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Background Human Rhinovirus (HRV) has been identified as the most common cause of acute respiratory infections and hospitalizations in premature children. It is unclear if premature children are more susceptible to HRV due to their decreased pulmonary reserve or because they have enhanced lower airway reactivity to HRV. Methods We conducted a retrospective analysis of the clinical respiratory presentation of all PCR-confirmed HRV infections in full-term and premature children aged ≤3 years in our institution. Standardized respiratory distress scores were developed to examine lower airway obstruction (i.e., wheezing, hyperinflation, and sub-costal retractions) along with markers of decreased pulmonary reserve (hypoxemia and tachypnea) in young children with HRV infections. Demographic and clinical variables were obtained from reviewing electronic medical records (EMR). Results This study included a total of 205 children; 71% of these children were born full-term (>37 weeks gestation), 10% preterm (32–37 weeks) and 19% severely premature (<32 weeks). Our results demonstrated that: 1) HRV infections in the first 3 years of life were associated with higher overall respiratory distress scores in severely premature children relative to children born preterm or full-term; 2) HRV-infected severely premature children ≤3 years old were more likely to have lower airway obstruction than HRV-infected children born preterm or full-term; and 3) other clinical signs of respiratory distress such as tachypnea and hypoxemia were not more common in severely premature than in preterm and full-term children during an HRV infection. Conclusions Our results indicate that HRV infections in severely premature children are associated with lower airway obstruction rather than hypoxemia or tachypnea. The latter suggests that enhanced airway reactivity is the underlying mechanism for the increased susceptibility to HRV in severely premature children. Longitudinal studies are needed to understand why premature babies develop airway hyper-reactivity to HRV and the long-term effects of early HRV infection in this population. [ABSTRACT FROM AUTHOR]

Background Cystic fibrosis (CF) is an autosomal recessive disease characterized by recurrent lung infections. Studies of the lung microbiome have shown an association between decreasing diversity and progressive disease. 454 pyrosequencing has frequently been used to study the lung microbiome in CF, but will no longer be supported. We sought to identify the benefits and drawbacks of using two state-of-the-art next generation sequencing (NGS) platforms, MiSeq and PacBio RSII, to characterize the CF lung microbiome. Each has its advantages and limitations. Methods Twelve samples of extracted bacterial DNA were sequenced on both MiSeq and PacBio NGS platforms. DNA was amplified for the V4 region of the 16S rRNA gene and libraries were sequenced on the MiSeq sequencing platform, while the full 16S rRNA gene was sequenced on the PacBio RSII sequencing platform. Raw FASTQ files generated by the MiSeq and PacBio platforms were processed in mothur v1.35.1. Results There was extreme discordance in alpha-diversity of the CF lung microbiome when using the two platforms. Because of its depth of coverage, sequencing of the 16S rRNA V4 gene region using MiSeq allowed for the observation of many more operational taxonomic units (OTUs) and higher Chao1 and Shannon indices than the PacBio RSII. Interestingly, several patients in our cohort had Escherichia , an unusual pathogen in CF. Also, likely because of its coverage of the complete 16S rRNA gene, only PacBio RSII was able to identify Burkholderia , an important CF pathogen. Conclusion When comparing microbiome diversity in clinical samples from CF patients using 16S sequences, MiSeq and PacBio NGS platforms may generate different results in microbial community composition and structure. It may be necessary to use different platforms when trying to correctly identify dominant pathogens versus measuring alpha-diversity estimates, and it would be important to use the same platform for comparisons to minimize errors in interpretation. [ABSTRACT FROM AUTHOR]