Global emergence and dissemination of enterococci as nosocomial pathogens: attack of the clones?

AM Guzman Prieto, W van Schaik… - Frontiers in …, 2016‏ - frontiersin.org
Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of
the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature …

Population genomics of bacterial host adaptation

SK Sheppard, DS Guttman, JR Fitzgerald - Nature Reviews Genetics, 2018‏ - nature.com
Some bacteria can transfer to new host species, and this poses a risk to human health.
Indeed, an estimated 60% of all human pathogens have originated from other animal …

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann… - Genome …, 2018‏ - genome.cshlp.org
Current methods struggle to reconstruct and visualize the genomic relationships of large
numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic …

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

M Nascimento, A Sousa, M Ramirez… - …, 2017‏ - academic.oup.com
Abstract Summary High Throughput Sequencing provides a cost effective means of
generating high resolution data for hundreds or even thousands of strains, and is rapidly …

BIGSdb: scalable analysis of bacterial genome variation at the population level

KA Jolley, MCJ Maiden - BMC bioinformatics, 2010‏ - Springer
Background The opportunities for bacterial population genomics that are being realised by
the application of parallel nucleotide sequencing require novel bioinformatics platforms …

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction

S Matamoros, JM Van Hattem, MS Arcilla, N Willemse… - Scientific reports, 2017‏ - nature.com
To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined
the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying …

PHYLOViZ: phylogenetic inference and data visualization for sequence based ty** methods

AP Francisco, C Vaz, PT Monteiro, J Melo-Cristino… - BMC …, 2012‏ - Springer
Background With the decrease of DNA sequencing costs, sequence-based ty** methods
are rapidly becoming the gold standard for epidemiological surveillance. These methods …

Toxoplasma gondii Genoty**: A Closer Look Into Europe

M Fernández-Escobar, G Schares… - Frontiers in cellular …, 2022‏ - frontiersin.org
Toxoplasma gondii is a major zoonotic agent which may cause harmful effects mainly in
pregnant and immunocompromised hosts. Despite many efforts on its genetic …

Antimicrobial-resistant Neisseria gonorrhoeae in Europe in 2020 compared with in 2013 and 2018: a retrospective genomic surveillance study

D Golparian, MJ Cole, L Sánchez-Busó, M Day… - The Lancet …, 2024‏ - thelancet.com
Background Regular quality-assured whole-genome sequencing linked to antimicrobial
resistance (AMR) and patient metadata is imperative to elucidate the shifting gonorrhoea …

A Study on Prevalence and Characterization of Bacillus cereus in Ready-to-Eat Foods in China

S Yu, P Yu, J Wang, C Li, H Guo, C Liu… - Frontiers in …, 2020‏ - frontiersin.org
Bacillus cereus is widely distributed in different food products and can cause a variety of
symptoms associated with food poisoning. Since ready-to-eat (RTE) foods are not commonly …