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Sielemann J, Sielemann K, Brejová B, Vinař T, Chauve C. plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph. Front Microbiol 2023; 14:1267695. [PMID: 37869681 PMCID: PMC10587606 DOI: 10.3389/fmicb.2023.1267695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023] Open
Abstract
Identification of plasmids from sequencing data is an important and challenging problem related to antimicrobial resistance spread and other One-Health issues. We provide a new architecture for identifying plasmid contigs in fragmented genome assemblies built from short-read data. We employ graph neural networks (GNNs) and the assembly graph to propagate the information from nearby nodes, which leads to more accurate classification, especially for short contigs that are difficult to classify based on sequence features or database searches alone. We trained plASgraph2 on a data set of samples from the ESKAPEE group of pathogens. plASgraph2 either outperforms or performs on par with a wide range of state-of-the-art methods on testing sets of independent ESKAPEE samples and samples from related pathogens. On one hand, our study provides a new accurate and easy to use tool for contig classification in bacterial isolates; on the other hand, it serves as a proof-of-concept for the use of GNNs in genomics. Our software is available at https://github.com/cchauve/plasgraph2 and the training and testing data sets are available at https://github.com/fmfi-compbio/plasgraph2-datasets.
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Affiliation(s)
- Janik Sielemann
- Computational Biology, Faculty of Biology, Center for Biotechnology & Graduate School Digital Infrastructures for the Life Sciences (DILS), Bielefeld Institute for Bioinformatics Infrastructure, Bielefeld University, Bielefeld, Germany
| | - Katharina Sielemann
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology & Graduate School Digital Infrastructures for the Life Sciences (DILS), Bielefeld Institute for Bioinformatics Infrastructure, Bielefeld University, Bielefeld, Germany
| | - Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
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Asano K, Hirose S, Narita K, Subsomwong P, Kawai N, Sukchawalit R, Nakane A. Extracellular vesicles from methicillin resistant Staphylococcus aureus stimulate proinflammatory cytokine production and trigger IgE-mediated hypersensitivity. Emerg Microbes Infect 2021; 10:2000-2009. [PMID: 34623928 PMCID: PMC8547819 DOI: 10.1080/22221751.2021.1991239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular vesicles (EVs) released from bacteria are enclosed particles carrying biological active molecules. They have been shown to play a role in bacterial communications and delivery of virulence factors to the host cells. Staphylococcus aureus is an opportunistic pathogen causing a variety of infections ranging from impetigo to septicaemia. The EVs released from S. aureus have a high potential to be used for vaccine development against S. aureus infections. However, it is important to clearly understand the impact of SaEVs on the host’s immune response. Our study demonstrated that purified EVs from a clinical isolated methicillin-resistant S. aureus (SaEVs) significantly stimulated proinflammatory cytokine production in mouse immune cells and induced host cell death. An impairment of cytokine production in the Toll-like receptor (TLR)-silenced macrophages suggested that SaEVs stimulate proinflammatory response via TLRs 2, 4 and 9. In mouse infection model, the results demonstrated that SaEV immunization did not provide protective effect. In contrast, all SaEV-immunized mice died within Day 1 after methicillin-resistant S. aureus (MRSA) infection. After MRSA infection for 3 h, the production of IL-6, TNF-α and IL-17 in the spleen of SaEV-immunized mice was significantly higher than that of control mice. On Day 5 after the second immunization, total IgE in the serum was significantly enhanced, and a high titre of Th2-related cytokines was remarkably induced after ex vivo stimulation of the spleen cells with SaEVs. These results suggested that MRSA-derived EVs act as an immunostimulant that induces inflammatory response and IgE-mediated hypersensitivity after MRSA infection.
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Affiliation(s)
- Krisana Asano
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan.,Department of Biopolymer and Health Science, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Shouhei Hirose
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Kouji Narita
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan.,Institute for Animal Experimentation, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Phawinee Subsomwong
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Noriaki Kawai
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Rojana Sukchawalit
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, Thailand
| | - Akio Nakane
- Department of Biopolymer and Health Science, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
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