Bacterial–bacterial interactions.

<p>The composition of nasopharyngeal microbiota is constantly subject to interactions between species. Bacterial species can interact with other bacterial species by competition and synergism. Synergism can be characterized by, for instance, the production of components that favors another species, as shown for the production of outer membrane vesicles. These may contain factors that are able to inactivate complement factor C3, thereby allowing another species to escape the immune system. Production of substances by one species, for example hydrogen peroxide (H₂O₂), may eliminate its competitor. The immune system may also be involved in competition, as one bacterium has fewer escape mechanisms to evade the immune system than another and therefore may use co-inhabitants to survive, whereas the reverse phenomenon (i.e., one species may trigger the immune system to combat the other species) may also occur. In addition, since PhC (phosphorylcholine) is shown to be immunogenic and some species may be able to switch off PhC expression whereas others cannot, there might be a selective advantage. Another form of competition involves competition for the same host receptor, as demonstrated for PhC and its receptor platelet activating factor receptor (PAFr). Moreover, one species may use neuraminidase to cut off the sialic acids (SA) that other bacteria may require for attachment to host receptors, therefore inhibiting adherence of the other bacterial species. H₂O₂, hydrogen peroxide; PAFr, platelet activating factor receptor; PhC, phosphorylcholine; NA, neuraminidase; SA, sialic acid (SA); rSA, receptor for sialic acids; Ab, antibodies.</p

Viral–bacterial interaction based on data available from human, animal, and in vitro studies.

<p>Virus (column one) and respective bacterium (column two) for which interactions were observed (column three), and source of evidence: from human studies (column four), animal studies (column five), or in vitro studies (column six) showing type of epithelium tested.</p><p>NA, data not available from literature.</p

Viral–bacterial interactions.

<p>(A) Viral–bacterial interaction on the respiratory epithelial surface. Viral presence is thought to predispose the respiratory niche to bacterial colonization by different mechanisms. First, viruses may render the epithelium more susceptible to bacterial colonization by altering the mucosal surfaces. Ciliae may be damaged, leading to decreased mucociliar function of the respiratory epithelium. Additionally, due to viral-induced damage and loss of integrity of the epithelium layer, bacterial colonization may be enhanced and translocation may be increased. Virus-infected cells may decrease the expression of antimicrobial peptides, as shown for β-defensins, thereby affecting the natural defense of the host epithelium. Viral neuraminidase (NA) activity is able to cleave sialic acids residues, thereby giving access to bacterial receptors that were covered by these residues. Finally, viruses may induce bacterial colonization and replication both directly and indirectly, the latter by inducing upregulation of various receptors required for bacterial adherence, including PAFr, CAECAM-1, P5F, ICAM-1, and G-protein. PAFr, platelet activating factor receptor; ICAM-1, intracellular adhesion molecule 1; P5 fimbriae, outer membrane protein P5-homologous fimbriae; CAECAM-1, carcinoembryonic adhesion molecule-1; PhC, phosphorylcholine; SA, sialic acids; rSA, receptor for sialic acids; NA, neuraminidase; mRNA, messenger RNA, AMPs, antimicrobial peptides. (B) Viral–bacterial interaction in relation to the host immune system. Viruses may also induce changes in immune function favorable to bacterial invasion: fewer NK cells may be recruited into the tissue and their functionality may be suboptimal as a consequence of viral infection. Virus-induced IFN-α and IFN-β may impair recruitment and functionality of neutrophils, and subsequently induce apoptosis of neutrophils recruited to combat the viral invader. Furthermore, IFN-γ seems to negatively affect the activity of macrophages. Viral-infected monocytes appear less effective in ingesting and killing bacteria, predisposing them to bacterial overgrowth and invasion. Viral infection seems to impair TLR pathways, induce production of the anti-inflammatory cytokine IL-10, and decrease the concentration of the pro-inflammatory cytokine TNF-α, generally affecting adequate immune responses to bacterial infections. Black arrows indicate increased (↑) or decreased (↓) activity or functionality of a cytokine. IFN, interferon; TNF, tumor necrosis factor; TLR, toll like receptor; IL, interleukin; NK cell, natural killer cell.</p

Viral detection in respiratory samples in asymptomatic children.

a<p>Related to geographical area.</p>b<p>Number of samples tested.</p>c<p>Stratified for season.</p>d<p>Picornavirus general.</p><p>M, months of age; Y, years of age; HRV, human rhinoviruses; EV, entero viruses; AdV, adeno viruses; HBoV, human bocavirus; RSV, respiratory syncytial virus; hMPV, human metapneumovirus; CoV, corona viruses; IV, influenza viruses; PIV, para-influenza viruses; NS, not specified.</p

Distribution and adjusted odds ratios^a,b for nasopharyngeal bacterial colonization, co-occurrence with each of the other bacteria, respiratory viruses and risk factors.

<p>Abbreviations: aOR, adjusted odds ratio; CI, confidence interval; NA, not applicable (i.e., not included in the model for that particular bacterial pathogen), RSV, respiratory syncytial virus.</p>a<p>Adjusted for age and all variables with a P value of <0.1 in univariate analysis.</p>b<p>Statistically significant associations are shown in bold.</p

Characteristics of the children, nasopharyngeal bacterial colonization and viral detection rates.

<p>Abbreviations: SD, standard deviation; NA, not applicable; PCV-7, 7-valent pneumococcal conjugate vaccine; URTI, upper respiratory tract infection.</p>a<p>Defined as more than 4 hours per week with at least one child from another family (yes/no).</p>b<p>Defined as use of an antibiotic, orally or intravenously administered with start date within 2 months before sampling date (yes/no). Of those, the prescribed antibiotic was amoxicillin (n = 69), penicillin (n = 1), amoxicillin/clavulanic acid (n = 3), a macrolide (n = 14; claritromycin (n = 8), azitromycin (n = 5), erythromycin (n = 1), a cephalosporin (n = 1, unknown type), and 3 unknowns.</p>c<p>Parent-reported presence of mild symptoms of an upper respiratory tract infection (eg, a runny nose) at the time of sampling (yes/no).</p>d<p>Presence of enteroviruses and human parechovirus was determined in a subgroup of samples (N = 831) due to insufficient amounts of remaining nasopharyngeal swab material or nucleic acids to run these tests. Missing values were imputed by the single imputation procedure in multivariate analysis models in which these viruses were included to retain statistical power.</p

Distribution and adjusted odds ratios^a,b for nasopharyngeal presence of the most common viruses, co-occurrence with each of the other respiratory viruses, bacteria and risk factors.

<p>Abbreviations: aOR, adjusted odds ratio; CI, confidence interval; NA, not applicable (i.e., not included in the model for that particular virus or pooled group of viruses), RSV, respiratory syncytial virus.</p>a<p>Adjusted for age and all variables with a P value of <0.1 in univariate analysis.</p>b<p>Statistically significant associations are shown in bold.</p

Graphical representation of interaction patterns.

<p>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, <i>S. pneumoniae</i>; HI, <i>H. influenzae</i>; MC, <i>M. catarrhalis</i>; SA, <i>S. aureus</i>; 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.</p