Whole genomes from bacteria collected at diagnostic units around the world 2020

Sidsel Nag; Gunhild Larsen; Judit Szarvas; Laura Elmlund Kohl Birkedahl; Gábor Máté Gulyás; Wojchiech Jakub Ciok; Timmie Mikkel 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; Lee Ann Turnbull; Simon Lévesque; Livia Berlinger; Kirstine Kobberoe Sogaard; Paula Diaz Guevara; Carolina Duarte Valderrama; Panagiota Maikanti; Jana Amlerova; Pavel Drevinek; Jan Tkadlec; Milica Dilas; Achim Kaasch; Henrik Torkil Westh; Mohamed Azzedine Bachtarzi; Wahiba Amhis; Carolina Elisabeth Satán Salazar; JoséEduardo E. Villacis; Mária Angeles Dominguez Lúzon; Dámaris Berbel Palau; Claire Duployez; Maxime Paluche; Solomon Asante-Sefa; Mie Moller; Margaret Ip; Ivana Mareković; 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 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 Sjogren Hendriksen; Frank Moller Aarestrup

doi:10.1038/s41597-023-02502-7

Whole genomes from bacteria collected at diagnostic units around the world 2020

Sidsel Nag^*, Gunhild Larsen, Judit Szarvas, Laura Elmlund Kohl Birkedahl, Gábor Máté Gulyás, Wojchiech Jakub Ciok, Timmie Mikkel 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 BegumDeyan Donchev, Mathew Diggle, Lee Ann Turnbull, Simon Lévesque, Livia Berlinger, Kirstine Kobberoe Sogaard, Paula Diaz Guevara, Carolina Duarte Valderrama, Panagiota Maikanti, Jana Amlerova, Pavel Drevinek, Jan Tkadlec, Milica Dilas, Achim Kaasch, Henrik Torkil Westh, Mohamed Azzedine Bachtarzi, Wahiba Amhis, Carolina Elisabeth Satán Salazar, JoséEduardo E. Villacis, Mária Angeles Dominguez Lúzon, Dámaris Berbel Palau, Claire Duployez, Maxime Paluche, Solomon Asante-Sefa, Mie Moller, Margaret Ip, Ivana Mareković, 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 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 Sjogren Hendriksen, Frank Moller Aarestrup

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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Abstract

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

Originalsprog	Engelsk
Artikelnummer	628
Tidsskrift	Scientific Data
Vol/bind	10
Udgave nummer	1
ISSN	2052-4463
DOI	https://doi.org/10.1038/s41597-023-02502-7
Status	Udgivet - 2023

Bibliografisk note

Publisher Copyright:
© 2023, Springer Nature Limited.

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10.1038/s41597-023-02502-7Licens: CC BY

FulltextForlagets udgivne version, 1,43 MBLicens: CC BY

Citationsformater

Nag, S., Larsen, G., Szarvas, J., Birkedahl, L. E. K., Gulyás, G. M., Ciok, W. J., Lagermann, T. M., Tafaj, S., Bradbury, S., Collignon, P., Daley, D., Dougnon, V., Fabiyi, K., Coulibaly, B., Dembélé, R., Nikiema, G., Magloire, N., Ouindgueta, I. J., Hossain, Z. Z., ... Aarestrup, F. M. (2023). Whole genomes from bacteria collected at diagnostic units around the world 2020. Scientific Data, 10(1), Artikel 628. https://doi.org/10.1038/s41597-023-02502-7

Nag, S, Larsen, G, Szarvas, J, Birkedahl, LEK, Gulyás, GM, Ciok, WJ, Lagermann, TM, Tafaj, S, Bradbury, S, Collignon, P, Daley, D, Dougnon, V, Fabiyi, K, Coulibaly, B, Dembélé, R, Nikiema, G, Magloire, N, Ouindgueta, IJ, Hossain, ZZ, Begum, A, Donchev, D, Diggle, M, Turnbull, LA, Lévesque, S, Berlinger, L, Sogaard, KK, Guevara, PD, Valderrama, CD, Maikanti, P, Amlerova, J, Drevinek, P, Tkadlec, J, Dilas, M, Kaasch, A, Westh, HT, Bachtarzi, MA, Amhis, W, Salazar, CES, Villacis, JE, Lúzon, MAD, Palau, DB, Duployez, C, Paluche, M, Asante-Sefa, S, Moller, M, Ip, M, Mareković, I, Pál-Sonnevend, A, Cocuzza, CE, Dambrauskiene, A, Macanze, A, Cossa, A, Mandomando, I, Nwajiobi-Princewill, P, Okeke, IN, Kehinde, AO, Adebiyi, I, Akintayo, I, Popoola, O, Onipede, A, Blomfeldt, A, Nyquist, NE, Bocker, K, Ussher, J, Ali, A, Ullah, N, Khan, H, Gustafson, NW, Jarrar, I, Al-Hamad, A, Luvira, V, Paveenkittiporn, W, Baran, I, Mwansa, JCL, Sikakwa, L, Yamba, K, Hendriksen, RS & Aarestrup, FM 2023, 'Whole genomes from bacteria collected at diagnostic units around the world 2020', Scientific Data, bind 10, nr. 1, 628. https://doi.org/10.1038/s41597-023-02502-7

