Ty** methods based on whole genome sequencing data

L Uelze, J Grützke, M Borowiak, JA Hammerl… - One Health …, 2020‏ - Springer
Whole genome sequencing (WGS) of foodborne pathogens has become an effective
method for investigating the information contained in the genome sequence of bacterial …

A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

HA Thorpe, R Booton, T Kallonen, MJ Gibbon… - Nature …, 2022‏ - nature.com
The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is
genetically and ecologically diverse. Many species are opportunistic pathogens and can …

Invasive pneumococcal disease 3 years after introduction of a reduced 1+ 1 infant 13-valent pneumococcal conjugate vaccine immunisation schedule in England: a …

M Bertran, JC D'Aeth, F Abdullahi, S Eletu… - The Lancet Infectious …, 2024‏ - thelancet.com
Background The UK transition from a 2+ 1 to a 1+ 1 infant immunisation schedule with the
13-valent pneumococcal conjugate vaccine (PCV13) on Jan 1, 2020, coincided with the start …

[HTML][HTML] Global genomic epidemiology of Streptococcus pyogenes

MG Jespersen, JA Lacey, SYC Tong… - Infection, Genetics and …, 2020‏ - Elsevier
Streptococcus pyogenes is one of the Top 10 human infectious disease killers worldwide
causing a range of clinical manifestations in humans. Colonizing a range of ecological …

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an …

SW Lo, RA Gladstone, AJ Van Tonder… - The Lancet Infectious …, 2019‏ - thelancet.com
Background Invasive pneumococcal disease remains an important health priority owing to
increasing disease incidence caused by pneumococci expressing non-vaccine serotypes …

Fast hierarchical Bayesian analysis of population structure

G Tonkin-Hill, JA Lees, SD Bentley… - Nucleic acids …, 2019‏ - academic.oup.com
We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly
identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering …

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

B Ekim, B Berger, R Chikhi - Cell systems, 2021‏ - cell.com
DNA sequencing data continue to progress toward longer reads with increasingly lower
sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of …

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

AK Pöntinen, J Top, S Arredondo-Alonso… - Nature …, 2021‏ - nature.com
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous
in animals and insects, representing a classical generalist microorganism. Here, we study E …

A bioinformatic analysis of integrative mobile genetic elements highlights their role in bacterial adaptation

MG Durrant, MM Li, BA Siranosian, SB Montgomery… - Cell host & …, 2020‏ - cell.com
Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however,
high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a …

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

SC Bayliss, HA Thorpe, NM Coyle, SK Sheppard… - …, 2019‏ - academic.oup.com
Background Cataloguing the distribution of genes within natural bacterial populations is
essential for understanding evolutionary processes and the genetic basis of adaptation …