Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants

Abstract

Traditional culture techniques have shown that increased bacterial colonization is associated with viral colonization; however, the influence of viral colonization on the whole microbiota composition is less clear. We thus aimed to understand the interaction of viral infections and the nasal microbiota in early life to appraise their roles in disease development. Thirty-two healthy, unselected infants were included in this prospective longitudinal cohort study within the first year of life. Biweekly nasal swabs (n = 559) were taken, and the microbiota was analyzed by 16S rRNA pyrosequencing, and 10 different viruses and 2 atypical bacteria were characterized by real-time PCR (combination of seven duplex samples). In contrast to asymptomatic human rhinovirus (HRV) colonization, symptomatic HRV infections were associated with lower alpha diversity (Shannon diversity index [SDI]), higher bacterial density (PCR concentration), and a difference in beta diversities (Jaccard and Bray-Curtis index) of the microbiota. In addition, infants with more frequent HRV infections had a lower SDI at the end of the study period. Overall, changes in the microbiota associated with symptomatic HRV infections were characterized by a loss of microbial diversity. The interaction between HRV infections and the nasal microbiota in early life might be of importance for later disease development and indicate a potential approach for future interventions. IMPORTANCE Respiratory viral infections are very frequent in infancy and of importance in acute and chronic disease development. Infections with human rhinovirus (HRV) are, e.g., associated with the later development of asthma. We found that only symptomatic HRV infections were associated with acute changes in the nasal microbiota, mainly characterized by a loss of microbial diversity. Infants with more frequent symptomatic HRV infections had a lower bacterial diversity at the end of the first year of life. Whether the interaction between viruses and the microbiota is one pathway contributing to asthma development will be assessed in the follow-ups of these children. Independent of that, measurements of microbial diversity might represent a potential marker for risk of later lung disease or monitoring of early life interventions.

Keywords: bacteriology; human rhinovirus; microbiota; pediatric infectious disease; respiratory viruses.

FIG 1

Study design. *, weekly telephone calls with standardized interviews regarding symptoms of lower and upper respiratory infections, wheeze, and/or cough; +, biweekly analysis of nasal swab samples, including analysis of the respiratory microbiota by PCR amplification of bacterial 16S rRNA and virological examination with multiplex PCR. 16S rRNA pyro seq., bacterial 16S rRNA pyrosequencing. Detailed explanation of analysis of viral colonization and the microbiota can be found in the Results section. Analysis I examined association of viral colonization and the microbiota in the same sample. Microbiota is used as the outcome parameter. Analysis II examined association of viral colonization and the microbiota within 3 weeks after viral colonization. Microbiota is used as the outcome parameter, and only samples free of virus after viral colonization are included for evaluation. Analysis III examined association of viral colonization and the microbiota within 3 weeks before viral colonization. Virus is used as the outcome parameter, and only samples free of virus before viral colonization are included for evaluation.

FIG 2

Beta diversity of the microbiota during HRV colonization. Shown is a comparison of the bacterial composition in samples without viral colonization to that in samples with asymptomatic and symptomatic HRV colonization. Weighted beta diversities are represented by using nonmetric multidimensional scaling (NMDS). Arrows indicate clustering of samples without viral colonization (no.virus), HRV colonization without symptoms (HRV.no.symp), and HRV infection with symptoms (HRV.symp). There is a significant difference in beta diversity during symptomatic HRV colonization (“Adonis” function of R; P = 0.04).

FIG 3

SDI values before, during, and after symptomatic HRV colonization. (A) Mean (95% CI) of SDI before, during, and after symptomatic HRV colonization. All samples are included. (B) Individual values of SDI before, during, and after symptomatic HRV colonization. Presented are only swabs with the following characteristics: three consecutive samples with the one before HRV colonization free of any viral colonization, the sample during HRV colonization without coinfection, and the sample after HRV colonization free of any viral colonization.

FIG 4

SDI at the end of the first year of life in relation to the number of viral colonizations throughout the whole year. Shown are the median SDIs of the nasal swabs taken in the last 3 months of the study period (box plots with minimum to maximum) grouped as from zero to two positive swabs and as more than two positive swabs for (A) symptomatic HRV (0 to 2, n = 18; >2, n = 13), (B) asymptomatic HRV (0 to 2, n = 20; >2, n = 11), and (C) symptomatic viral infections other than HRV (0 to 2, n = 21; >2, n = 10). Coinfections are only included for symptomatic viral infections other than HRV. A lower SDI was found in infants with more frequent symptomatic HRV colonization (P = 0.015) but not with more frequent asymptomatic HRV colonization (P = 0.2) or more frequent symptomatic viral colonization other than HRV (P = 0.1).