4 files

TWIW database dump

posted on 2023-03-03, 10:06 authored by Sidsel Nag, Laura Elmlund Kohl BirkedahlLaura Elmlund Kohl Birkedahl, Timmie LagermannTimmie Lagermann, Wojciech Jakub Ciok, Gábor Máté Gulyás, Frank Møller AarestrupFrank Møller Aarestrup

Two Weeks in the World is a global research collaboration which seeks to shed light on various aspects of antimicrobial resistance. The research project has resulted in a dataset of 3100 clinically relevant bacterial  genomes with pertaining metadata. “Clinically relevant” refers to the fact that the bacteria from which the genomes were obtained, were all concluded as being a cause of clinical manifestations of infection. The metadata refers to the data describing  the infection from which the bacteria was obtained, like geographic origin and approximate collection date. The bacteria were collected from 59 microbiological diagnostic units in 35 countries around the world during 2020. The data from the project consists of tabular data and genomic sequence data. The tabular data is available as a mysql dump (relational database) and as csv files. The tabular data includes the infection metadata, the results from bioinformatic analyses (species prediction, identification of acquired resistance genes and phylogenetic analysis) as well as the pertaining accession numbers of the individual genomic sequence data, which are available through the European Nucleotide Archive (ENA). At time of submission, the project also has a dedicated web app, from which data can be browsed and downloaded: https://twiw.genomicepidemiology.org/ 

This complete dataset is created and shared according to the FAIR principles and has large reuse potential within the research fields of antimicrobial resistance, clinical microbiology and global health.


Novo Nordisk Fonden NNF16OC0021856

EC | Horizon 2020 Framework Programme 874735

Versatile Emerging infectious disease Observatory

European Commission

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ORCID for corresponding depositor