Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2016 |
| Outros Autores: | , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/17895 |
Resumo: | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ. Brasil. |
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Fróes, Adriana M.Mota, Fábio F. daCuadrat, Rafael R. C.Dávila, Alberto M. R.2017-02-23T16:27:21Z2017-02-23T16:27:21Z2016FRÓES, Adriana M. et al. Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases. Frontiers in Microbiology, Frontiers in Microbiology, v.7, Article 1790, 15p, Nov. 2016.1664-302Xhttps://www.arca.fiocruz.br/handle/icict/1789510.3389/fmicb.2016.01790engFrontiers MediaDiversidade filogenéticaEsgoto hospitalarMetagenomes AmbientaisSerinaβ-lactamAntibióticosserine β-lactamaseshospital sewagemetagenomeHidden-Markov-Modelphylogenetic diversityDistribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databasesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ. Brasil.β-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as β-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine β-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available. Also, we propose a Hidden-Markov-Model approach to screen potential serine β-lactamases genes (in public environments samples and generated hospital sewage data), exploring its evolutionary relationships. Due to the high variability in β-lactamases, we used a position-specific scoring matrix search method (RPS-BLAST) against conserved domain database profiles (CDD, Pfam, and COG) followed by visual inspection to detect conserved motifs, to increase the reliability of the results and remove possible false positives. We were able to identify novel β-lactamases from Brazilian hospital sewage and to estimate relative abundance of its types. The highest relative abundance found in SZ was the Class A (50%), while Class D is predominant in NZ (55%). CfxA (65%) and ACC (47%) types were the most abundant genes detected in SZ, while in NZ the most frequent were OXA-10 (32%), CfxA (28%), ACC (21%), CEPA (20%), and FOX (19%). Phylogenetic analysis revealed β-lactamases from Brazilian hospital sewage grouped in the same clade and close to sequences belonging to Firmicutes and Bacteroidetes groups, but distant from potential β-lactamases screened from public environmental data, that grouped closer to β-lactamases of Proteobacteria. Our results demonstrated that HMM-based approach identified homologs of serine β-lactamases, indicating the specificity and high sensitivity of this approach in large datasets, contributing for the identification and classification of a large number of homologous genes, comprising possible new ones. Phylogenetic analysis revealed the potential reservoir of β-lactam resistance genes in the environment, contributing to understanding the evolution and dissemination of these genes.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/17895/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALadriana_froes_etal_IOC_2016.pdfadriana_froes_etal_IOC_2016.pdfapplication/pdf3634032https://www.arca.fiocruz.br/bitstream/icict/17895/2/adriana_froes_etal_IOC_2016.pdf7c46bcadcfb95fd20f649d9b3ebcd5dfMD52data sheet 1.docdata sheet 1.docMaterial Suplementarapplication/msword1397760https://www.arca.fiocruz.br/bitstream/icict/17895/3/data%20sheet%201.doca6feb00e644d76f9a137741e607f3320MD53TEXTadriana_froes_etal_IOC_2016.pdf.txtadriana_froes_etal_IOC_2016.pdf.txtExtracted 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| dc.title.pt_BR.fl_str_mv |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| title |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| spellingShingle |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases Fróes, Adriana M. Diversidade filogenética Esgoto hospitalar Metagenomes Ambientais Serina β-lactam Antibióticos serine β-lactamases hospital sewage metagenome Hidden-Markov-Model phylogenetic diversity |
| title_short |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| title_full |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| title_fullStr |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| title_full_unstemmed |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| title_sort |
Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases |
| author |
Fróes, Adriana M. |
| author_facet |
Fróes, Adriana M. Mota, Fábio F. da Cuadrat, Rafael R. C. Dávila, Alberto M. R. |
| author_role |
author |
| author2 |
Mota, Fábio F. da Cuadrat, Rafael R. C. Dávila, Alberto M. R. |
| author2_role |
author author author |
| dc.contributor.author.fl_str_mv |
Fróes, Adriana M. Mota, Fábio F. da Cuadrat, Rafael R. C. Dávila, Alberto M. R. |
| dc.subject.other.pt_BR.fl_str_mv |
Diversidade filogenética Esgoto hospitalar Metagenomes Ambientais Serina β-lactam Antibióticos |
| topic |
Diversidade filogenética Esgoto hospitalar Metagenomes Ambientais Serina β-lactam Antibióticos serine β-lactamases hospital sewage metagenome Hidden-Markov-Model phylogenetic diversity |
| dc.subject.en.pt_BR.fl_str_mv |
serine β-lactamases hospital sewage metagenome Hidden-Markov-Model phylogenetic diversity |
| description |
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ. Brasil. |
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2016 |
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2016 |
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2017-02-23T16:27:21Z |
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2017-02-23T16:27:21Z |
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FRÓES, Adriana M. et al. Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases. Frontiers in Microbiology, Frontiers in Microbiology, v.7, Article 1790, 15p, Nov. 2016. |
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https://www.arca.fiocruz.br/handle/icict/17895 |
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1664-302X |
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10.3389/fmicb.2016.01790 |
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FRÓES, Adriana M. et al. Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases. Frontiers in Microbiology, Frontiers in Microbiology, v.7, Article 1790, 15p, Nov. 2016. 1664-302X 10.3389/fmicb.2016.01790 |
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