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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2022; 10:80. [PMID: 35847383 PMCID: PMC9243550 DOI: 10.12688/f1000research.39214.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Affiliation(s)
| | - Marco Fabbri
- European Commission Joint Research Centre, Ispra, Italy
| | | | | | - Guy Van den Eede
- European Commission Joint Research Centre, Ispra, Italy
- European Commission Joint Research Centre, Geel, Belgium
| | - Erik Alm
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Catherine Carrillo
- Ottawa Laboratory – Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | | | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teresa Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, Madrid, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul Hammer
- BIOMES. NGS GmbH c/o Technische Hochschule Wildau, Wildau, Germany
| | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, Lyon, France
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Thierry Naas
- French-NRC for CPEs, Service de Bactériologie-Hygiène, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | | | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | | | - John Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Lukas M. Weber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Present address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2021; 10:80. [DOI: 10.12688/f1000research.39214.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 01/12/2023] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Mitsutake K, Watanabe N, Karaushi H, Tarumoto N, Koyama S, Ebihara Y, Yoshitake A, Nakajima H. Thoracic aortic mycotic aneurysm due to Staphylococcus argenteus: A case report. J Infect Chemother 2020; 26:1213-1215. [PMID: 32839112 DOI: 10.1016/j.jiac.2020.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 11/17/2022]
Abstract
Staphylococcus argenteus was subdivided as a novel species from Staphylococcus aureus in 2014. We herein report a case of mycotic aneurysm caused by S. argenteus. A 59-year-old woman with diabetes and schizophrenia visited at the emergency room because of falling. Chest computed tomography revealed a left humerus fracture and a thoracic aortic aneurysm. With her elevated WBC count and CRP level, she was suspected to have a mycotic aneurysm. After being transferred to our hospital, vascular graft replacement surgery was performed. Isolates of blood cultures and surgical specimens were identified as S. argenteus by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MAS MALDI Biotyper Ver. 8.0). Although S. argenteus lacks staphyloxanthin, a carotenoid pigment, it is coagulase positive. In addition to traditional and automated biochemical identification systems, even MALDI-TOF MAS may misidentify the organism as S. aureus depending on its version. S. argenteus should be considered when coagulase-negative Staphylococcus like colonies are obtained from samples of S. aureus infection. To our knowledge, this is the first case of aortic mycotic aneurysm caused by S. argenteus in Japan. Although S. argenteus is considered less virulent than Staphylococcus aureus, we should closely monitor the prevalence and the clinical impact of this pathogen on community-acquired infections and health care-associated infections.
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Affiliation(s)
- Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan.
| | - Noriyuki Watanabe
- Department of Laboratory Medicine, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Haruka Karaushi
- Department of Pharmacy, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Sachie Koyama
- Department of Laboratory Medicine, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Yasuhiro Ebihara
- Department of Laboratory Medicine, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Akihiro Yoshitake
- Department of Cardiovascular Surgery, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Hiroyuki Nakajima
- Department of Cardiovascular Surgery, Saitama International Medical Center, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1298, Japan
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Kozajda A, Jeżak K, Kapsa A. Airborne Staphylococcus aureus in different environments-a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:34741-34753. [PMID: 31654301 PMCID: PMC6900272 DOI: 10.1007/s11356-019-06557-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/23/2019] [Indexed: 05/22/2023]
Abstract
The aim of the literature review was to describe the environments where the presence of airborne Staphylococcus aureus was confirmed and to catalogue the most often used methods and conditions of bioaerosol sampling to identify the bacteria. The basis for searching of studies on S. aureus in the bioaerosol in different environments was PubMed database resources from the years 1990-2019 (May). The review included studies which were carried on in selected environments: hospitals and other health care facilities, large-scale animal breeding, wastewater treatment plants, residential areas, educational institutions, and other public places. The highest concentrations and genetic diversity of identified S. aureus strains, including MRSA (methicillin-resistant S. aureus), have been shown in large-scale animal breeding. The role of the airborne transmission in dissemination of infection caused by these pathogens is empirically confirmed in environmental studies. Commonly available, well-described, and relatively inexpensive methods of sampling, identification, and subtyping guarantee a high reliability of results and allow to obtain fast and verifiable outcomes in environmental studies on air transmission routes of S. aureus strains.
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Affiliation(s)
- Anna Kozajda
- Nofer Institute of Occupational Medicine, 8 Teresy Str, 91-348, Łódź, Poland.
| | - Karolina Jeżak
- Nofer Institute of Occupational Medicine, 8 Teresy Str, 91-348, Łódź, Poland
| | - Agnieszka Kapsa
- Nofer Institute of Occupational Medicine, 8 Teresy Str, 91-348, Łódź, Poland
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