Publications – Center for Communicable Disease Dynamics

Viral factors in influenza pandemic risk assessment.

Author(s): Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CAJournal: ElifePMID: 27834632 November 2016

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of…

Improving Control of Antibiotic-Resistant Gonorrhea by Integrating Research Agendas Across Disciplines: Key Questions Arising From Mathematical Modeling.

Author(s): Grad YH, Goldstein E, Lipsitch M, White PJJournal: J Infect DisPMID: 26518045 March 2016

The rise in gonococcal antibiotic resistance and the threat of untreatable infection are focusing attention on strategies to limit the…

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.

Author(s): Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WPJournal: Sci DataPMID: 26528397 October 2015

Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have…

Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks.

Author(s): Lipsitch M, Donnelly CA, Fraser C, Blake IM, Cori A, Dorigatti I, Ferguson NM, Garske T, Mills HL, Riley S, Van Kerkhove MD, Hernán MAJournal: PLoS Negl Trop DisPMID: 26181387 July 2015

Estimating the case-fatality risk (CFR)-the probability that a person dies from an infection given that they are a case-is a…

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.

Author(s): Li Y, Croucher NJ, Thompson CM, Trzciński K, Hanage WP, Lipsitch MJournal: BMC GenomicsPMID: 25956132 May 2015

Understanding genetic determinants of a microbial phenotype generally involves creating and comparing isogenic strains differing at the locus of interest,…

Selective and genetic constraints on pneumococcal serotype switching.

Author(s): Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WPJournal: PLoS GenetPMID: 25826208 March 2015

Streptococcus pneumoniae isolates typically express one of over 90 immunologically distinguishable polysaccharide capsules (serotypes), which can be classified into "serogroups"…

Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced.

Author(s): Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WPJournal: BMC Infect DisPMID: 25887323 February 2015

The success of 7-valent pneumococcal conjugate vaccination (PCV-7) introduced to the US childhood immunization schedule in 2000 was partially offset…

Improving pandemic influenza risk assessment.

Author(s): Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JDJournal: ElifePMID: 25321142 October 2014

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As…

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

Author(s): Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser CJournal: PLoS GenetPMID: 24786281 May 2014

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity…

Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset.

Author(s): Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WPJournal: PLoS OnePMID: 23667472 May 2013

Staphylococcus aureus exhibits tropisms to many distinct animal hosts. While spillover events can occur wherever there is an interface between…