Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing
Cyanobacteria are ubiquitous in freshwater environments, but their role in aquatic resistome remains unclear. In this work, we performed whole genome sequencing on 43 cyanobacterial strains isolated from Portuguese fresh/wastewaters. From 43 available non-axenic unicyanoabacterial cultures (containi...
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2025-05-01
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| author | Duarte Balata Tânia Rosado Francisco Pina-Martins Vera Manageiro Carina Menezes Eugénia Ferreira Octávio S. Paulo Manuela Caniça Elsa Dias |
| author_facet | Duarte Balata Tânia Rosado Francisco Pina-Martins Vera Manageiro Carina Menezes Eugénia Ferreira Octávio S. Paulo Manuela Caniça Elsa Dias |
| author_sort | Duarte Balata |
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| description | Cyanobacteria are ubiquitous in freshwater environments, but their role in aquatic resistome remains unclear. In this work, we performed whole genome sequencing on 43 cyanobacterial strains isolated from Portuguese fresh/wastewaters. From 43 available non-axenic unicyanoabacterial cultures (containing only one cyanobacterial strain and their co-occurring bacteria), it was possible to recover 41 cyanobacterial genomes from the genomic assemblies using a genome binning software, 26 of which were classified as high-quality based on completeness, contamination, N50 and contig number thresholds. By using the comprehensive antibiotic resistance database (CARD) on the assembled samples, we detected four antibiotic resistance gene (ARG) variants, conferring resistance in pathogenic bacteria to tetracyclines, fluoroquinolones (<i>adeF</i>-type) and macrolides (<i>ermF</i>-type, <i>mefC</i>-type and <i>mphG</i>-type). Among these, <i>adeF</i>-type was the most prevalent gene, found across 11 cyanobacterial genomes from the Nostocales order. <i>Planktothrix</i> presented the highest variety of close ARG matches, with hits for the macrolide resistance genes <i>ermF</i>-type, <i>mefC</i>-type and <i>mphG-</i>type. An analysis of the genomic assemblies also revealed an additional 12 ARGs in bacteria from the phyla Firmicutes, Proteobacteria and Bacteroidetes, present in the cyanobacterial cultures, foreseeing the horizontal gene transfer of ARGs with cyanobacteria. Additionally, more than 200 partial ARGs were detected on each recovered cyanobacterial genome, allowing for future studies of antibiotic resistance genotype/phenotype in cyanobacteria. These findings highlight the importance of further efforts to understand the role of cyanobacteria on the aquatic resistome from a One Health perspective. |
| format | Article |
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| publishDate | 2025-05-01 |
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| spelling | doaj-art-309fc4a0775b4e67a1f102619fd66f552025-08-20T03:16:34ZengMDPI AGMicroorganisms2076-26072025-05-01136125210.3390/microorganisms13061252Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome SequencingDuarte Balata0Tânia Rosado1Francisco Pina-Martins2Vera Manageiro3Carina Menezes4Eugénia Ferreira5Octávio S. Paulo6Manuela Caniça7Elsa Dias8Centre for Ecology, Evolution and Environmental Changes (CE3C) & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, PortugalLaboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, PortugalCentre for Ecology, Evolution and Environmental Changes (CE3C) & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, PortugalNational Reference Laboratory of Antibiotic Resistance and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, PortugalLaboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, PortugalNational Reference Laboratory of Antibiotic Resistance and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, PortugalCentre for Ecology, Evolution and Environmental Changes (CE3C) & CHANGE—Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, PortugalNational Reference Laboratory of Antibiotic Resistance and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, PortugalLaboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, PortugalCyanobacteria are ubiquitous in freshwater environments, but their role in aquatic resistome remains unclear. In this work, we performed whole genome sequencing on 43 cyanobacterial strains isolated from Portuguese fresh/wastewaters. From 43 available non-axenic unicyanoabacterial cultures (containing only one cyanobacterial strain and their co-occurring bacteria), it was possible to recover 41 cyanobacterial genomes from the genomic assemblies using a genome binning software, 26 of which were classified as high-quality based on completeness, contamination, N50 and contig number thresholds. By using the comprehensive antibiotic resistance database (CARD) on the assembled samples, we detected four antibiotic resistance gene (ARG) variants, conferring resistance in pathogenic bacteria to tetracyclines, fluoroquinolones (<i>adeF</i>-type) and macrolides (<i>ermF</i>-type, <i>mefC</i>-type and <i>mphG</i>-type). Among these, <i>adeF</i>-type was the most prevalent gene, found across 11 cyanobacterial genomes from the Nostocales order. <i>Planktothrix</i> presented the highest variety of close ARG matches, with hits for the macrolide resistance genes <i>ermF</i>-type, <i>mefC</i>-type and <i>mphG-</i>type. An analysis of the genomic assemblies also revealed an additional 12 ARGs in bacteria from the phyla Firmicutes, Proteobacteria and Bacteroidetes, present in the cyanobacterial cultures, foreseeing the horizontal gene transfer of ARGs with cyanobacteria. Additionally, more than 200 partial ARGs were detected on each recovered cyanobacterial genome, allowing for future studies of antibiotic resistance genotype/phenotype in cyanobacteria. These findings highlight the importance of further efforts to understand the role of cyanobacteria on the aquatic resistome from a One Health perspective.https://www.mdpi.com/2076-2607/13/6/1252antibiotic resistanceaquatic resistomefreshwater bacteriacyanobacteriagenomebioinformatics pipeline |
| spellingShingle | Duarte Balata Tânia Rosado Francisco Pina-Martins Vera Manageiro Carina Menezes Eugénia Ferreira Octávio S. Paulo Manuela Caniça Elsa Dias Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing Microorganisms antibiotic resistance aquatic resistome freshwater bacteria cyanobacteria genome bioinformatics pipeline |
| title | Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing |
| title_full | Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing |
| title_fullStr | Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing |
| title_full_unstemmed | Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing |
| title_short | Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing |
| title_sort | prediction of antibiotic resistance genes in cyanobacterial strains by whole genome sequencing |
| topic | antibiotic resistance aquatic resistome freshwater bacteria cyanobacteria genome bioinformatics pipeline |
| url | https://www.mdpi.com/2076-2607/13/6/1252 |
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