; Whyte, Lyle; Turnbaugh, Peter; Hanage, William P.; Dantas, Gautam; Desai, Michael M (Public Library of Science, 2013-07-02)
      Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms ...
    • Fuzzy species revisited 

      Hanage, William P. (BioMed Central, 2013)
    • Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 

      Grad, Yonatan Hagai; Lipsitch, Marc; Feldgarden, M.; Arachchi, H. M.; Cerqueira, G. C.; Fitzgerald, Michael L.; Godfrey, P.; Haas, Brandon Russell; Murphy, C. I.; Russ, C.; Sykes, Sean; Walker, B. J.; Wortman, J. R.; Young, Sarah; Zeng, Q.; Abouelleil, A.; Bochicchio, J.; Chauvin, S.; DeSmet, T.; Gujja, S.; Mccowan, Caryn Alissa; Montmayeur, A.; Steelman, S.; Frimodt-Moller, J.; Petersen, A. M.; Struve, C.; Krogfelt, K. A.; Bingen, E.; Weill, F.-X.; Lander, Eric Steven; Nusbaum, C.; Birren, B. W.; Hung, Deborah Tan; Hanage, William P. (Proceedings of the National Academy of Sciences, 2012)
      The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia ...
    • Global Phylogenomic Analysis of Nonencapsulated Streptococcus pneumoniae Reveals a Deep-Branching Classic Lineage That Is Distinct from Multiple Sporadic Lineages 

      Hilty, Markus; Wüthrich, Daniel; Salter, Susannah J.; Engel, Hansjürg; Campbell, Samuel; Sá-Leão, Raquel; de Lencastre, Hermínia; Hermans, Peter; Sadowy, Ewa; Turner, Paul; Chewapreecha, Claire; Diggle, Mathew; Pluschke, Gerd; McGee, Lesley; Köseoğlu Eser, Özgen; Low, Donald E.; Smith-Vaughan, Heidi; Endimiani, Andrea; Küffer, Marianne; Dupasquier, Mélanie; Beaudoing, Emmanuel; Weber, Johann; Bruggmann, Rémy; Hanage, William P.; Parkhill, Julian; Hathaway, Lucy J.; Mühlemann, Kathrin; Bentley, Stephen D. (Oxford University Press, 2014)
      The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also ...
    • Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution 

      Mostowy, Rafal; Croucher, Nicholas J.; Hanage, William P.; Harris, Simon R.; Bentley, Stephen; Fraser, Christophe (Public Library of Science, 2014)
      The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive ...
    • Historical Zoonoses and Other Changes in Host Tropism of Staphylococcus aureus, Identified by Phylogenetic Analysis of a Population Dataset 

      Shepheard, Marcus A.; Fleming, Vicki M.; Connor, Thomas R.; Corander, Jukka; Feil, Edward J.; Fraser, Christophe; Hanage, William P. (Public Library of Science, 2013)
      Background: Staphylococcus aureus exhibits tropisms to many distinct animal hosts. While spillover events can occur wherever there is an interface between host species, changes in host tropism only occur with the establishment ...
    • 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 ...
    • Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage 

      Chang, Qiuzhi; Lipsitch, Marc; Hanage, William P. (Cambridge University Press (CUP), 2015)
      BACKGROUND Staphylococcus aureus is a common cause of bacterial infections worldwide. It is most commonly carried in and transmitted from the anterior nares. Hosts are known to vary in their proclivity for S. aureus nasal ...
    • The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome 

      Azarian, Taj; Grant, Lindsay R.; Arnold, Brian John; Hammitt, Laura L.; Reid, Raymond; Santosham, Mathuram; Weatherholtz, Robert; Goklish, Novalene; Thompson, Claudette M.; Bentley, Stephen D.; O’Brien, Katherine L.; Hanage, William P.; Lipsitch, Marc (Public Library of Science (PLoS), 2018)
      In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination ...