Viral detection is often asymptomatic and occasionally prolonged, especially for bocavirus and rhinovirus. In clinical settings, the interpretation of positive PCR tests, particularly in young children and those who live with them, may be confounded.

Proven influenza infection in children results in substantial hospital resource utilization and morbidity. Nationwide, the median hospital costs may total 55 million dollars. Our data support the Advisory Committee on Immunization's recommendations to expand the use of influenza vaccine to children > 2 years of age.

PNP is a serious and increasingly common complication of S. pneumoniae pneumonia in Utah. Infection with serotype 3 is associated with an increased risk of developing PNP. The increase in the incidence of infection due to nonvaccine serotypes reported worldwide and the changing epidemiology of invasive pneumococcal disease should be considered when developing vaccine strategies.

BackgroundHigh-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.ResultsWe present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface.ConclusionsTaxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0969-1) contains supplementary material, which is available to authorized users.

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