Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing

Autor: Amogelang R. Raphenya, James Robertson, Casper Jamin, Leonardo de Oliveira Martins, Finlay Maguire, Andrew G. McArthur, John P. Hays

Publikováno v: Scientific Data, Vol 9, Iss 1, Pp 1-6 (2022)

Measurement(s) bacterial genomes Technology Type(s) next generation DNA sequencing Factor Type(s) None Sample Characteristic - Organism Bacterium Sample Characteristic - Environment Varying Sample Characteristic - Location World

Externí odkaz: https://doaj.org/article/45bd6d4200de4d5f8027242b3875bdf5

Appearance of vanD-positive Enterococcus faecium in a tertiary hospital in the Netherlands: prevalence of vanC and vanD in hospitalized patients

Autor: Jacky Flipse, Christian J. H. von Wintersdorff, Julius M. van Niekerk, Casper Jamin, Frank H. van Tiel, Henrik Hasman, Lieke B. van Alphen

Publikováno v: Scientific Reports, Vol 9, Iss 1, Pp 1-9 (2019)

Abstract Vancomycin-resistant enterococci (VRE) can rapidly spread through hospitals. Therefore, our hospital employs a screening program whereby rectal swabs are screened for the presence of vanA and vanB, and only PCR-positive broths are cultured o

Externí odkaz: https://doaj.org/article/5908c34a0722486ca2c365deb7ec7aaf

AMR Benchmarking dataset - Mapped ReadSets - 3

Autor: James Robertson, John Hays, Casper Jamin, Leonardo de Oliveira Martins, Amos Raphenya

Benchmarking dataset for AMR detection pipelines for assemblies focusing on ESKAPE pathogens in addition to Salmonella. This dataset consists of closed genomes from NCBI where paired-end Illumina data was available. The closed genomes from NCBI are p

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0e16a84ff4686024ebf6a0e0b4c7bd3d

Centre-specific bacterial pathogen typing affects infection-control decision making

Autor: Jordy P. M. Coolen, Heiman F. L. Wertheim, Lieke B van Alphen, John W. A. Rossen, Sébastien Matamoros, Paul H. M. Savelkoul, Casper Jamin

Publikováno v: Microbial genomics, 7(8):000612. AMER SOC MICROBIOLOGY
Microbial Genomics, 7
Coolen, J P M, Jamin, C, Savelkoul, P H M, Rossen, J W A, Wertheim, H F L, Matamoros, S B P & van Alphen, L B 2021, ' Centre-specific bacterial pathogen typing affects infection-control decision making ', Microbial Genomics, vol. 7, no. 8, 000612 . https://doi.org/10.1099/mgen.0.000612
Microbial Genomics, 7(8):000612. Microbiology Society
Microbial Genomics
Microbial Genomics, 7, 8

Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e6a081aaab5aff71379f9e757145749d
https://research.rug.nl/en/publications/587f238b-29c2-4a43-a9c9-2c654a6b1112

Higher Prevalence of

Autor: Heike E F, Becker, Casper, Jamin, Liene, Bervoets, Annemarie, Boleij, Pan, Xu, Marie J, Pierik, Frank R M, Stassen, Paul H M, Savelkoul, John, Penders, Daisy M A E, Jonkers

Publikováno v: Frontiers in Microbiology

Bacteroides fragilis has previously been linked to Crohn’s disease (CD) exacerbations, but results are inconsistent and underlying mechanisms unknown. This study investigates the epidemiology of B. fragilis and its virulence factors bft (enterotoxi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::b89396b5d945c02cdce91d6f051f5e18
https://pubmed.ncbi.nlm.nih.gov/34168621