Gen??mica comparativa de Shigella spp. isoladas de crian??as com doen??as diarreicas na Amaz??nia

• Author(s): Ver??osa, Jo??o Victor de Melo
• Date: 2019
• Origin: Oasisbr
• Subject(s): Shigella; Gen??mica; Bioinform??tica; Shigelose; SST3; CI??NCIAS BIOL??GICAS
• Document Type: Master thesis
• Language: Portuguese

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FAPEAM - Funda????o de Amparo ?? Pesquisa do Estado do Amazonas

92 981041214

Diarrhea is the second leading cause of child mortality in the world. Diarrheal diseases include shigellosis, a disease characterized by the presence of mucus and blood in the faeces, in addition to fever, colic and tenesms. Currently, around 165 million cases of the disease occur worldwide, with 1.5 million deaths a year. This disease has as its etiologic agent the Shigella, being four species belonging to this genus: S. flexneri, S. sonnei, S. boydii and S. dysenteriae; the first two being the most endemic in the world. The pathogenicity of Shigella is dependent on the Type 3 Secretion System (T3SS), located in pINV, an invasion plasmid found in all species of the genus. T3SS expresses proteins that dribble the host's immune system, causing the bacteria to lodge and multiply within the intestinal epithelial cells. Besides the SST3, Type 2 (T2SS) and 6 (T6SS) Secretion Systems can be found in Shigella, the first in S. boydii and the second, more recently described, in S. sonnei. A study conducted by the group Diagn??stico e Controle de Doen??asInfecciosasna Amaz??nia (DCDIA) in 2009, stool samples were collected from 1339 children, in which 30 strains of Shigella were found. From these, 7 were selected, which followed for the complete sequencing of their genomes in the Illumina HiSeq 2500 equipment. The contigs were assembled using the approach de novo in the Velvet software and the scaffolds assembled by ABACAS. The annotation was made by the Prokka pipeline. The samples were classified from the comparison of sequences in several databases, such as Genbank, using the tool BLAST, RDP and SILVA. Of the 7 bacteria, 4 were classified as S. flexneri and 3, as S. boydii, a species rarely found outside India. With an annotation made by KAAS, metabolic pathways were visualized in the KEGG using the Pathway package, in which the T6SS was identified in the 3 representatives of S. boydii. This system guarantees a competitive adaptive advantage for the bacteria and may be the answer as to why the number of S. boydii cases outside India has increased.

A diarreia ?? a segunda maior causa de mortalidade infantil no mundo. Dentre as doen??as diarreicas, destaca-se a shigelose, uma doen??a caracterizada pela presen??a de muco e sangue nas fezes, al??m de febre, c??lica e tenesmos. Atualmente no mundo, ocorrem cerca de 165 milh??es de casos da doen??a com 1,5 milh??es de mortes por ano. Essa doen??a tem como seu agente etiol??gico a Shigella, sendo quatro esp??cies pertencentes a este g??nero: S. flexneri, S. sonnei, S. boydii e S. dysenteriae; sendo as duas primeiras as mais end??micas no mundo. A patogenicidade da Shigella ?? dependente do Sistema de Secre????o do Tipo 3 (SST3), localizado no pINV, um plasm??deo de invas??o encontrado em todas as esp??cies do g??nero. O SST3 expressa prote??nas que driblam o sistema imunol??gico do hospedeiro, fazendo com que a bact??ria consiga se alojar e multiplicar-se dentro das c??lulas epiteliais do intestino. Al??m do SST3, podem ser encontrados na Shigella os Sistemas de Secre????o Tipo II (SST2) e VI (SST6), o primeiro em S. boydii e o segundo, mais recentemente descrito, em S. sonnei. Um estudo realizado pelo grupo Diagn??stico e Controle de Doen??as Infecciosas na Amaz??nia (DCDIA) em 2009, foram coletadas amostras de fezes de 1339 crian??as, no qual foram encontradas 30 cepas de Shigella. Destas, foram selecionadas 7, que seguiram para o sequenciamento completo de seus genomas no equipamento Illumina HiSeq 2500. Os contigs foram montados utilizando a abordagem de novo, no software Velvet e os scaffolds montados pelo ABACAS. A anota????o foi feita pelo pipeline do Prokka. As amostras foram classificadas a partir da compara????o de sequencias em v??rios bancos de dados, como Genbank, utilizando a ferramenta BLAST, RDP e SILVA. Das 7 bact??rias, 4 foram classificadas como S. flexneri e 3, como S. boydii, uma esp??cie raramente encontrada fora da ??ndia. Com uma anota????o feita pelo KAAS, foram visualizadas vias metab??licas no KEGG, utilizando o pacote Pathway, no qual foi identificado o SST6 nas 3 representantes da S. boydii. Esse sistema garante uma vantagem adaptativa competitiva para a bact??ria, podendo ser a resposta do porqu?? o n??mero de casos com S. boydii fora da ??ndia tem crescido.

Achei bem simples e f??cil de fazer!