@article{07f297a44feb4c2f9983d7a1868534c7,

title = "Whole genomes from bacteria collected at diagnostic units around the world 2020",

abstract = "The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.",

author = "Sidsel Nag and Gunhild Larsen and Judit Szarvas and Birkedahl, {Laura Elmlund Kohl} and Guly{\'a}s, {G{\'a}bor M{\'a}t{\'e}} and Ciok, {Wojchiech Jakub} and Lagermann, {Timmie Mikkel} and Silva Tafaj and Susan Bradbury and Peter Collignon and Denise Daley and Victorien Dougnon and Kafayath Fabiyi and Boubacar Coulibaly and Ren{\'e} Demb{\'e}l{\'e} and Georgette Nikiema and Natama Magloire and Ouindgueta, {Isidore Juste} and Hossain, {Zenat Zebin} and Anowara Begum and Deyan Donchev and Mathew Diggle and Turnbull, {Lee Ann} and Simon L{\'e}vesque and Livia Berlinger and Sogaard, {Kirstine Kobberoe} and Guevara, {Paula Diaz} and Valderrama, {Carolina Duarte} and Panagiota Maikanti and Jana Amlerova and Pavel Drevinek and Jan Tkadlec and Milica Dilas and Achim Kaasch and Westh, {Henrik Torkil} and Bachtarzi, {Mohamed Azzedine} and Wahiba Amhis and Salazar, {Carolina Elisabeth Sat{\'a}n} and Villacis, {Jos{\'e}Eduardo E.} and L{\'u}zon, {M{\'a}ria Angeles Dominguez} and Palau, {D{\'a}maris Berbel} and Claire Duployez and Maxime Paluche and Solomon Asante-Sefa and Mie Moller and Margaret Ip and Ivana Marekovi{\'c} and Agnes P{\'a}l-Sonnevend and Cocuzza, {Clementiza Elvezia} and Asta Dambrauskiene and Alexandre Macanze and Anelsio Cossa and In{\'a}cio Mandomando and Philip Nwajiobi-Princewill and Okeke, {Iruka N.} and Kehinde, {Aderemi O.} and Ini Adebiyi and Ifeoluwa Akintayo and Oluwafemi Popoola and Anthony Onipede and Anita Blomfeldt and Nyquist, {Nora Elisabeth} and Kiri Bocker and James Ussher and Amjad Ali and Nimat Ullah and Habibullah Khan and Gustafson, {Natalie Weiler} and Ikhlas Jarrar and Arif Al-Hamad and Viravarn Luvira and Wantana Paveenkittiporn and Irmak Baran and Mwansa, {James C.L.} and Linda Sikakwa and Kaunda Yamba and Hendriksen, {Rene Sjogren} and Aarestrup, {Frank Moller}",

note = "Funding Information: The authors would like to acknowledge Rolf Sommer Kaas and Thomas Nordahl Petersen for assisting in creating the necessary in-house data management infrastructure to enable compliance with FAIR and Baptiste Avot with assistance in data upload. A contribution also goes to Frederik Duus M{\o}ller for creating summary scripts for KmerFinder and ResFinder, enabling easy extraction of summary output from these analyses as well as to Victor Hyltoft for maintaining the TWIW web app. The authors would also like to acknowledge Ana Rita Bastos Rebelo for guidance and advice in relation to the assessment of the genomes generated and how to validate these. The authors would also like to thank Martin Koliba for technical support and expertise related to the development of the data-sharing infrastructure and partner database and to Christina Aaby Svendsen, Jacob Dyring Jensen, Michella Oppenheuser, Birthe S. Rosenkvist Lund, Hanne N{\o}rgaard Nielsen & Hanne Mordhorst for assisting in sample handling and processing in the laboratory. Lastly, the authors thank medical laboratory scientists and other staff at participating sites that contributed to isolate and data collection. Publisher Copyright: {\textcopyright} 2023, Springer Nature Limited.",

year = "2023",

doi = "10.1038/s41597-023-02502-7",

language = "English",

volume = "10",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "nature publishing group",

number = "1",

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TY - JOUR

T1 - Whole genomes from bacteria collected at diagnostic units around the world 2020

