Publications – Center for Communicable Disease Dynamics

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles SJournal: Nat CommunPMID: 37907520 October 2023

Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts…

Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles SJournal: bioRxiv October 2022

Genomic surveillance provides a data source complementary to contact tracing to resolve putative transmission chains. However, the role of within-host…

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.

Author(s): Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WPJournal: Nat MicrobiolPMID: 32042129 February 2020

Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does…

Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13.

Author(s): Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WPJournal: Microb GenomPMID: 30777813 February 2019

The 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large paediatric carriage sample…

Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009.

Author(s): Chang Q, Abuelaish I, Biber A, Jaber H, Callendrello A, Andam CP, Regev-Yochay G, Hanage WP, On Behalf Of The Picr Study GroupJournal: Euro SurveillPMID: 30153881 August 2018

BackgroundRemarkably high carriage prevalence of a community-associated meticillin-resistant (MRSA) strain of sequence type (ST) 22 in the Gaza strip was…

Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.

Author(s): Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WPJournal: J Clin MicrobiolPMID: 28100596 April 2017

Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic-resistant strains throughout the 2000s. However, diseases caused…

Diversification of bacterial genome content through distinct mechanisms over different timescales.

Author(s): Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WPJournal: Nat CommunPMID: 25407023 November 2014

Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification.…