Publications – Center for Communicable Disease Dynamics

Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.

Author(s): Carroll AC, Mortimer L, Ghosh H, Reuter S, Grundmann H, Břinda K, Hanage WP, Li A, Paterson A, Purssell A, Rooney A, Yee NR, Coburn B, Able-Thomas S, Antonio M, McGeer A, MacFadden DRJournal: Microbiol SpectrPMID: 39611823 November 2024

Timely diagnostic tools are needed to improve antibiotic treatment. Pairing metagenomic sequencing with genomic neighbor typing algorithms may support rapid…

SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics.

Author(s): Wikle NB, Tran TN, Gentilesco B, Leighow SM, Albert E, Strong ER, Břinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MFJournal: Sci AdvPMID: 35080987 January 2022

State-level reopenings in late spring 2020 facilitated the resurgence of severe acute respiratory syndrome coronavirus 2 transmission. Here, we analyze…

Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes.

Author(s): Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang TJournal: Proc Natl Acad Sci U S APMID: 34453008 August 2021

Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.

Author(s): Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang TJournal: Proc Natl Acad Sci U S APMID: 33975908 May 2021

Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.

Author(s): Che Y, Yang Y, Xu X, Břinda K, Polz MF, Hanage WP, Zhang TJournal: Proc Natl Acad Sci U S APMID: 33526659 February 2021

It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little…

Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli.

Author(s): MacFadden DR, Coburn B, Břinda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WPJournal: Antimicrob Agents ChemotherPMID: 32152083 March 2020

Rising antibiotic resistance increasingly compromises empiric treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empiric…

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…