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Leekitcharoenphon P, Otani S, Szarvas J, Mzee T, Kumburu H, Møller FD, Aarestrup FM. The first complete genome sequence of Staphylococcus aureus ST5477. Microbiol Resour Announc 2024; 13:e0100423. [PMID: 38179915 PMCID: PMC10868164 DOI: 10.1128/mra.01004-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
This study presents the first complete genome of Staphylococcus aureus ST5477, one of the most common sequence types (ST) from bovine in eastern Africa. The genome consists of a 2,723,132-bp circular chromosome and a 3,044-bp plasmid. This strain was collected in 2017 from cow milk in Tanzania.
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Affiliation(s)
- Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Judit Szarvas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tutu Mzee
- Ifakara Health Institute, Bagamoyo Branch, Bagamoyo, Tanzania
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Kilimanjaro, Tanzania
| | - Frederik Duus Møller
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Rahman N, O'Cathail C, Zyoud A, Sokolov A, Oude Munnink B, Grüning B, Cummins C, Amid C, Nieuwenhuijse DF, Visontai D, Yuan DY, Gupta D, Prasad DK, Gulyás GM, Rinck G, McKinnon J, Rajan J, Knaggs J, Skiby JE, Stéger J, Szarvas J, Gueye K, Papp K, Hoek M, Kumar M, Ventouratou MA, Bouquieaux MC, Koliba M, Mansurova M, Haseeb M, Worp N, Harrison PW, Leinonen R, Thorne R, Selvakumar S, Hunt S, Venkataraman S, Jayathilaka S, Cezard T, Maier W, Waheed Z, Iqbal Z, Aarestrup FM, Csabai I, Koopmans M, Burdett T, Cochrane G. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microb Genom 2024; 10:001188. [PMID: 38358325 PMCID: PMC10926692 DOI: 10.1099/mgen.0.001188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 01/14/2024] [Indexed: 02/16/2024] Open
Abstract
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.
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Affiliation(s)
- Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Colman O'Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ahmad Zyoud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Bas Oude Munnink
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Björn Grüning
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Clara Amid
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | | | - Dávid Visontai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - David Yu Yuan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Divyae K. Prasad
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Gábor Máté Gulyás
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jasmine McKinnon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeff Knaggs
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeffrey Edward Skiby
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - József Stéger
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Judit Szarvas
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Khadim Gueye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Krisztián Papp
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Maarten Hoek
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Marianna A. Ventouratou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Martin Koliba
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Milena Mansurova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Muhammad Haseeb
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nathalie Worp
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Peter W. Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ross Thorne
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sandeep Selvakumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sundar Venkataraman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Timothée Cezard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wolfgang Maier
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Istvan Csabai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Marion Koopmans
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
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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 L, 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 J, 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. Whole genomes from bacteria collected at diagnostic units around the world 2020. Sci Data 2023; 10:628. [PMID: 37717051 PMCID: PMC10505216 DOI: 10.1038/s41597-023-02502-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/23/2023] [Indexed: 09/18/2023] Open
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.
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Affiliation(s)
- Sidsel Nag
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark.
