Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria

Abstract

Background: High rates of potentially pathogenic bacteria and respiratory viruses can be detected in the upper respiratory tract of healthy children. Investigating presence of and associations between these pathogens in healthy individuals is still a rather unexplored field of research, but may have implications for interpreting findings during disease.

Methodology/principal findings: We selected 986 nasopharyngeal samples from 433 6- to 24-month-old healthy children that had participated in a randomized controlled trial. We determined the presence of 20 common respiratory viruses using real-time PCR. Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Staphylococcus aureus were identified by conventional culture methods. Information on risk factors was obtained by questionnaires. We performed multivariate logistic regression analyses followed by partial correlation analysis to identify the overall pattern of associations. S. pneumoniae colonization was positively associated with the presence of H. influenzae (adjusted odds ratio 1.60, 95% confidence interval 1.18-2.16), M. catarrhalis (1.78, 1.29-2.47), human rhinoviruses (1.63, 1.19-2.22) and enteroviruses (1.97, 1.26-3.10), and negatively associated with S. aureus presence (0.59, 0.35-0.98). H. influenzae was positively associated with human rhinoviruses (1.63, 1.22-2.18) and respiratory syncytial viruses (2.78, 1.06-7.28). M. catarrhalis colonization was positively associated with coronaviruses (1.99, 1.01-3.93) and adenoviruses (3.69, 1.29-10.56), and negatively with S. aureus carriage (0.42, 0.25-0.69). We observed a strong positive association between S. aureus and influenza viruses (4.87, 1.59-14.89). In addition, human rhinoviruses and enteroviruses were positively correlated (2.40, 1.66-3.47), as were enteroviruses and human bocavirus, WU polyomavirus, parainfluenza viruses, and human parechovirus. A negative association was observed between human rhinoviruses and coronaviruses.

Conclusions/significance: Our data revealed high viral and bacterial prevalence rates and distinct bacterial-bacterial, viral-bacterial and viral-viral associations in healthy children, hinting towards the complexity and potential dynamics of microbial communities in the upper respiratory tract. This warrants careful consideration when associating microbial presence with specific respiratory diseases.

Conflict of interest statement

Competing Interests: DB declares to have received consulting fees from Pfizer. EAMS declares to have received unrestricted research support from Pfizer and Baxter, consulting fees from Pfizer and GlaxoSmithKline, lecturing fees from Pfizer, and grant support for vaccine studies from Pfizer and GlaxoSmithKline. RHV declares to have received research support from GlaxoSmithKline and Pfizer for vaccine studies and consulting fees from GlaxoSmithKline. None of the fees or grants listed here were received for the research described in this paper. For all other authors no conflicts of interest were declared. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1. Graphical representation of interaction patterns.

Visualization of the partial correlations between bacteria and viruses (A) and epidemiologic drivers (risk factors) of those interactions (B). The patterns depicted here result from partial correlation network analysis and are visualized by Cytoscape. Bacteria are shown in blue, respiratory viruses in orange and risk factors in grey boxes. The solid lines represent associations with a p-value less than 0.01, the dashed lines represent associations with a p-value between 0.01 and 0.05. Green lines indicate positively correlated variables; red lines indicate negative correlations. The thickness of the line indicates the magnitude of the correlation. Abbreviations: SP, S. pneumoniae; HI, H. influenzae; MC, M. catarrhalis; SA, S. aureus; HRV, human rhinovirus, EV, enterovirus; HBoV, human bocavirus; WUPyV, WU polyomavirus; HCoV, human coronavirus; PIV, parainfluenza virus; HAdV, human adenovirus; IV, influenza virus; HPeV, human parechovirus; RSV, respiratory syncytial virus; AB, antibiotic use within 2 months before sampling; ‘crowding’ was entered into the model as a variable combining the presence of siblings (yes/no) and day care attendance (yes/no); 0 = no siblings and no day care attendance, 1 = siblings present, but not attending day care, or vice versa, and 2 = siblings present and attending day care.