Autor(es):
Macedo, Rita ; Isidro, Joana ; Ferreira, Rita ; Pinto, Miguel ; Borges, Vítor ; Duarte, Sílvia ; Vieira, Luís ; Gomes, João Paulo
Data: 2023
Identificador Persistente: http://hdl.handle.net/10400.18/8973
Origem: Repositório Científico do Instituto Nacional de Saúde
Assunto(s): Mycobacterium tuberculosis; RNA-baits; Molecular Capture; Resistance; Surveillance; Target Enrichment; Drug Therapy; Epidemiology; Microbiology; Genetics; Whole Genome Sequencing; Tuberculosis; nfecções Respiratórias; Resistência aos Antimicrobianos
Descrição
The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n = 100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, Santa Clara, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Moreover, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, 9, and 1 samples were 3+, 2+, and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance prediction, essentially in settings when culture is not routinely performed or for samples that fail to grow.
