Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences

Macedo, Rita; Isidro, Joana; Ferreira, Rita; Pinto, Miguel; Borges, Vítor; Duarte, Sílvia; Vieira, Luís; Gomes, João Paulo

http://hdl.handle.net/10400.18/8973

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Abstract(s)

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.

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(This article belongs to the Special Issue CRISPR-Cas in Genomic Manipulation and Antimicrobial Resistance)

Keywords

Mycobacterium tuberculosis RNA-baits Molecular Capture Resistance Surveillance Target Enrichment Drug Therapy Epidemiology Microbiology Genetics Whole Genome Sequencing Tuberculosis nfecções Respiratórias Resistência aos Antimicrobianos