| | - Gunhild Larsen
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
| | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
| | | | - Gábor Máté Gulyás
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
| | - Wojchiech Jakub Ciok
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
| | - Timmie Mikkel Lagermann
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
| | - Silva Tafaj
- Microbiology Department, University Hospital "Shefqet Ndroqi", Rruga Dr. Shefqet Ndroqi. Sauk, Tirana, 1044, Albania
| | - Susan Bradbury
- Microbiology Department, Canberra Hospital, Gilmore Cresent, Garran, 2605, Australian Capital Territory, Australia
| | - Peter Collignon
- Microbiology Department, Canberra Hospital, Gilmore Cresent, Garran, 2605, Australian Capital Territory, Australia
| | - Denise Daley
- Department of Microbiology, PathWest Laboratory Medicine, Fiona Stanley Hospital, 9 Robin Warren Drive, Murdoch, 6150, Western Australia, Australia
| | - Victorien Dougnon
- 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
| | - Kafayath Fabiyi
- 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
| | - Boubacar Coulibaly
- Department of Laboratory, Nouna Health Research Centre, Rue Namory Keita, Nouna, Burkina Faso
| | - René Dembélé
- Training and Research Unit in Applied Sciences and Technologies/Biochemistry-microbiology, University of Dedougou, Dedougou, 176, Boucle du Mouhoun, Burkina Faso
| | - Georgette Nikiema
- Training and Research Unit in Applied Sciences and Technologies/Biochemistry-microbiology, University of Dedougou, Dedougou, 176, Boucle du Mouhoun, Burkina Faso
| | - Natama Magloire
- Clinical Research Unit of Nanoro, National Institutes of Medical Research, Ouagadougou, 176, Burkina Faso
| | | | | | - Anowara Begum
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Deyan Donchev
- Clinical Laboratory of Microbiology and Virology, University Hospital "Lozenetz", Str. Kozyak 1, Sofia, 1407, Sofia, Bulgaria
| | | | | | - Simon Lévesque
- 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
| | | | - Kirstine Kobberoe Sogaard
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, Basel, 4031, Switzerland
| | - Paula Diaz Guevara
- Microbiology Group, Instituto Nacional de Salud, Avenida Calle 26·51-20 CAN, Bogotá, 111321, Colombia
| | | | - Panagiota Maikanti
- Charalampous, Microbiology Department, National Reference Laboratory for Antimicrobial Resistance Surveillance, Nicosia General Hospital, 215, Paleos Dromos Lefkosia-Lemesos str., Strovolos, 2029, Nicosia, Cyprus
| | - Jana Amlerova
- Department of Microbiology, University Hospital in Plzen, Edvarda Benese 1128/13, Plzen, 305 99, Czech Republic
| | - Pavel Drevinek
- Department of Medical Microbiology, Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic
| | - Jan Tkadlec
- Department of Medical Microbiology, Motol University Hospital, V Uvalu 84, Prague, 15006, Czech Republic
| | - Milica Dilas
- Otto-von-Guericke University, Magdebourg, Germany
| | - Achim Kaasch
- Otto-von-Guericke University, Magdebourg, Germany
| | - Henrik Torkil Westh
- Klinisk Mikrobiologisk Afdeling, Hvidovre Hospital, Kettegårds Allé, Hvidovre, 2650, Denmark
| | - Mohamed Azzedine Bachtarzi
- Laboratoire de Microbiologie Clinique, Centre Hospitalo-universitaire, 1 place du 1er Mai 1945, Algiers, 16000, Algeria
| | - Wahiba Amhis
- Laboratoire de Microbiologie Clinique, Centre Hospitalo-universitaire, 1 place du 1er Mai 1945, Algiers, 16000, Algeria
| | - Carolina Elisabeth Satán Salazar
- National Reference Center for Antimicrobial Resistance, National Institute of Public Health Research "Dr. Leopoldo Izquieta Pérez", Iquique N14-285, Quito, 170403, Pichicha, Ecuador
| | - JoséEduardo Villacis
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quinto, 1701-2184, Pichincha, Ecuador
| | | | | | - Claire Duployez
- Institute of Microbiology, Centre Hospitalier Universitaire de Lille, Rue du Pr. Jules Leclercq, Lille, 59037, France
| | - Maxime Paluche
- Bacteriology laboratory, Centre hospitalier de Valenciennes, Avenue Désandrouin, Valenciennes, 59300, France
| | - Solomon Asante-Sefa
- Sekondi Public Health Laboratory, Ghana Health Service, Effia Nkwanta Regional Hospital, Effia Nkwanta Regional Hospital, Takoradi, Ghana
| | - Mie Moller
- Dronning Ingrids Hospital, Nuuk, Greenland
| | - Margaret Ip
- Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ivana Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Kišpatićeva 12, Zagreb, 10000, Croatia
| | - Agnes Pál-Sonnevend
- Medical Microbiology and Immunology, University of Pecs Medical School, Szigeti ut 12, Pecs, 7631, Hungary
| | | | - Asta Dambrauskiene
- Laboratory Medicine Department, Hospital of Lithuanian University of Health Sciences Kauno klinikos, Eiveniu Str. 2, Kaunas, 50161, Lithuania
| | | | - Anelsio Cossa
- Centro de Investigação em Saúde de Manhiça, Manhiça, Mozambique
| | | | | | - Iruka N Okeke
- Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Aderemi O Kehinde
- College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- University College of Ibadan, Ibadan, Oyo State, Nigeria
| | - Ini Adebiyi
- Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- University College of Ibadan, Ibadan, Oyo State, Nigeria
| | - Ifeoluwa Akintayo
- College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Oluwafemi Popoola
- College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- University College of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Anita Blomfeldt
- Department of Microbiology and Infection Control, Akershus University Hospital, Sykehusveien 25, Lørenskog, 1478, Norway
| | - Nora Elisabeth Nyquist
- Department of Microbiology and Infection Control, Akershus University Hospital, Sykehusveien 25, Lørenskog, 1478, Norway
| | - Kiri Bocker
- Southern Community Laboratories, University of Otago, 472 George Street, Otago, 9016, Dunedin, New Zealand
| | - James Ussher
- Southern Community Laboratories, University of Otago, 472 George Street, Otago, 9016, Dunedin, New Zealand
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Habibullah Khan
- Molecular Diagnostic Section, Khyber Teaching Hospital (KTH), University Road, Peshawar, 25120, Pakistan
| | - Natalie Weiler Gustafson
- Departamento de Bacteriologia, Laboratorio Central de Salud Publico, Avenida Venezuela y Tte Escurra, Asunción, CP, 1429, Paraguay
| | - Ikhlas Jarrar
- Basic Medical Sciences Department, Arab American University, AAUP st., Zababdeh, P240, Jenin, Palestine
| | - Arif Al-Hamad
- Division of Clinical Microbiology, Qatif Central Hospital, 3213 Dharan-Jubail Expressway, Al-Qatif, 32654-7376, Eastern Province, Saudi Arabia
| | - Viravarn Luvira
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Bangkok, 10400, Thailand
| | | | - Irmak Baran
- Medical Microbiology Department, Karadeniz Technical University Farabi Hospital, Farabi Hastanesi, Trabzon, 61080, Ortahisar, Turkey
| | | | | | | | - Rene Sjogren Hendriksen
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
| | - Frank Moller Aarestrup
- National Food Institute, Technical University of Denmark, Kemitorvet, Kgs, Lyngby, 2800, Denmark
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Aytan-Aktug D, Grigorjev V, Szarvas J, Clausen PTLC, Munk P, Nguyen M, Davis JJ, Aarestrup FM, Lund O. SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies. Microbiol Spectr 2022; 10:e0264122. [PMID: 36377945 PMCID: PMC9769690 DOI: 10.1128/spectrum.02641-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.
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Affiliation(s)
- Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Vladislav Grigorjev
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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5
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Aytan-Aktug D, Clausen PTLC, Szarvas J, Munk P, Otani S, Nguyen M, Davis JJ, Lund O, Aarestrup FM. PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest. mSystems 2022; 7:e0118021. [PMID: 35382558 PMCID: PMC9040769 DOI: 10.1128/msystems.01180-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning-specifically, random forests. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level; the models achieved Matthews correlation coefficients of 0.662 and 0.867 at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool is available online through the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/). IMPORTANCE Antimicrobial resistance is a global health threat to humans and animals, causing high mortality and morbidity while effectively ending decades of success in fighting against bacterial infections. Plasmids confer extra genetic capabilities to the host organisms through accessory genes that can encode antimicrobial resistance and virulence. In addition to lateral inheritance, plasmids can be transferred horizontally between bacterial taxa. Therefore, detection of the host range of plasmids is crucial for understanding and predicting the dissemination trajectories of extrachromosomal genes and bacterial evolution as well as taking effective countermeasures against antimicrobial resistance.
