Genômica comparativa de Shigella spp. isoladas de crianças com doenças diarreicas na Amazônia

Abstract

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 Diagnóstico e Controle de DoençasInfecciosasna Amazônia (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.