Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends
Abstract Few studies have analyzed the role of the lung microbiome in the diagnosis of pulmonary coinfection in ventilated ICU COVID-19 patients. We characterized the lung microbiota in COVID-19 patients with severe pneumonia on invasive mechanical ventilation using full-length 16S rRNA gene sequenc...
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| Format: | Article |
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Nature Portfolio
2024-12-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-81738-8 |
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| author | Francisco José Molina Luz Elena Botero Juan Pablo Isaza Luz Elena Cano Lucelly López Luis Valdés Angela J. Arévalo Arbeláez Isabel Moreno Laura S. Pérez Restrepo Jaime Usuga Karl Ciuoderis Juan Pablo Hernandez Rubén López-Aladid Laia Fernández Antoni Torres |
| author_facet | Francisco José Molina Luz Elena Botero Juan Pablo Isaza Luz Elena Cano Lucelly López Luis Valdés Angela J. Arévalo Arbeláez Isabel Moreno Laura S. Pérez Restrepo Jaime Usuga Karl Ciuoderis Juan Pablo Hernandez Rubén López-Aladid Laia Fernández Antoni Torres |
| author_sort | Francisco José Molina |
| collection | DOAJ |
| description | Abstract Few studies have analyzed the role of the lung microbiome in the diagnosis of pulmonary coinfection in ventilated ICU COVID-19 patients. We characterized the lung microbiota in COVID-19 patients with severe pneumonia on invasive mechanical ventilation using full-length 16S rRNA gene sequencing and established its relationship with coinfections, mortality, and the need for mechanical ventilation for more than 7 days. This study included 67 COVID-19 ICU patients. DNA extracted from mini-bronchoalveolar lavage fluid and endotracheal aspirates was amplified by PCR with specific 16S primers (27F and 1492R). General and relative bacterial abundance analysis was also conducted. Alpha diversity was measured by the Shannon and Simpson indices, and differences in the microbiota were established using beta diversity. A linear discriminant analysis (LDA) effect size algorithm was implemented to describe biomarkers. Streptococcus spp. represented 51% of the overall microbial abundance. There were no differences in alpha diversity between the analyzed variables. There was variation in bacterial composition between samples that had positive and negative cultures. The genera Veillonella sp., Granulicatella sp., Enterococcus sp. and Lactiplantibacillus sp., with LDA scores > 2, were biomarkers associated with negative cultures. Rothia sp., with an LDA score > 2, was a biomarker associated with mortality. |
| format | Article |
| id | doaj-art-e9598963d67643dd993c6bcd36942d4d |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-e9598963d67643dd993c6bcd36942d4d2024-12-08T12:24:41ZengNature PortfolioScientific Reports2045-23222024-12-0114111010.1038/s41598-024-81738-8Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trendsFrancisco José Molina0Luz Elena Botero1Juan Pablo Isaza2Luz Elena Cano3Lucelly López4Luis Valdés5Angela J. Arévalo Arbeláez6Isabel Moreno7Laura S. Pérez Restrepo8Jaime Usuga9Karl Ciuoderis10Juan Pablo Hernandez11Rubén López-Aladid12Laia Fernández13Antoni Torres14Facultad de Medicina, Escuela de Ciencias de la Salud, Universidad Pontificia BolivarianaFacultad de Medicina, Escuela de Ciencias de la Salud, Universidad Pontificia BolivarianaFacultad de Medicina, Escuela de Ciencias de la Salud, Universidad Pontificia BolivarianaFacultad de Medicina, Escuela de Ciencias de la Salud, Universidad Pontificia BolivarianaFacultad de Medicina, Escuela de Ciencias de la Salud, Universidad Pontificia BolivarianaFacultad de Medicina, Escuela de Ciencias de la Salud, Universidad Pontificia BolivarianaGHI One Health Colombia, Universidad Nacional de ColombiaGHI One Health Colombia, Universidad Nacional de ColombiaGHI One Health Colombia, Universidad Nacional de ColombiaGHI One Health Colombia, Universidad Nacional de ColombiaGHI One Health Colombia, Universidad Nacional de ColombiaGHI One Health Colombia, Universidad Nacional de ColombiaCellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Abstract Few studies have analyzed the role of the lung microbiome in the diagnosis of pulmonary coinfection in ventilated ICU COVID-19 patients. We characterized the lung microbiota in COVID-19 patients with severe pneumonia on invasive mechanical ventilation using full-length 16S rRNA gene sequencing and established its relationship with coinfections, mortality, and the need for mechanical ventilation for more than 7 days. This study included 67 COVID-19 ICU patients. DNA extracted from mini-bronchoalveolar lavage fluid and endotracheal aspirates was amplified by PCR with specific 16S primers (27F and 1492R). General and relative bacterial abundance analysis was also conducted. Alpha diversity was measured by the Shannon and Simpson indices, and differences in the microbiota were established using beta diversity. A linear discriminant analysis (LDA) effect size algorithm was implemented to describe biomarkers. Streptococcus spp. represented 51% of the overall microbial abundance. There were no differences in alpha diversity between the analyzed variables. There was variation in bacterial composition between samples that had positive and negative cultures. The genera Veillonella sp., Granulicatella sp., Enterococcus sp. and Lactiplantibacillus sp., with LDA scores > 2, were biomarkers associated with negative cultures. Rothia sp., with an LDA score > 2, was a biomarker associated with mortality.https://doi.org/10.1038/s41598-024-81738-8 |
| spellingShingle | Francisco José Molina Luz Elena Botero Juan Pablo Isaza Luz Elena Cano Lucelly López Luis Valdés Angela J. Arévalo Arbeláez Isabel Moreno Laura S. Pérez Restrepo Jaime Usuga Karl Ciuoderis Juan Pablo Hernandez Rubén López-Aladid Laia Fernández Antoni Torres Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends Scientific Reports |
| title | Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends |
| title_full | Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends |
| title_fullStr | Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends |
| title_full_unstemmed | Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends |
| title_short | Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends |
| title_sort | deciphering the lung microbiota in covid 19 patients insights from culture analysis filmarray pneumonia panel ventilation impact and mortality trends |
| url | https://doi.org/10.1038/s41598-024-81738-8 |
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