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Affiliation(s)
- Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Judit Szarvas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, Illinois, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, Illinois, USA
| | - Ole Lund
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Szarvas J, Rebelo AR, Bortolaia V, Leekitcharoenphon P, Schrøder Hansen D, Nielsen HL, Nørskov-Lauritsen N, Kemp M, Røder BL, Frimodt-Møller N, Søndergaard TS, Coia JE, Østergaard C, Westh H, Aarestrup FM. Danish Whole-Genome-Sequenced Candida albicans and Candida glabrata Samples Fit into Globally Prevalent Clades. J Fungi (Basel) 2021; 7:jof7110962. [PMID: 34829249 PMCID: PMC8622182 DOI: 10.3390/jof7110962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Candida albicans and Candida glabrata are opportunistic fungal pathogens with increasing incidence worldwide and higher-than-expected prevalence in Denmark. We whole-genome sequenced yeast isolates collected from Danish Clinical Microbiology Laboratories to obtain an overview of the Candida population in the country. The majority of the 30 C. albicans isolates were found to belong to three globally prevalent clades, and, with one exception, the remaining isolates were also predicted to cluster with samples from other geographical locations. Similarly, most of the eight C. glabrata isolates were predicted to be prevalent subtypes. Antifungal susceptibility testing proved all C. albicans isolates to be susceptible to both azoles and echinocandins. Two C. glabrata isolates presented azole-resistant phenotypes, yet all were susceptible to echinocandins. There is no indication of causality between population structure and resistance phenotypes for either species.
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Affiliation(s)
- Judit Szarvas
- Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (A.R.R.); (V.B.); (P.L.); (F.M.A.)
- Correspondence:
| | - Ana Rita Rebelo
- Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (A.R.R.); (V.B.); (P.L.); (F.M.A.)
| | - Valeria Bortolaia
- Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (A.R.R.); (V.B.); (P.L.); (F.M.A.)
| | - Pimlapas Leekitcharoenphon
- Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (A.R.R.); (V.B.); (P.L.); (F.M.A.)
| | | | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, 9100 Aalborg, Denmark;
| | | | - Michael Kemp
- Department of Clinical Microbiology, Odense University Hospital, 5000 Odense, Denmark;
| | - Bent Løwe Røder
- Department of Clinical Microbiology, Slagelse Hospital, 4200 Slagelse, Denmark;
| | | | | | - John Eugenio Coia
- Department of Clinical Microbiology, Sydvestjysk Hospital, 6700 Esbjerg, Denmark;
| | - Claus Østergaard
- Department of Clinical Microbiology, Vejle Hospital, 7100 Vejle, Denmark;
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, 2650 Hvidovre, Denmark;
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Frank Møller Aarestrup
- Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (A.R.R.); (V.B.); (P.L.); (F.M.A.)
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Szarvas J, Bartels MD, Westh H, Lund O. Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting. Front Microbiol 2021; 12:636608. [PMID: 33868194 PMCID: PMC8047125 DOI: 10.3389/fmicb.2021.636608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.
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Affiliation(s)
- Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mette Damkjaer Bartels
- MRSA Knowledge Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
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Villabruna N, Izquierdo Lara RW, Szarvas J, Koopmans MPG, de Graaf M. Phylogenetic Investigation of Norovirus Transmission between Humans and Animals. Viruses 2020; 12:v12111287. [PMID: 33182775 PMCID: PMC7698157 DOI: 10.3390/v12111287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 01/03/2023] Open
Abstract
Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. One hypothesis is that new human infections may be seeded from an animal reservoir, as human noroviruses have occasionally been detected in animal species. The majority of these sequences were identified as older GII.4 variants, but a variety of other GIIs and GIs have been detected as well. While these sequences share at least 94% nt similarity with human strains, most of them are >98% identical to human strains. The fact that these strains were detected in animals after they had been detected through human surveillance to be already circulating in humans suggests human-to-animal transmission.
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Affiliation(s)
- Nele Villabruna
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Ray W. Izquierdo Lara
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (N.V.); (R.W.I.L.); (M.P.G.K.)
