Publications

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

Author(s): MacFadden DR, McGeer A, Athey T, Perusini S, Olsha R, Li A, Eshaghi A, Gubbay JB, Hanage WPJournal: Emerg Infect DisPMID: 29460729 March 2018

Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic…

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Author(s): Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WPJournal: GeneticsPMID: 29330348 March 2018

The impact of epistasis on the evolution of multi-locus traits depends on recombination. While sexually reproducing eukaryotes recombine so frequently…

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Author(s): Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJJournal: Nat Ecol EvolPMID: 29038424 December 2017

Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often cocirculate in the…

Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data.

Author(s): Worby CJ, Lipsitch M, Hanage WPJournal: Am J EpidemiolPMID: 29149252 November 2017

Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected…

Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period.

Author(s): Lee GM, Kleinman K, Pelton S, Lipsitch M, Huang SS, Lakoma M, Dutta-Linn M, Rett M, Hanage WP, Finkelstein JAJournal: PediatricsPMID: 28978716 November 2017

Rates of invasive pneumococcal disease have declined since widespread introduction of pneumococcal conjugate vaccines (PCVs) in the United States. We…

Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi.

Author(s): Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DBJournal: VaccinePMID: 28711389 August 2017

Pneumococcal infections cause a high death toll in Sub Saharan Africa (SSA) but the recently rolled out pneumococcal conjugate vaccines…

Surveillance of pneumococcal colonization and invasive pneumococcal disease reveals shift in prevalent carriage serotypes in Massachusetts’ children to relatively low invasiveness.

Author(s): Yildirim I, Little BA, Finkelstein J, Lee G, Hanage WP, Shea K, Pelton SI, T., he Massachusetts Dept. of Public Health.Journal: VaccinePMID: 28645717 July 2017

Following the introduction of pneumococcal conjugate vaccines (PCV), overall nasopharyngeal colonization rates have not changed significantly, however a dramatic and…