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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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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] [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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3
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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4
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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] [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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5
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Clausen PTLC. Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining. Bioinformatics 2022; 39:6858462. [PMID: 36453849 PMCID: PMC9805563 DOI: 10.1093/bioinformatics/btac774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
MOTIVATION The neighbor-joining (NJ) algorithm is a widely used method to perform iterative clustering and forms the basis for phylogenetic reconstruction in several bioinformatic pipelines. Although NJ is considered to be a computationally efficient algorithm, it does not scale well for datasets exceeding several thousand taxa (>100 000). Optimizations to the canonical NJ algorithm have been proposed; these optimizations are, however, achieved through approximations or extensive memory usage, which is not feasible for large datasets. RESULTS In this article, two new algorithms, dynamic neighbor joining (DNJ) and heuristic neighbor joining (HNJ), are presented, which optimize the canonical NJ method to scale to millions of taxa without increasing the memory requirements. Both DNJ and HNJ outperform the current gold standard methods to construct NJ trees, while DNJ is guaranteed to produce exact NJ trees. AVAILABILITY AND IMPLEMENTATION https://bitbucket.org/genomicepidemiology/ccphylo.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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6
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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] [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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Timme RE, Wolfgang WJ, Balkey M, Venkata SLG, Randolph R, Allard M, Strain E. Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. ONE HEALTH OUTLOOK 2020; 2:20. [PMID: 33103064 PMCID: PMC7568946 DOI: 10.1186/s42522-020-00026-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings. Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.
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Affiliation(s)
- Ruth E. Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740 USA
| | | | - Maria Balkey
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740 USA
| | | | - Robyn Randolph
- Association of Public Health Laboratories, Silver Spring, MD USA
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740 USA
| | - Errol Strain
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD USA
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