- Correspondence:
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Szarvas J, Ahrenfeldt J, Cisneros JLB, Thomsen MCF, Aarestrup FM, Lund O. Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform. Commun Biol 2020; 3:137. [PMID: 32198478 PMCID: PMC7083913 DOI: 10.1038/s42003-020-0869-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/03/2020] [Indexed: 11/09/2022] Open
Abstract
Public health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria. The computational methods have not kept up with the deluge of data and the need for real-time results. We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance. The data is divided into sets by mapping to reference genomes, then consensus sequences are generated. Nucleotide based genetic distance is calculated between the sequences in each set, and isolates are clustered together at 10 single-nucleotide polymorphisms. Phylogenetic trees are inferred from the non-redundant sequences and the clustered isolates are added back. The method is accurate at grouping outbreak strains together, while discriminating them from non-outbreak strains. The pipeline is applied in Evergreen Online, which processes publicly available sequencing data from foodborne bacterial pathogens on a daily basis, updating phylogenetic trees as needed.
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Affiliation(s)
- Judit Szarvas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Johanne Ahrenfeldt
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jose Luis Bellod Cisneros
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Halász K, Geösel A, Szarvas J, Virágh N, Hajdú C, Lukács N. Occurrence of double-stranded RNA species in champignon and their relation to Mushroom Virus X symptoms. Acta Alimentaria 2014. [DOI: 10.1556/aalim.2013.0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Szarvas J, Geösel A, Pál K, Naár Z, Győrfi J. Comparative studies of the cultivable king oyster mushroom [ Pleurotus eryngii(DC.: Fr.) Quél.] Isolates by RAPD-PCR method. Acta Alimentaria 2011. [DOI: 10.1556/aalim.40.2011.suppl.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sántha E, Szarvas J, Szabó L, Répásy G. [Active movement therapy after flexor tendon suture using a new dynamic control splint]. HANDCHIR MIKROCHIR P 1998; 30:312-6. [PMID: 9816512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The authors constructed a new dynamic guiding splint assisting the active mobilisation after flexor tendon repair distal to the wrist. In these cases, the "inverse" wrist position seems to be the best position for mobilisation. This means that finger flexion should be carried out during wrist extension, and finger extension during wrist flexion. The splint guides and co-ordinates the movements of the wrist and the fingers, and it limits the free usage of the hand.
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Affiliation(s)
- E Sántha
- Abteilung für Unfallchirurgie und Handchirurgie, Szent György-Krankenhauses in Székesfehérvár, Ungarn
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Sántha E, Szarvas J, Répásy G. [Does the flexed position of the wrist releave the stress on the suture in the flexor tendon?]. Magy Traumatol Ortop Kezseb Plasztikai Seb 1993; 36:261-267. [PMID: 8364661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Authors have examined the optimal position of the wrist from the viewpoint of active motion during the postoperative care, after the suture of the flexor tendons of the hand. Based on clinical and cadaveric experiences a motion of the wrist (inverse) in contrary direction to the motion of the fingers is suggested i. e. flexion of the fingers in wrist extension and vice versa. The tendon injuries distally and proximally from the wrist are discussed separately.
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Affiliation(s)
- E Sántha
- Fejér megyei Szent György Kórház Traumatológiai és Kézsebészeti Osztályának közleménye
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Sántha E, Szarvas J, Varga G, Varga M. [Contralateral autotransplantation of an upper limb]. HANDCHIR MIKROCHIR P 1988; 20:259-62. [PMID: 3181824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A case report of a contralateral autotransplantation after severe bilateral upper limb injury is presented. The left arm just above the elbow was replanted onto the stump of the right upper arm.
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Affiliation(s)
- E Sántha
- Abteilung für Unfallchirurgie und Handchirurgie. Staatlichen Krankenhauses in Székesfehérvár, Ungarn
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Háciková S, Krejcí L, Brozek B, Szarvas J. [Corneal pachymetry during gradual adaptation to contact lenses in low and medium myopia]. Cesk Oftalmol 1985; 41:107-10. [PMID: 3995608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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