Typing 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 …
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 …
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 …
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 …
[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 …
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 …
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 …
Minimal standards for the description of new genera and species of rhizobia and agrobacteria
PM De Lajudie, M Andrews, J Ardley… - … of systematic and …, 2019 - microbiologyresearch.org
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the
International Committee on Systematics of Prokaryotes review recent developments in …
International Committee on Systematics of Prokaryotes review recent developments in …
Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics
Abstract Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for
which a commercial vaccine for humans is not available. Employing the advantages of high …
which a commercial vaccine for humans is not available. Employing the advantages of high …