Publicação
Comparative resistome, virulome and mobilome analysis of metagenomes from wild and farm animals
| Resumo: | Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability of horizontal gene transfer, bacteria are capable of “borrowing” and “lending” defensive and evasive maneuvers against antibiotics from other neighboring bacteria. As a consequence of antibiotic use, the frequency of antibiotic-resistant bacteria increases in the microbiome, eventually containing mobile genetic elements coding for antimicrobial resistance genes, thus favoring the dissemination of these genes which can lead to the ineffectiveness of the antibiotic. Furthermore, recent studies have shown that, as a side effect of antibiotic intake in medicine, people may be selecting more virulent strains. The quick rise of resistant bacteria threatens the effectiveness of antibiotics worldwide. For this reason, it is crucial to understand the relationship between antibiotic resistance (AR), virulence factors (VF) and mobile genetic elements (MGEs). With this project, we aim to study the metagenomes of domesticated and wild animals. To have an understanding of the impact of AR pollution and dissemination, we created a bioinformatic workflow to make a comparative study of the richness and diversity of the determinants of bacterial AR, VFs and MGEs in the microbiomes of domestic and wild animals. We retrieved metagenomic files of geese, mice, horses and yaks from NCBI, MG-RAST and NCBC, and utilized MetaSPADES and Prokka to assemble, annotate and translate them. In order to compare the richness and diversity of the animals’ microbiomes, we used two files for each metagenome: one with the complete DNA sequence (FNA) and another one in which the translated proteins were clustered at 90% identity. We used these files as input for BLAST and ran them against dedicated databases for AR (Resfinder), VFs (VFDB) and MGEs (ICEberg, ReTrIn, Prophage DB). Afterwards, each BLAST output file was prepared and normalized for statistical analysis using R. Kruskal-Wallis and Wilcoxon tests were applied to compare the orthologs in the microbiomes of the animals’ and linear regression and correlation coefficient were used to study the relationship between AR, VFs and MGEs. We were unable to create to validate scientific knowledge from our dataset due to its small sample size, but we were successful in defining and testing a bioinformatic workflow to compare the metagenomes of domestic and wild animals. |
|---|---|
| Autores principais: | Figueiredo, João Filipe Mendes Gil Correia |
| Assunto: | metagenomas resistência antibiótica fatores de virulência elementos genéticos móveis BLAST Teses de mestrado - 2023 |
| Ano: | 2023 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso restrito |
| Instituição associada: | Universidade de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório da Universidade de Lisboa |
| Resumo: | Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability of horizontal gene transfer, bacteria are capable of “borrowing” and “lending” defensive and evasive maneuvers against antibiotics from other neighboring bacteria. As a consequence of antibiotic use, the frequency of antibiotic-resistant bacteria increases in the microbiome, eventually containing mobile genetic elements coding for antimicrobial resistance genes, thus favoring the dissemination of these genes which can lead to the ineffectiveness of the antibiotic. Furthermore, recent studies have shown that, as a side effect of antibiotic intake in medicine, people may be selecting more virulent strains. The quick rise of resistant bacteria threatens the effectiveness of antibiotics worldwide. For this reason, it is crucial to understand the relationship between antibiotic resistance (AR), virulence factors (VF) and mobile genetic elements (MGEs). With this project, we aim to study the metagenomes of domesticated and wild animals. To have an understanding of the impact of AR pollution and dissemination, we created a bioinformatic workflow to make a comparative study of the richness and diversity of the determinants of bacterial AR, VFs and MGEs in the microbiomes of domestic and wild animals. We retrieved metagenomic files of geese, mice, horses and yaks from NCBI, MG-RAST and NCBC, and utilized MetaSPADES and Prokka to assemble, annotate and translate them. In order to compare the richness and diversity of the animals’ microbiomes, we used two files for each metagenome: one with the complete DNA sequence (FNA) and another one in which the translated proteins were clustered at 90% identity. We used these files as input for BLAST and ran them against dedicated databases for AR (Resfinder), VFs (VFDB) and MGEs (ICEberg, ReTrIn, Prophage DB). Afterwards, each BLAST output file was prepared and normalized for statistical analysis using R. Kruskal-Wallis and Wilcoxon tests were applied to compare the orthologs in the microbiomes of the animals’ and linear regression and correlation coefficient were used to study the relationship between AR, VFs and MGEs. We were unable to create to validate scientific knowledge from our dataset due to its small sample size, but we were successful in defining and testing a bioinformatic workflow to compare the metagenomes of domestic and wild animals. |
|---|