Publicação
Transição das tecnologias “tradicionais” de tipagem para a tecnologia de sequenciação total do genoma para o estudo e caracterização molecular de agentes patogénicos transmitidos por alimentos e água
| Resumo: | Infectious Diseases, in particular food- and waterborne diseases (FWD), are critical public health concerns nowadays, reinforcing that public health laboratories should establish accurate strategies that allow a proper epidemiological surveillance of the causative infectious agents. With the advances in the whole genome sequencing (WGS) technologies, and associated bioinformatics, genome-based typing tools are becoming the gold standard methodology for laboratory epidemiological monitoring of FWD, with recognized benefits for public health. In the present study, we aimed at starting the implementation of WGS/bioinformatics techniques (in place of traditional typing methods) for routine epidemiological surveillance of FWD-associated pathogens, more specifically of four of the most clinically relevant bacterial pathogens: Listeria monocytogenes, Salmonella enterica, verocytotoxin-producing Escherichia coli (VTEC) and Campylobacter jejuni. The WGS of multiple bacterial isolates (n= 89) firstly allowed us to apply and test multiple bioinformatics tools for in silico capture of the typing data routinely provided by the traditional pheno- and genotyping techniques. In general, high levels of concordance were reached, opening good perspectives that backwards compatibility with “historical” typing data may be ensured during this technology transfer process. Subsequently, in order to test novel genome-based typing tools for routine surveillance of FWD, we implemented and assayed core genome multilocus sequence typing (cgMLST) schemes and core-genome SNP-based strategies, with unequivocal gains regarding the discriminatory power. Moreover, the results were particularly concordantly between the two strategies, which also stood when applying either “assembly-free” or “de novo assembly-based” core-genome SNP-based strategies. Finally, our insights on the potential of WGS/bioinformatics to predict bacterial virulence and antimicrobial susceptibility profiles provided very optimistic perspectives for the future routine application of WGS for such purposes. In conclusion, the present study constitutes an unequivocally important step towards the application of genome-based typing tools as the future gold standard technique for routine epidemiological surveillance of FWD in Portugal. |
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| Autores principais: | Ferreira, Marta Patrícia Ribeiro |
| Assunto: | Food- and waterborne diseases Epidemiological surveillance Traditional typing methodologies Whole-genome sequencing Bioinformatics Teses de mestrado - 2017 |
| Ano: | 2017 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório da Universidade de Lisboa |
| Resumo: | Infectious Diseases, in particular food- and waterborne diseases (FWD), are critical public health concerns nowadays, reinforcing that public health laboratories should establish accurate strategies that allow a proper epidemiological surveillance of the causative infectious agents. With the advances in the whole genome sequencing (WGS) technologies, and associated bioinformatics, genome-based typing tools are becoming the gold standard methodology for laboratory epidemiological monitoring of FWD, with recognized benefits for public health. In the present study, we aimed at starting the implementation of WGS/bioinformatics techniques (in place of traditional typing methods) for routine epidemiological surveillance of FWD-associated pathogens, more specifically of four of the most clinically relevant bacterial pathogens: Listeria monocytogenes, Salmonella enterica, verocytotoxin-producing Escherichia coli (VTEC) and Campylobacter jejuni. The WGS of multiple bacterial isolates (n= 89) firstly allowed us to apply and test multiple bioinformatics tools for in silico capture of the typing data routinely provided by the traditional pheno- and genotyping techniques. In general, high levels of concordance were reached, opening good perspectives that backwards compatibility with “historical” typing data may be ensured during this technology transfer process. Subsequently, in order to test novel genome-based typing tools for routine surveillance of FWD, we implemented and assayed core genome multilocus sequence typing (cgMLST) schemes and core-genome SNP-based strategies, with unequivocal gains regarding the discriminatory power. Moreover, the results were particularly concordantly between the two strategies, which also stood when applying either “assembly-free” or “de novo assembly-based” core-genome SNP-based strategies. Finally, our insights on the potential of WGS/bioinformatics to predict bacterial virulence and antimicrobial susceptibility profiles provided very optimistic perspectives for the future routine application of WGS for such purposes. In conclusion, the present study constitutes an unequivocally important step towards the application of genome-based typing tools as the future gold standard technique for routine epidemiological surveillance of FWD in Portugal. |
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