Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosis Article Swipe
Rita Ferreira
,
Luís Coelho
,
João Dourado Santos
,
Daniel Sobral
,
Joana Isidro
,
Verónica Mixão
,
Miguel Pinto
,
Alexandra Nunes
,
Maria José Borrego
,
Sílvia Lopo
,
Mónica Oleastro
,
Rita Sousa
,
Paula Palminha
,
Cristina Veríssimo
,
Maria João Gargaté
,
Raquel Guiomar
,
Rita Cordeiro
,
Rita Macedo
,
Maria Paula Bajanca-Lavado
,
Paulo Paixão
,
Sílvia Duarte
,
Luís Vieira
,
Vítor Borges
,
João Paulo Gomes
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3389/fmicb.2025.1656831
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3389/fmicb.2025.1656831
Probe-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.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fmicb.2025.1656831
- https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1656831/pdf
- OA Status
- gold
- References
- 70
- OpenAlex ID
- https://openalex.org/W4415172617
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https://openalex.org/W4415172617Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3389/fmicb.2025.1656831Digital Object Identifier
- Title
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Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosisWork title
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
-
2025-10-14Full publication date if available
- Authors
-
Rita Ferreira, Luís Coelho, João Dourado Santos, Daniel Sobral, Joana Isidro, Verónica Mixão, Miguel Pinto, Alexandra Nunes, Maria José Borrego, Sílvia Lopo, Mónica Oleastro, Rita Sousa, Paula Palminha, Cristina Veríssimo, Maria João Gargaté, Raquel Guiomar, Rita Cordeiro, Rita Macedo, Maria Paula Bajanca-Lavado, Paulo Paixão, Sílvia Duarte, Luís Vieira, Vítor Borges, João Paulo GomesList of authors in order
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https://doi.org/10.3389/fmicb.2025.1656831Publisher landing page
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https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1656831/pdfDirect link to full text PDF
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goldOpen access status per OpenAlex
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https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1656831/pdfDirect OA link when available
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| publication_date | 2025-10-14 |
| publication_year | 2025 |
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| abstract_inverted_index.85.3% | 174 |
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