Publication
Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences
| dc.contributor.author | Macedo, Rita | |
| dc.contributor.author | Isidro, Joana | |
| dc.contributor.author | Ferreira, Rita | |
| dc.contributor.author | Pinto, Miguel | |
| dc.contributor.author | Borges, Vítor | |
| dc.contributor.author | Duarte, Sílvia | |
| dc.contributor.author | Vieira, Luís | |
| dc.contributor.author | Gomes, João Paulo | |
| dc.date.accessioned | 2024-01-24T16:32:41Z | |
| dc.date.available | 2024-01-24T16:32:41Z | |
| dc.date.issued | 2023-02-02 | |
| dc.description | (This article belongs to the Special Issue CRISPR-Cas in Genomic Manipulation and Antimicrobial Resistance) | pt_PT |
| dc.description.abstract | 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. | pt_PT |
| dc.description.sponsorship | The acquisition of WGS-associated equipment used in this study (including the Illumina NextSeq 2000) was funded by the HERA project (Grant/2021/PHF/23776) supported by the European Commission through the European Centre for Disease Control and Prevention and partially funded by the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020—Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT). | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.citation | Int J Mol Sci. 2023 Feb 2;24(3):2912. doi: 10.3390/ijms24032912 | pt_PT |
| dc.identifier.doi | 10.3390/ijms24032912 | pt_PT |
| dc.identifier.issn | 1661-6596 | |
| dc.identifier.uri | http://hdl.handle.net/10400.18/8973 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.publisher | MDPI | pt_PT |
| dc.relation | National Facility for genome sequencing and analysis | |
| dc.relation.publisherversion | https://www.mdpi.com/1422-0067/24/3/2912 | pt_PT |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | pt_PT |
| dc.subject | Mycobacterium tuberculosis | pt_PT |
| dc.subject | RNA-baits | pt_PT |
| dc.subject | Molecular Capture | pt_PT |
| dc.subject | Resistance | pt_PT |
| dc.subject | Surveillance | pt_PT |
| dc.subject | Target Enrichment | pt_PT |
| dc.subject | Drug Therapy | pt_PT |
| dc.subject | Epidemiology | pt_PT |
| dc.subject | Microbiology | pt_PT |
| dc.subject | Genetics | pt_PT |
| dc.subject | Whole Genome Sequencing | pt_PT |
| dc.subject | Tuberculosis | pt_PT |
| dc.subject | nfecções Respiratórias | pt_PT |
| dc.subject | Resistência aos Antimicrobianos | pt_PT |
| dc.title | Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences | pt_PT |
| dc.type | journal article | |
| dspace.entity.type | Publication | |
| oaire.awardTitle | National Facility for genome sequencing and analysis | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/9444 - RNIIIE/PINFRA%2F22184%2F2016/PT | |
| oaire.citation.issue | 3 | pt_PT |
| oaire.citation.startPage | 2912 | pt_PT |
| oaire.citation.title | International Journal of Molecular Sciences | pt_PT |
| oaire.citation.volume | 24 | pt_PT |
| oaire.fundingStream | 9444 - RNIIIE | |
| project.funder.identifier | http://doi.org/10.13039/501100001871 | |
| project.funder.name | Fundação para a Ciência e a Tecnologia | |
| rcaap.embargofct | Acesso de acordo com a política editorial da revista. | pt_PT |
| rcaap.rights | openAccess | pt_PT |
| rcaap.type | article | pt_PT |
| relation.isProjectOfPublication | 3b8a803c-37e5-4354-93f5-6410d7fb2af7 | |
| relation.isProjectOfPublication.latestForDiscovery | 3b8a803c-37e5-4354-93f5-6410d7fb2af7 |