Publicação
Pan-genome comparison between Streptococcus dysgalactiae subsp. equisimilis isolates from human and animal sources
| Resumo: | Streptococcus dysgalactiae subsp. equisimilis (SDSE) is being increasingly reported not only in human infections, but also colonizes various animal species, although no genomic analysis has been done to clarify the genomic identity and taxonomy of the isolates from animal origin. To assess the differences between SDSE isolates from human and animal sources, a pan-genome comparison was performed with a collection of SDSE isolates from human (n=29) and animal (n=32) sources. The collection was de novo assembled and annotated, with quality control performed after the assembly. Three datasets where used in the pan-genome analysis, one with the 61 SDSE samples, a second with the addition of a Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) genome sequence and the third with the option to not split paralogous genes. Three different clades were distinguishable in all analysis, one containing isolates recovered from human sources (n=26), other containing isolates recovered from horses (n=15), and the third clade containing isolates recovered from various hosts, including human, horse, pig, dog, chicken, fish, duck, iguana and cow. To assess if the variation detected through the pan-genomic analysis was detectable in techniques to index and catalogue strain variation, the core-genome of the 61 SDSE was studied through MultiLocus Sequence Typing (MLST) and core-genome MultiLocus Sequence Typing (cgMLST). The exclusive accessory genome of the clades containing isolates recovered exclusively from human and horses was studies, preliminarily through clustergrams and queries done to the pan-genome obtained. Gene association studies were carried out in the pan-genome regarding the three SDSE clades, with the significantly associated genes present in at least 90% of the isolates of the human and horse clade being selected as the respective exclusive accessory genome. The exclusive accessory genome for the human clade is composed by 40 genes, changing to 45 genes when the paralogous genes are not split, and the exclusive accessory genome for the horse clade is composed by 22 genes, changing to 20 genes when the paralogous genes are not split. The gene ontology terms for the genes in the exclusive accessory genome of the two clades were retrieved. The exclusive accessory genomes for each clade were evaluated for potential virulence factors that could explain the host specificity of the clades, having found several homologous genes, recognized as virulence factors in Streptococcus pyogenes in the human SDSE clade, and diverse potential virulence factors for the horse SDSE clade. |
|---|---|
| Autores principais: | Mendes, Catarina Inês Marques de Sousa |
| Assunto: | Sequenciação de Alto Débito Pan-genoma Genoma acessório exclusivo Estudos de associação génica Teses de mestrado - 2016 |
| Ano: | 2016 |
| 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: | Streptococcus dysgalactiae subsp. equisimilis (SDSE) is being increasingly reported not only in human infections, but also colonizes various animal species, although no genomic analysis has been done to clarify the genomic identity and taxonomy of the isolates from animal origin. To assess the differences between SDSE isolates from human and animal sources, a pan-genome comparison was performed with a collection of SDSE isolates from human (n=29) and animal (n=32) sources. The collection was de novo assembled and annotated, with quality control performed after the assembly. Three datasets where used in the pan-genome analysis, one with the 61 SDSE samples, a second with the addition of a Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) genome sequence and the third with the option to not split paralogous genes. Three different clades were distinguishable in all analysis, one containing isolates recovered from human sources (n=26), other containing isolates recovered from horses (n=15), and the third clade containing isolates recovered from various hosts, including human, horse, pig, dog, chicken, fish, duck, iguana and cow. To assess if the variation detected through the pan-genomic analysis was detectable in techniques to index and catalogue strain variation, the core-genome of the 61 SDSE was studied through MultiLocus Sequence Typing (MLST) and core-genome MultiLocus Sequence Typing (cgMLST). The exclusive accessory genome of the clades containing isolates recovered exclusively from human and horses was studies, preliminarily through clustergrams and queries done to the pan-genome obtained. Gene association studies were carried out in the pan-genome regarding the three SDSE clades, with the significantly associated genes present in at least 90% of the isolates of the human and horse clade being selected as the respective exclusive accessory genome. The exclusive accessory genome for the human clade is composed by 40 genes, changing to 45 genes when the paralogous genes are not split, and the exclusive accessory genome for the horse clade is composed by 22 genes, changing to 20 genes when the paralogous genes are not split. The gene ontology terms for the genes in the exclusive accessory genome of the two clades were retrieved. The exclusive accessory genomes for each clade were evaluated for potential virulence factors that could explain the host specificity of the clades, having found several homologous genes, recognized as virulence factors in Streptococcus pyogenes in the human SDSE clade, and diverse potential virulence factors for the horse SDSE clade. |
|---|