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Ty** methods based on whole genome sequencing data
Whole genome sequencing (WGS) of foodborne pathogens has become an effective
method for investigating the information contained in the genome sequence of bacterial …
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
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 …
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 …
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 …
13-valent pneumococcal conjugate vaccine (PCV13) on Jan 1, 2020, coincided with the start …
[HTML][HTML] Global genomic epidemiology of Streptococcus pyogenes
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 …
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 …
Background Invasive pneumococcal disease remains an important health priority owing to
increasing disease incidence caused by pneumococci expressing non-vaccine serotypes …
increasing disease incidence caused by pneumococci expressing non-vaccine serotypes …
Fast hierarchical Bayesian analysis of population structure
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 …
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
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 …
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
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 …
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
Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however,
high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a …
high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a …
PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
Background Cataloguing the distribution of genes within natural bacterial populations is
essential for understanding evolutionary processes and the genetic basis of adaptation …
essential for understanding evolutionary processes and the genetic basis of adaptation …