Logo do repositório
 
Publicação

Probe-based metagenomic pathogen detection

2025-10Artigo científico Acesso aberto
Ver registo simples
dc.contributor.authorFerreira, Rita
dc.contributor.authorCoelho, Luís
dc.contributor.authorSantos, João Dourado
dc.contributor.authorSobral, Daniel
dc.contributor.authorIsidro, Joana
dc.contributor.authorMixão, Verónica
dc.contributor.authorPinto, Miguel
dc.contributor.authorNunes, Alexandra
dc.contributor.authorBorrego, Maria José
dc.contributor.authorLopo, Sílvia
dc.contributor.authorOleastro, Mónica
dc.contributor.authorSousa, Rita
dc.contributor.authorPalminha, Paula
dc.contributor.authorVeríssimo, Cristina
dc.contributor.authorGargaté, Maria João
dc.contributor.authorGuiomar, Raquel
dc.contributor.authorCordeiro, Rita
dc.contributor.authorMacedo, Rita
dc.contributor.authorBajanca-Lavado, Paula
dc.contributor.authorPaixão, Paulo
dc.contributor.authorPaixão, Paulo
dc.contributor.authorDuarte, Sílvia
dc.contributor.authorVieira, Luís
dc.contributor.authorBorges, Vítor
dc.contributor.authorGomes, João Paulo
dc.contributor.institutionNOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
dc.contributor.institutionComprehensive Health Research Centre (CHRC) - pólo NMS
dc.contributor.pblFrontiers Research Foundation
dc.date.accessioned2025-11-19T21:10:36Z
dc.date.available2025-11-19T21:10:36Z
dc.date.issued2025-10
dc.descriptionPublisher Copyright: Copyright © 2025 Ferreira, Coelho, Santos, Sobral, Isidro, Mixão, Pinto, Nunes, Borrego, Lopo, Oleastro, Sousa, Palminha, Veríssimo, Gargaté, Guiomar, Cordeiro, Macedo, Bajanca-Lavado, Paixão, Duarte, Vieira, Borges and Gomes.
dc.description.abstractProbe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance of two Illumina probe-based panels, the Respiratory and the Urinary Pathogen ID panels (RPIP and UPIP), using 99 clinical samples of 15 different matrices (e.g., cerebrospinal fluid, plasma, serum, urine, swabs, biopsies, etc.) available from Portuguese National Reference Laboratories. This sample set involved 114 “PCR-positive hits” (Ct values range of 9.7–41.3; median of 28.4) for 52 non-redundant human pathogens. For a more detailed bioinformatics assessment, as a complement of the Illumina turnkey solution (Explify), we applied an extended version of our INSaFLU-TELEVIR(+) metagenomics pipeline. Whereas Explify analyses resulted in an initial detection frequency of 73.7% (84/114), the subsequent application of INSaFLU-TELEVIR(+), including taxonomic classification followed by confirmatory read mapping, enabled an overall detection proportion of 79.8% (91/114) of the PCR-positive hits. This translated into a detection rate increment from 54.3% (19/35) to 65.7% (23/35) for bacteria, and from 85.3% (58/68) to 89.7% (61/68) for viruses. The implemented workflow was also very satisfactory for samples with qPCR Ct values above 30, with an overall detection frequency of 71.8% (28/39) when compared with the 92.0% (46/50) observed for those with Ct ≤ 30. In summary, this study validated and established a pioneering approach at the Portuguese National Institute of Health to support clinicians in complex diagnosis, contributing to advance diagnostic capabilities toward a more informed clinical decision and potential improvement of infectious disease outcomes.en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent3529253
dc.identifier.doi10.3389/fmicb.2025.1656831
dc.identifier.issn1664-302X
dc.identifier.otherPURE: 135033892
dc.identifier.otherPURE UUID: a701fb18-2399-4544-bc88-120d4749cb8c
dc.identifier.otherScopus: 105019974894
dc.identifier.urihttp://hdl.handle.net/10362/191083
dc.identifier.urlhttps://www.scopus.com/pages/publications/105019974894
dc.language.isoeng
dc.peerreviewedyes
dc.subjectbioinformatics analysis
dc.subjectINSaFLU-TELEVIR
dc.subjectmetagenomics
dc.subjectmNGS
dc.subjectnext-generation sequencing
dc.subjectpathogen detection
dc.subjectMicrobiology
dc.subjectMicrobiology (medical)
dc.subjectSDG 3 - Good Health and Well-being
dc.titleProbe-based metagenomic pathogen detectionen
dc.title.subtitleadvancing laboratory capacity for complex diagnosisen
dc.typejournal article
degois.publication.titleFrontiers in Microbiology
degois.publication.volume16
dspace.entity.typePublication
person.familyNamePaixão
person.givenNamePaulo
person.identifier.orcid0000-0002-4294-0872
person.identifier.scopus-author-id6508103792
rcaap.rightsopenAccess
relation.isAuthorOfPublication05b765bd-f025-43ee-8cf5-2e54ceb007cb
relation.isAuthorOfPublication.latestForDiscovery05b765bd-f025-43ee-8cf5-2e54ceb007cb

Ficheiros

Principais
A mostrar 1 - 1 de 1
Miniatura
Nome:
fmicb-16-1656831.pdf
Tamanho:
3.37 MB
Formato:
Adobe Portable Document Format
Ver/Abrir

Coleções

NMS: CHRC - Artigos em revista internacional com arbitragem científica