JCI - Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children

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JCI - Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children
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Cracking the puzzle of lower respiratory tract infections in children jclinicalinvest

We enrolled children aged 31 days to 18 years who were expected to require mechanical ventilation via endotracheal tube for at least 72 hours.

Parents or other legal guardians of eligible patients were approached for consent by study-trained staff as soon as possible after intubation. Waiver of consent was granted for TA samples to be obtained from standard-of-care suctioning of the endotracheal tube until the parents or guardians could be approached for informed consent.

Prospectively collected clinical data were recorded in a web-based research database maintained by the CPCCRN data-coordinating center at the University of Utah, Salt Lake City, Utah, USA.Enrolled patients received standard-of-care clinical respiratory microbiologic diagnostics, as ordered by treating clinicians at each study site. These diagnostics included NP swab respiratory viral testing by multiplex PCR and/or TA bacterial and fungal semiquantitative cultures.

Genes were retained for differential expression analysis if they had at least 10 counts in at least 20% of the samples included in the analysis. DE analyses were performed with the R package limma , using quantile normalization and the voom method.tests , as implemented in limma, and adjusted for multiple hypothesis testing with the Benjamini-Hochberg method. Tests with< 0.05 were considered significant.

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