Publications – Center for Communicable Disease Dynamics

A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.

Author(s): Sánchez-Busó L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, Argimón S, Ma KC, Mortimer TD, Golparian D, Cole MJ, Grad YH, Martin I, Raphael BH, Shafer WM, Town K, Wi T, Harris SR, Unemo M, Aanensen DMJournal: Genome MedPMID: 33875000 April 2021

The distribution and spread of susceptible and resistant Neisseria gonorrhoeae across demographic groups in a major metropolitan center.

Author(s): Mortimer TD, Pathela P, Crawley A, Rakeman JL, Lin Y, Harris SR, Blank S, Schillinger JA, Grad YHJournal: Clin Infect DisPMID: 32829411 August 2020

Genomic epidemiology studies of gonorrhea in the United States have primarily focused on national surveillance for antibiotic resistance, and patterns…

Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae.

Author(s): Ma KC, Mortimer TD, Hicks AL, Wheeler NE, Sánchez-Busó L, Golparian D, Taiaroa G, Rubin DHF, Wang Y, Williamson DA, Unemo M, Harris SR, Grad YHJournal: Nat CommunPMID: 32807804 August 2020

Neisseria gonorrhoeae is an urgent public health threat due to rapidly increasing incidence and antibiotic resistance. In contrast with the…

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013.

Author(s): Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch MJournal: J Infect DisPMID: 27638945 November 2016

Treatment of Neisseria gonorrhoeae infection is empirical and based on population-wide susceptibilities. Increasing antimicrobial resistance underscores the potential importance of…

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.

Author(s): Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, Kamng'ona AW, Parkhill J, French N, Heyderman RS, Kadioglu A, Everett DB, Bentley SD, Hanage WPJournal: MBioPMID: 27677790 September 2016

Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many…

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.

Author(s): Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill JJournal: PLoS GenetPMID: 25101644 August 2014

Traditional genetic association studies are very difficult in bacteria, as the generally limited recombination leads to large linked haplotype blocks,…

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone.

Author(s): Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SDJournal: BMC BiolPMID: 24957517 June 2014

Pneumococcal β-lactam resistance was first detected in Iceland in the late 1980s, and subsequently peaked at almost 25% of clinical…

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…

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study.

Author(s): Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S, Lipsitch MJournal: Lancet Infect DisPMID: 24462211 March 2014

The emergence of Neisseria gonorrhoeae with decreased susceptibility to extended spectrum cephalosporins raises the prospect of untreatable gonorrhoea. In the…

Bacterial genomes in epidemiology–present and future.

Author(s): Croucher NJ, Harris SR, Grad YH, Hanage WPJournal: Philos Trans R Soc Lond B Biol SciPMID: 23382424 February 2013

Sequence data are well established in the reconstruction of the phylogenetic and demographic scenarios that have given rise to outbreaks…