Nasopharyngeal Microbiome Composition During Acute Respiratory Illnesses and Asymptomatic Periods in Young Peruvian Children

Background:

Changes in respiratory microbiota may be associated with the pathogenesis of acute respiratory illness (ARI), but these relationships are poorly understood. We sought to characterize and compare nasopharyngeal (NP) microbiome composition during ARI and asymptomatic periods among children <3 years of age enrolled in a prospective cohort study in Peru.

Methods:

Bacterial 16S ribosomal sequencing was performed on DNA extracts from a cross-sectional convenience sample of NP specimens from children during ARI (n=9) and asymptomatic (n=10) periods. NP samples were also tested for several common respiratory viruses by real-time RT-PCR.  The composition and diversity of the NP microbiome samples were compared between groups.

Results:

Eight of 9 (89%) of samples collected during ARI and 4 of 10 (40%) samples from asymptomatic periods had ³1 virus detected, most commonly rhinovirus. ARI samples were dominated by a smaller number of more highly abundant taxa relative to asymptomatic samples. The mean Shannon diversity index was significantly lower (indicating less diversity) in ARI samples (1.63, SD 0.79) compared to asymptomatic (3.07, SD 1.86) samples (p=0.049; Figure 1). There was a lower abundance of Moraxella (p=0.041), Paracoccus (p=0.006), and Staphylococcus haemolyticus (p=0.002) in ARI compared with asymptomatic samples. There was a trend toward higher abundance of Haemophilus influenzae in ARI samples, but this did not reach statistical significance (p=0.079). There was no difference in the abundance of the genus Streptococcus between groups (p=0.42). Relative abundance of specific taxa by sample type and viral detection are highlighted in Figure 2.

Conclusion:

The composition and diversity of NP microbiota varies significantly between ARI and asymptomatic periods. Future studies will explore other metrics of diversity and the relationship between viruses detected and nasopharyngeal microbiota.