AU - Nag, Sidsel

AU - Larsen, Gunhild

AU - Szarvas, Judit

AU - Birkedahl, Laura Elmlund Kohl

AU - Gulyás, Gábor Máté

AU - Ciok, Wojchiech Jakub

AU - Lagermann, Timmie Mikkel

AU - Tafaj, Silva

AU - Bradbury, Susan

AU - Collignon, Peter

AU - Daley, Denise

AU - Dougnon, Victorien

AU - Fabiyi, Kafayath

AU - Coulibaly, Boubacar

AU - Dembélé, René

AU - Nikiema, Georgette

AU - Magloire, Natama

AU - Ouindgueta, Isidore Juste

AU - Hossain, Zenat Zebin

AU - Begum, Anowara

AU - Donchev, Deyan

AU - Diggle, Mathew

AU - Turnbull, Lee Ann

AU - Lévesque, Simon

AU - Berlinger, Livia

AU - Sogaard, Kirstine Kobberoe

AU - Guevara, Paula Diaz

AU - Valderrama, Carolina Duarte

AU - Maikanti, Panagiota

AU - Amlerova, Jana

AU - Drevinek, Pavel

AU - Tkadlec, Jan

AU - Dilas, Milica

AU - Kaasch, Achim

AU - Westh, Henrik Torkil

AU - Bachtarzi, Mohamed Azzedine

AU - Amhis, Wahiba

AU - Salazar, Carolina Elisabeth Satán

AU - Villacis, JoséEduardo E.

AU - Lúzon, Mária Angeles Dominguez

AU - Palau, Dámaris Berbel

AU - Duployez, Claire

AU - Paluche, Maxime

AU - Asante-Sefa, Solomon

AU - Moller, Mie

AU - Ip, Margaret

AU - Mareković, Ivana

AU - Pál-Sonnevend, Agnes

AU - Cocuzza, Clementiza Elvezia

AU - Dambrauskiene, Asta

AU - Macanze, Alexandre

AU - Cossa, Anelsio

AU - Mandomando, Inácio

AU - Nwajiobi-Princewill, Philip

AU - Okeke, Iruka N.

AU - Kehinde, Aderemi O.

AU - Adebiyi, Ini

AU - Akintayo, Ifeoluwa

AU - Popoola, Oluwafemi

AU - Onipede, Anthony

AU - Blomfeldt, Anita

AU - Nyquist, Nora Elisabeth

AU - Bocker, Kiri

AU - Ussher, James

AU - Ali, Amjad

AU - Ullah, Nimat

AU - Khan, Habibullah

AU - Gustafson, Natalie Weiler

AU - Jarrar, Ikhlas

AU - Al-Hamad, Arif

AU - Luvira, Viravarn

AU - Paveenkittiporn, Wantana

AU - Baran, Irmak

AU - Mwansa, James C.L.

AU - Sikakwa, Linda

AU - Yamba, Kaunda

AU - Hendriksen, Rene Sjogren

AU - Aarestrup, Frank Moller

N1 - Funding Information: The authors would like to acknowledge Rolf Sommer Kaas and Thomas Nordahl Petersen for assisting in creating the necessary in-house data management infrastructure to enable compliance with FAIR and Baptiste Avot with assistance in data upload. A contribution also goes to Frederik Duus Møller for creating summary scripts for KmerFinder and ResFinder, enabling easy extraction of summary output from these analyses as well as to Victor Hyltoft for maintaining the TWIW web app. The authors would also like to acknowledge Ana Rita Bastos Rebelo for guidance and advice in relation to the assessment of the genomes generated and how to validate these. The authors would also like to thank Martin Koliba for technical support and expertise related to the development of the data-sharing infrastructure and partner database and to Christina Aaby Svendsen, Jacob Dyring Jensen, Michella Oppenheuser, Birthe S. Rosenkvist Lund, Hanne Nørgaard Nielsen & Hanne Mordhorst for assisting in sample handling and processing in the laboratory. Lastly, the authors thank medical laboratory scientists and other staff at participating sites that contributed to isolate and data collection. Publisher Copyright: © 2023, Springer Nature Limited.

PY - 2023

Y1 - 2023

N2 - The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

AB - The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

U2 - 10.1038/s41597-023-02502-7

DO - 10.1038/s41597-023-02502-7

M3 - Journal article

C2 - 37717051

AN - SCOPUS:85171410753

SN - 2052-4463

VL - 10

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 628

ER -