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Authors
Abstract(s)
A tuberculose continua a ser um grave problema de saúde pública, apesar de ser uma doença evitável e tratável. A Organização Mundial de Saúde estima que 1,5 milhões de pessoas morrem de tuberculose ano após ano e acredita-se que cerca de um quarto da população mundial esteja infectada.
A Letónia é um dos países europeus de alta prioridade no controlo da tuberculose e tem uma das taxas mais altas de tuberculose multirresistente do mundo, apesar de ter um programa de controlo bem estabelecido. Prevenção, detecção precoce e resposta rápida e eficaz aos surtos são elementos essenciais para controlar a propagação da tuberculose.
Durante um período de dez anos, foram colhidas sete amostras de uma família de cinco pessoas da Letónia. Realizámos análises genómicas dos sete isolados com o intuito de desvendar a cadeia de transmissão, investigar a origem de dois casos recorrentes e revelar a possível existência de resistência aos medicamentos.
Preparámos bibliotecas genómicas e sequenciámos os isolados com o Ion Proton. Para analisar as sequências genómicas, efectuámos uma análise bioinformática para a detecção de variantes em todo o genoma, que incluiu o alinhamento das reads contra o genoma de referência H37Rv, o local indel realignment, variant calling e a detecção de variantes estruturais.
No total, foram encontrados 6 variantes estruturais, e detectámos 1029 SNPs de alta qualidade, dos quais 9 eram filogeneticamente informativos e 17 diferenciavam os isolados. Com base Spoligotyping in silico, os isolados pertenciam à sub-família T1. Ao comparar os nossos dados com os da lista de SNPs filogeneticamente específicos, as estirpes estudadas faziam parte da sub-linhagem Haarlem. Não foram encontrados polimorfismos robustos nos genes associados à resistência aos medicamentos, pelo que os isolados foram classificados como susceptíveis a todas os medicamentos anti-tuberculose. Dois doentes tiveram casos recorrentes que definimos como reinfecções. Gerámos hipóteses para estabelecer a cadeia de transmissão, apoiadas pelos limites definidos no número de SNPs e pelos dados das árvores filogenéticas de máxima verossimilhança.
Embora tenhamos utilizado um método de alta resolução, os dados do WGS não foram suficientes para determinar sem ambiguidade a direcção da transmissão do surto. Os dados da epidemiologia molecular precisavam da epidemiologia clássica e da informação clínica para investigar eficazmente este surto.
Tuberculosis remains a serious public health problem even though it is a preventable and treatable disease. World Health Organization estimates that 1.5 million people die from tuberculosis year after year and roughly one quarter of the world’s population is believed to be infected. Latvia is one of Europe’s high-priority countries for tuberculosis control and has one of the highest rates of multi-drug resistant tuberculosis in the world, despite having a well-established control programme. Prevention, early detection and quick and effective response to outbreaks are essential elements to control the spread of tuberculosis. Over a period of ten years, seven samples were collected from a family of five people from Latvia. We performed genomic analysis of the seven isolates in order to unravel the chain of transmission, investigate the origin of two recurrent cases and reveal the possible existence of drug resistance. We prepared genomic libraries and we sequenced the isolates using the Ion Proton platform. To analyze the genomic sequences, we caried out bioinformatic analysis using a pipeline for genome-wide variant detection, that included alignment of the reads against the reference H37Rv genome, local indel realignment, variant calling and structural variant detection. Overall, 6 structural variants were found, and we detected 1029 high-quality SNPs, from which 9 were phylogenetically informative and 17 differentiated the isolates. Based on in silico Spoligotyping the isolates belonged to the T1 sub-family and when using phylogenetic specific SNPs, the studied strains were determined to be part of the Haarlem sub-lineage. No robust polymorphisms in genes associated with drug resistance were found, therefore the isolates were classified susceptible to all anti-tuberculosis drugs. Two patients had recurrent cases that we defined as re-infections. We generated hypotheses in order to establish the routes of transmission, supported by the defined cut-offs in the number of SNPs and the data from the maximum likelihood phylogenetic trees. Although we used a high-resolution method, the WGS data was not enough to determine the direction of transmission within the cluster unambiguously. The molecular epidemiology data needed to be combined with classical epidemiology and clinical information to effectively investigate this household transmission cluster.
Tuberculosis remains a serious public health problem even though it is a preventable and treatable disease. World Health Organization estimates that 1.5 million people die from tuberculosis year after year and roughly one quarter of the world’s population is believed to be infected. Latvia is one of Europe’s high-priority countries for tuberculosis control and has one of the highest rates of multi-drug resistant tuberculosis in the world, despite having a well-established control programme. Prevention, early detection and quick and effective response to outbreaks are essential elements to control the spread of tuberculosis. Over a period of ten years, seven samples were collected from a family of five people from Latvia. We performed genomic analysis of the seven isolates in order to unravel the chain of transmission, investigate the origin of two recurrent cases and reveal the possible existence of drug resistance. We prepared genomic libraries and we sequenced the isolates using the Ion Proton platform. To analyze the genomic sequences, we caried out bioinformatic analysis using a pipeline for genome-wide variant detection, that included alignment of the reads against the reference H37Rv genome, local indel realignment, variant calling and structural variant detection. Overall, 6 structural variants were found, and we detected 1029 high-quality SNPs, from which 9 were phylogenetically informative and 17 differentiated the isolates. Based on in silico Spoligotyping the isolates belonged to the T1 sub-family and when using phylogenetic specific SNPs, the studied strains were determined to be part of the Haarlem sub-lineage. No robust polymorphisms in genes associated with drug resistance were found, therefore the isolates were classified susceptible to all anti-tuberculosis drugs. Two patients had recurrent cases that we defined as re-infections. We generated hypotheses in order to establish the routes of transmission, supported by the defined cut-offs in the number of SNPs and the data from the maximum likelihood phylogenetic trees. Although we used a high-resolution method, the WGS data was not enough to determine the direction of transmission within the cluster unambiguously. The molecular epidemiology data needed to be combined with classical epidemiology and clinical information to effectively investigate this household transmission cluster.
Description
Trabalho Final de Mestrado Integrado, Ciências Farmacêuticas, 2020, Universidade de Lisboa, Faculdade de Farmácia.
Keywords
Tuberculose Letónia Mycobacterium tuberculosis Whole-genome sequencing Mestrado integrado - 2020