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Abstract Body

Timely and accurate diagnosis of lower respiratory tract infections (LRTIs) in young children admitted to the hospital are critical in developing effective clinical treatment plans, which will reduce hospital stays, duration of illness, and the burden on children and families. Metagenomic testing allows the detection of pathogens directly from clinical specimens without a priori knowledge of target sequences. Metagenomics uses genome sequencing and bioinformatics techniques to identify and characterize microorganisms, including viruses, fungi, and bacteria. By determining the entire genomic sequence of a pathogen, scientists and clinicians can decipher not just the organism, but also the strain type which informs transmission patterns and identify sequences known to be antimicrobial resistance (AMR) markers. AMR markers inform treatment options by indicating which antivirals or antibiotics will not or less efficiently be effective against the target pathogen. Moreover, metagenomics allows the detection of co-infections, which regularly can be the cause of death in patients with a severe LRTI. However, high levels of genetic material from both host and normal microflora limit the sensitivity of detection for this method. An enrichment-based sequencing workflow using capture probes can be used to increase sensitivity. Capture probes are more tolerant of mismatches in target sequences than are PCR primers and probes, making them suitable for use with high-diversity targets like RNA viruses. This approach simultaneously enriches target regions of interest while effectively depleting background sequences. Here, an overview of the different technologies will be given, requirements for implementation will be discussed, and case studies will be presented.