TWIW database dump

dataset

posted on 2023-07-10, 06:31 authored by Sidsel Nag, Gunhild Larsen, Judit Szarvas, Laura Elmlund Kohl BirkedahlLaura Elmlund Kohl Birkedahl, Gábor Máté Gulyás, Wojciech Jakub Ciok, Timmie M. R. Lagermann, Silva Tafaj, Susan Bradbury, Peter Collignon, Denise Daley, Victorien Dougnon, Kafayath Fabiyi, Boubacar Coulibaly, René Dembélé, Georgette Nikiema, Natama Magloire, Isidore Juste Ouindgueta, Zenat Zebin Hossain, Anowara Begum, Deyan Donchev, Mathew Diggle, LeeAnn Turnbull, Simon Lévesque, Livia Berlinger, Kirstine Kobberoe Søgaard, Paula Diaz Guevara, Carolina Duarte Valderrama, Panagiota Maikanti, Jana Amlerova, Pavel Drevinek, Jan Tkadlec, Milica Dilas, Achim J. Kaasch, HenrikTorkil Westh, Mohamed Azzedine Bachtarzi, Wahiba Amhis, Carolina Elizabeth Satán Salazar, José Eduardo Villacis, Mária Angeles Dominguez Lúzon, Dàmaris Berbel Palau, Claire Duployez, Maxime Paluch, Solomon Asante-Sefa, Mie Møller, Margaret Ip, Ivana Marecović, Agnes Pál-Sonnevend, Clementiza Elvezia Cocuzza, Asta Dambrauskiene, Alexandre Macanze, Anelsio Cossa, Inácio Mandomando, Philip Nwajiobi-Princewill, Iruka N. Okeke, Aderemi O. Kehinde, Ini Adebiyi, Ifeoluwa Akintayo, Oluwafemi Popoola, Anthony Onipede, Anita Blomfeldt, Nora Elisabeth Nyquist, Kiri Bocker, James Ussher, Amjad Ali, Nimat UllahNimat Ullah, Habibullah Khan, Natalie Weiler Gustafson, Ikhlas Jarrar, Arif Al-Hamad, Viravarn Luvira, Wantana Paveenkittiporn, Irmak Baran, James C. L. Mwansa, Linda Sikakwa, Kaunda Yamba, Rene Sjøgren Hendriksen, 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.

.v2: Author list and readme has been updated. And a file containing column descriptions, for the database dump, has been added: TWIW_dbcolumns_explained.csv.