A brief history of bird flu

SJ Lycett, F Duchatel, P Digard - … Transactions of the …, 2019‏ - royalsocietypublishing.org
In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50
million people. A century later, with the advent of sequencing technology and corresponding …

Outbreak analytics: a develo** data science for informing the response to emerging pathogens

JA Polonsky, A Baidjoe, ZN Kamvar… - … of the Royal …, 2019‏ - royalsocietypublishing.org
Despite continued efforts to improve health systems worldwide, emerging pathogen
epidemics remain a major public health concern. Effective response to such outbreaks relies …

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

R Bouckaert, TG Vaughan… - PLoS computational …, 2019‏ - journals.plos.org
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary …

Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients

R León-Sampedro, J DelaFuente, C Díaz-Agero… - Nature …, 2021‏ - nature.com
Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern
in clinical settings worldwide. Two fundamentally different processes shape the …

Patterns of within-host genetic diversity in SARS-CoV-2

G Tonkin-Hill, I Martincorena, R Amato, ARJ Lawson… - elife, 2021‏ - elifesciences.org
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become
a major public health focus for many governments around the world. The modest mutation …

Gut to lung translocation and antibiotic mediated selection shape the dynamics of Pseudomonas aeruginosa in an ICU patient

RM Wheatley, JD Caballero, TE van der Schalk… - Nature …, 2022‏ - nature.com
Bacteria have the potential to translocate between sites in the human body, but the
dynamics and consequences of within-host bacterial migration remain poorly understood …

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

X Didelot, C Fraser, J Gardy… - Molecular biology and …, 2017‏ - academic.oup.com
Genomic data are increasingly being used to understand infectious disease epidemiology.
Isolates from a given outbreak are sequenced, and the patterns of shared variation are used …

Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis

F Coll, KE Raven, GM Knight, B Blane… - The Lancet …, 2020‏ - thelancet.com
Background Whole-genome sequencing (WGS) can be used in genomic epidemiology
investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted …

[HTML][HTML] Understanding the transmission of foot-and-mouth disease virus at different scales

DJ Paton, S Gubbins, DP King - Current opinion in virology, 2018‏ - Elsevier
Highlights•FMDV is readily transmitted via direct and indirect contact between hosts.•The
role of low-probability events is difficult to recreate and model.•Sequences can be combined …

High-resolution map** of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain

Y Xu, I Cancino-Muñoz, M Torres-Puente… - PLoS …, 2019‏ - journals.plos.org
Background Whole genome sequencing provides better delineation of transmission clusters
in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal …