. 2023 Sep 16;10(1):628.

doi: 10.1038/s41597-023-02502-7.

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

Sidsel Nag¹, Gunhild Larsen², Judit Szarvas², Laura Elmlund Kohl Birkedahl², Gábor Máté Gulyás², Wojchiech Jakub Ciok², Timmie Mikkel Lagermann², Silva Tafaj³, Susan Bradbury⁴, Peter Collignon⁴, Denise Daley⁵, Victorien Dougnon⁶, Kafayath Fabiyi⁶, Boubacar Coulibaly⁷, René Dembélé⁸, Georgette Nikiema⁸, Natama Magloire⁹, Isidore Juste Ouindgueta¹⁰, Zenat Zebin Hossain¹¹, Anowara Begum¹¹, Deyan Donchev¹², Mathew Diggle¹³, LeeAnn Turnbull¹³, Simon Lévesque¹⁴, Livia Berlinger¹⁵, Kirstine Kobberoe Sogaard¹⁶, Paula Diaz Guevara¹⁷, Carolina Duarte Valderrama¹⁷, Panagiota Maikanti¹⁸, Jana Amlerova¹⁹, Pavel Drevinek²⁰, Jan Tkadlec²⁰, Milica Dilas²¹, Achim Kaasch²¹, Henrik Torkil Westh²², Mohamed Azzedine Bachtarzi²³, Wahiba Amhis²³, Carolina Elisabeth Satán Salazar²⁴, JoséEduardo Villacis²⁵, Mária Angeles Dominguez Lúzon²⁶, Dámaris Berbel Palau²⁷, Claire Duployez²⁸, Maxime Paluche²⁹, Solomon Asante-Sefa³⁰, Mie Moller³¹, Margaret Ip³², Ivana Mareković³³, Agnes Pál-Sonnevend³⁴, Clementiza Elvezia Cocuzza³⁵, Asta Dambrauskiene³⁶, Alexandre Macanze³⁷, Anelsio Cossa³⁷, Inácio Mandomando³⁷, Philip Nwajiobi-Princewill³⁸, Iruka N Okeke³⁹, Aderemi O Kehinde^{40

41}, Ini Adebiyi^{39

41}, Ifeoluwa Akintayo⁴⁰, Oluwafemi Popoola^{40

41}, Anthony Onipede⁴², Anita Blomfeldt⁴³, Nora Elisabeth Nyquist⁴³, Kiri Bocker⁴⁴, James Ussher⁴⁴, Amjad Ali⁴⁵, Nimat Ullah⁴⁵, Habibullah Khan⁴⁶, Natalie Weiler Gustafson⁴⁷, Ikhlas Jarrar⁴⁸, Arif Al-Hamad⁴⁹, Viravarn Luvira⁵⁰, Wantana Paveenkittiporn⁵¹, Irmak Baran⁵², James C L Mwansa⁵³, Linda Sikakwa⁵⁴, Kaunda Yamba⁵⁵, Rene Sjogren Hendriksen², Frank Moller Aarestrup²

Affiliations

¹ National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark. jassd_nf@hotmail.com.
² National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark.
³ Microbiology Department, University Hospital "Shefqet Ndroqi", Rruga Dr. Shefqet Ndroqi. Sauk, Tirana, 1044, Albania.
⁴ Microbiology Department, Canberra Hospital, Gilmore Cresent, Garran, 2605, Australian Capital Territory, Australia.
⁵ Department of Microbiology, PathWest Laboratory Medicine, Fiona Stanley Hospital, 9 Robin Warren Drive, Murdoch, 6150, Western Australia, Australia.
⁶ Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 PO Box, Abomey-Calavi, 2009, Cotonou, Benin.
⁷ Department of Laboratory, Nouna Health Research Centre, Rue Namory Keita, Nouna, Burkina Faso.
⁸ Training and Research Unit in Applied Sciences and Technologies/Biochemistry-microbiology, University of Dedougou, Dedougou, 176, Boucle du Mouhoun, Burkina Faso.
⁹ Clinical Research Unit of Nanoro, National Institutes of Medical Research, Ouagadougou, 176, Burkina Faso.
¹⁰ Department, University of Joseph KI-ZERBO, Street, Ouagadouogou, Burkina Faso.
¹¹ Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
¹² Clinical Laboratory of Microbiology and Virology, University Hospital "Lozenetz", Str. Kozyak 1, Sofia, 1407, Sofia, Bulgaria.
¹³ Alberta Precision Laboratories, Alberta, Canada.
¹⁴ Service de microbiologie, Centre Integré Universitaire de Santé et de services sociaux de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, 3001 12è avenue Nord, Sherbrooke, J1H 5N4, Québec, Canada.
¹⁵ Department, Bioanalytica AG, Luzern, 6006, Switzerland.
¹⁶ Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, Basel, 4031, Switzerland.
¹⁷ Microbiology Group, Instituto Nacional de Salud, Avenida Calle 26·51-20 CAN, Bogotá, 111321, Colombia.
¹⁸ Charalampous, Microbiology Department, National Reference Laboratory for Antimicrobial Resistance Surveillance, Nicosia General Hospital, 215, Paleos Dromos Lefkosia-Lemesos str., Strovolos, 2029, Nicosia, Cyprus.
¹⁹ Department of Microbiology, University Hospital in Plzen, Edvarda Benese 1128/13, Plzen, 305 99, Czech Republic.
²⁰ Department of Medical Microbiology, Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic.
²¹ Otto-von-Guericke University, Magdebourg, Germany.
²² Klinisk Mikrobiologisk Afdeling, Hvidovre Hospital, Kettegårds Allé, Hvidovre, 2650, Denmark.
²³ Laboratoire de Microbiologie Clinique, Centre Hospitalo-universitaire, 1 place du 1er Mai 1945, Algiers, 16000, Algeria.
²⁴ National Reference Center for Antimicrobial Resistance, National Institute of Public Health Research "Dr. Leopoldo Izquieta Pérez", Iquique N14-285, Quito, 170403, Pichicha, Ecuador.
²⁵ Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quinto, 1701-2184, Pichincha, Ecuador.
²⁶ Department of Pathology and Experimental Therapy, Universitat de Barcelona, Barcelona, Spain.
²⁷ Microbiology Department, Hospital de Bellvitge, Barcelona, 10587, Spain.
²⁸ Institute of Microbiology, Centre Hospitalier Universitaire de Lille, Rue du Pr. Jules Leclercq, Lille, 59037, France.
²⁹ Bacteriology laboratory, Centre hospitalier de Valenciennes, Avenue Désandrouin, Valenciennes, 59300, France.
³⁰ Sekondi Public Health Laboratory, Ghana Health Service, Effia Nkwanta Regional Hospital, Effia Nkwanta Regional Hospital, Takoradi, Ghana.
³¹ Dronning Ingrids Hospital, Nuuk, Greenland.
³² Chinese University of Hong Kong, Shatin, Hong Kong.
³³ Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Kišpatićeva 12, Zagreb, 10000, Croatia.
³⁴ Medical Microbiology and Immunology, University of Pecs Medical School, Szigeti ut 12, Pecs, 7631, Hungary.
³⁵ Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy.
³⁶ Laboratory Medicine Department, Hospital of Lithuanian University of Health Sciences Kauno klinikos, Eiveniu Str. 2, Kaunas, 50161, Lithuania.
³⁷ Centro de Investigação em Saúde de Manhiça, Manhiça, Mozambique.
³⁸ National Hospital Abuja, Abuja, Nigeria.
³⁹ Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
⁴⁰ College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.
⁴¹ University College of Ibadan, Ibadan, Oyo State, Nigeria.
⁴² Obafemi Awolowo University, Ile-Ife, Nigeria.
⁴³ Department of Microbiology and Infection Control, Akershus University Hospital, Sykehusveien 25, Lørenskog, 1478, Norway.
⁴⁴ Southern Community Laboratories, University of Otago, 472 George Street, Otago, 9016, Dunedin, New Zealand.
⁴⁵ Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.
⁴⁶ Molecular Diagnostic Section, Khyber Teaching Hospital (KTH), University Road, Peshawar, 25120, Pakistan.
⁴⁷ Departamento de Bacteriologia, Laboratorio Central de Salud Publico, Avenida Venezuela y Tte Escurra, Asunción, CP, 1429, Paraguay.
⁴⁸ Basic Medical Sciences Department, Arab American University, AAUP st., Zababdeh, P240, Jenin, Palestine.
⁴⁹ Division of Clinical Microbiology, Qatif Central Hospital, 3213 Dharan-Jubail Expressway, Al-Qatif, 32654-7376, Eastern Province, Saudi Arabia.
⁵⁰ Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand.
⁵¹ Department of Medical Sciences, National Institute of Health, Sariburi, Thailand.
⁵² Medical Microbiology Department, Karadeniz Technical University Farabi Hospital, Farabi Hastanesi, Trabzon, 61080, Ortahisar, Turkey.
⁵³ Lusaka Apex Medical School, Lusaka, Zambia.
⁵⁴ Levy Mwanawasa Teaching Hospital, Lusaka, Zambia.
⁵⁵ University Teaching Hospital, Lusaka, Zambia.

PMID: 37717051
PMCID: PMC10505216
DOI: 10.1038/s41597-023-02502-7

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

Sidsel Nag et al. Sci Data. 2023.

. 2023 Sep 16;10(1):628.

doi: 10.1038/s41597-023-02502-7.

Authors

Affiliations

¹ National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark. jassd_nf@hotmail.com.
² National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark.
³ Microbiology Department, University Hospital "Shefqet Ndroqi", Rruga Dr. Shefqet Ndroqi. Sauk, Tirana, 1044, Albania.
⁴ Microbiology Department, Canberra Hospital, Gilmore Cresent, Garran, 2605, Australian Capital Territory, Australia.
⁵ Department of Microbiology, PathWest Laboratory Medicine, Fiona Stanley Hospital, 9 Robin Warren Drive, Murdoch, 6150, Western Australia, Australia.
⁶ Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 PO Box, Abomey-Calavi, 2009, Cotonou, Benin.
⁷ Department of Laboratory, Nouna Health Research Centre, Rue Namory Keita, Nouna, Burkina Faso.
⁸ Training and Research Unit in Applied Sciences and Technologies/Biochemistry-microbiology, University of Dedougou, Dedougou, 176, Boucle du Mouhoun, Burkina Faso.
⁹ Clinical Research Unit of Nanoro, National Institutes of Medical Research, Ouagadougou, 176, Burkina Faso.
¹⁰ Department, University of Joseph KI-ZERBO, Street, Ouagadouogou, Burkina Faso.
¹¹ Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
¹² Clinical Laboratory of Microbiology and Virology, University Hospital "Lozenetz", Str. Kozyak 1, Sofia, 1407, Sofia, Bulgaria.
¹³ Alberta Precision Laboratories, Alberta, Canada.
¹⁴ Service de microbiologie, Centre Integré Universitaire de Santé et de services sociaux de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, 3001 12è avenue Nord, Sherbrooke, J1H 5N4, Québec, Canada.
¹⁵ Department, Bioanalytica AG, Luzern, 6006, Switzerland.
¹⁶ Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, Basel, 4031, Switzerland.
¹⁷ Microbiology Group, Instituto Nacional de Salud, Avenida Calle 26·51-20 CAN, Bogotá, 111321, Colombia.
¹⁸ Charalampous, Microbiology Department, National Reference Laboratory for Antimicrobial Resistance Surveillance, Nicosia General Hospital, 215, Paleos Dromos Lefkosia-Lemesos str., Strovolos, 2029, Nicosia, Cyprus.
¹⁹ Department of Microbiology, University Hospital in Plzen, Edvarda Benese 1128/13, Plzen, 305 99, Czech Republic.
²⁰ Department of Medical Microbiology, Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic.
²¹ Otto-von-Guericke University, Magdebourg, Germany.
²² Klinisk Mikrobiologisk Afdeling, Hvidovre Hospital, Kettegårds Allé, Hvidovre, 2650, Denmark.
²³ Laboratoire de Microbiologie Clinique, Centre Hospitalo-universitaire, 1 place du 1er Mai 1945, Algiers, 16000, Algeria.
²⁴ National Reference Center for Antimicrobial Resistance, National Institute of Public Health Research "Dr. Leopoldo Izquieta Pérez", Iquique N14-285, Quito, 170403, Pichicha, Ecuador.
²⁵ Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quinto, 1701-2184, Pichincha, Ecuador.
²⁶ Department of Pathology and Experimental Therapy, Universitat de Barcelona, Barcelona, Spain.
²⁷ Microbiology Department, Hospital de Bellvitge, Barcelona, 10587, Spain.
²⁸ Institute of Microbiology, Centre Hospitalier Universitaire de Lille, Rue du Pr. Jules Leclercq, Lille, 59037, France.
²⁹ Bacteriology laboratory, Centre hospitalier de Valenciennes, Avenue Désandrouin, Valenciennes, 59300, France.
³⁰ Sekondi Public Health Laboratory, Ghana Health Service, Effia Nkwanta Regional Hospital, Effia Nkwanta Regional Hospital, Takoradi, Ghana.
³¹ Dronning Ingrids Hospital, Nuuk, Greenland.
³² Chinese University of Hong Kong, Shatin, Hong Kong.
³³ Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Kišpatićeva 12, Zagreb, 10000, Croatia.
³⁴ Medical Microbiology and Immunology, University of Pecs Medical School, Szigeti ut 12, Pecs, 7631, Hungary.
³⁵ Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy.
³⁶ Laboratory Medicine Department, Hospital of Lithuanian University of Health Sciences Kauno klinikos, Eiveniu Str. 2, Kaunas, 50161, Lithuania.
³⁷ Centro de Investigação em Saúde de Manhiça, Manhiça, Mozambique.
³⁸ National Hospital Abuja, Abuja, Nigeria.
³⁹ Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
⁴⁰ College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.
⁴¹ University College of Ibadan, Ibadan, Oyo State, Nigeria.
⁴² Obafemi Awolowo University, Ile-Ife, Nigeria.
⁴³ Department of Microbiology and Infection Control, Akershus University Hospital, Sykehusveien 25, Lørenskog, 1478, Norway.
⁴⁴ Southern Community Laboratories, University of Otago, 472 George Street, Otago, 9016, Dunedin, New Zealand.
⁴⁵ Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.
⁴⁶ Molecular Diagnostic Section, Khyber Teaching Hospital (KTH), University Road, Peshawar, 25120, Pakistan.
⁴⁷ Departamento de Bacteriologia, Laboratorio Central de Salud Publico, Avenida Venezuela y Tte Escurra, Asunción, CP, 1429, Paraguay.
⁴⁸ Basic Medical Sciences Department, Arab American University, AAUP st., Zababdeh, P240, Jenin, Palestine.
⁴⁹ Division of Clinical Microbiology, Qatif Central Hospital, 3213 Dharan-Jubail Expressway, Al-Qatif, 32654-7376, Eastern Province, Saudi Arabia.
⁵⁰ Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand.
⁵¹ Department of Medical Sciences, National Institute of Health, Sariburi, Thailand.
⁵² Medical Microbiology Department, Karadeniz Technical University Farabi Hospital, Farabi Hastanesi, Trabzon, 61080, Ortahisar, Turkey.
⁵³ Lusaka Apex Medical School, Lusaka, Zambia.
⁵⁴ Levy Mwanawasa Teaching Hospital, Lusaka, Zambia.
⁵⁵ University Teaching Hospital, Lusaka, Zambia.

PMID: 37717051
PMCID: PMC10505216
DOI: 10.1038/s41597-023-02502-7

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1**
Country representation. The countries represented in the study are shown with colour coding according to the WHO-defined regions they belong to.

**Fig. 2**
Summary description of samples in the dataset. (a) Number of genera identified in the dataset and accounting for the 90 percent majority groups in the dataset, (b) major pathogen-source combinations accounting for the majority of the dataset and (c) Area depiction of 9 major genera (black circles) and represented species (grey circles) in the dataset.

**Fig. 3**
Project pipeline and framework – tasks in green were performed by DTU and tasks in yellow were performed by partners. DNA extraction was performed by some partners, who could not dispatch swabs.

**Fig. 4**
Schematic of the genome validation process employed in the qc_species_parser_v3.py.

See this image and copyright information in PMC

References

1. Reygaert WC. An overview of the antimicrobial resistance mechanisms of bacteria. Aims Microbiology. 2018;4:482–501. doi: 10.3934/microbiol.2018.3.482. - DOI - PMC - PubMed
1. Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clinical Microbiology Reviews. 2018;31:e00088–17. doi: 10.1128/CMR.00088-17. - DOI - PMC - PubMed
1. Antimicrobial resistance in g7 countries and beyond: policy brief. https://www.oecd.org/els/health-systems/Antimicrobial-Resistance-in-G7-C... Last accessed April 2022 (2015).
1. Global action plan for antimicrobial resistance. https://www.who.int/publications/i/item/9789241509763 Last accessed April 2022 (2016).
1. Drug-resistant infections; a threat to our economic future. https://documents.worldbank.org/curated/en/323311493396993758/pdf/114679... Last accessed April 2022 (2017).

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Molecular Biology Databases