Figures
- FIGURE 1
Flow chart of the study population. ARI: acute respiratory tract infection.
- FIGURE 2
Composition of the most common clusters at the a) onset of the first acute respiratory tract infection (swab A) and b) 3 weeks later (swab B) illustrated as bacterial abundances of the five most common bacterial families with the remaining grouped as “Others”. Clusters with sizes of <5% are not depicted.
- FIGURE 3
Results of hierarchical clustering based on the microbial composition at the onset of the first acute respiratory tract infection (swab A) and 3 weeks later (swab B). The size of the circles and the numbers inside indicate the number of individuals assigned to each cluster. The connecting bars indicate the transition from one particular cluster to another between swabs A and B; the size of the bars corresponds to the number of transitioning individuals. The dominating bacterial families in the clusters are as follows. A1: Moraxellaceae; A2: Moraxellaceae and Streptococcaeae; A3: Streptococcaceae; A4: “Others”; A5: Pasteurellaceae; B1: Moraxellaceae; B2: “Others”; B3: Streptococcaceae. Areas in the circles of darker green on the left side of the panel indicate the proportion of infants at swab A in each cluster who were asymptomatic at swab B compared to the proportion of symptomatic infants at swab B (lighter green). Areas in the circles of darker orange on the right side of the panel indicate the proportion of asymptomatic infants at swab B compared to the proportion of symptomatic infants (lighter orange). SDI: Shannon Diversity Index, presented as the median value.
Tables
- TABLE 1
Baseline characteristics of the study population
Total participants n (% male) 167 (57) Mean±sd gestational age weeks 39.3±2.0 Mean±sd birth weight kg 3.3±0.55 Caesarean section 25 (15) Season of birth Spring 62 (37) Summer 44 (26) Autumn 32 (19) Winter 29 (17) Mean±sd (range) age at ARI weeks 29.9±12.5 (2–52) Season at first ARI Spring 40 (24) Summer 14 (8) Autumn 38 (23) Winter 75 (45) Increased atopy risk 109 (65) Childcare attendance 32 (19) Breastfeeding status at time of ARI# 99 (60) Environmental tobacco smoke exposure 24 (14) Other siblings (living in the same household) 106 (63) One sibling 75 (45) ≥2 siblings 31 (19) Data are presented as n (%), unless otherwise stated. ARI: acute respiratory tract infection. #: infants being breastfed at the time of ARI.
- TABLE 2
Abundances of bacterial families and alpha diversity measurements at the onset of the acute respiratory tract infection (ARI) and 3 weeks after the onset
At ARI onset (swab A) 3 weeks after ARI onset (swab B) Bacterial family abundance % Moraxellaceae 52.4 (66.5) 49.5 (66.2) Streptococcaceae 19.2 (41.03) 16.31 (33.9) Corynebacteriaceae 0.1 (0.7) 0.2 (1.1)# Pasteurellaceae 0.4 (1.9) 0.3 (1.5) Staphylococcaceae 0.1 (0.6) 0.1 (0.6) “Others” 6.6 (14.7) 9.4 (27.3)# Alpha diversity measurements SDI 1.0 (0.8) 1.1 (1.2)¶ Bacterial richness 33 (35) 38 (36)¶ Data are presented as median (interquartile range). SDI: Shannon Diversity Index. #: abundance of Corynebacteriaceae and “Others” were significantly different between swab A and swab B (p=0.002 and 0.004, respectively, Wilcoxon signed rank sum test); ¶: SDI and bacterial richness are lower at swab A compared to swab B (p=0.013 and 0.052, respectively, Wilcoxon signed rank sum test).
- TABLE 3
Infant clusters at the onset of acute respiratory tract infection (swab A) and subsequent presence of symptoms
Cluster (n=165) p-value A1 (n=56) A2 (n=51) A3 (n=31) A4 (n=14) A5 (n=13) Symptomatic after 1 week 38 (67.8) 43 (84.3) ↑ 19 (61.3) 8 (53.3) 9 (69.2) 0.121# Symptomatic after 2 weeks 17 (30.4) 19 (37.3) ↑ 4 (12.9) ↓ 1 (7.1) ↓ 4 (30.8) 0.061¶ Symptomatic after 3 weeks 19 (33.9) 12 (23.5) 8 (25.8) 4 (28.6) 5 (38.5) 0.754¶ Continuously symptomatic for ≥3 weeks 13 (23.3) 9 (17.6) 2 (6.5) ↓ 1 (7.1) 3 (23.1) 0.329¶ Data are presented as n (%), unless otherwise stated. Statistical analyses were performed using #: Chi-squared; or ¶: Fisher's exact test. Significant overrepresentation (↑) and significant underrepresentation (↓) of presence of symptoms in the clusters was assessed by enrichment analysis. The dominating bacterial families in the clusters are as follows. A1: Moraxellaceae; A2: Moraxellaceae and Streptococcaeae; A3: Streptococcaceae; A4: “Others”; A5: Pasteurellaceae.
- TABLE 4
Infant clusters 3 weeks after onset of acute respiratory tract infection (ARI) (swab B) and subsequent presence of symptoms after the onset of the first ARI
Cluster (n=155) B1 (n=96) B2 (n=34) B3 (n=25) p-value Symptomatic after 1 week 70 (72.9) 22 (64.7) 16 (64.0) 0.135# Symptomatic after 2 weeks 28 (30.2) 5 (14.7) ↓ 9 (36.0) 0.454# Symptomatic after 3 weeks 27 (29.2) 2 (5.9) ↓ 14 (56.0) ↑ <0.001¶ Continuously symptomatic for ≥3 weeks 16 (16.7) 1 (2.9) ↓ 9 (36.0) ↑ 0.010¶ Data are presented as n (%), unless otherwise stated. Statistical analyses were performed using #: Chi-squared; or ¶: Fisher's exact test. Significant overrepresentation (↑) and significant underrepresentation (↓) of presence of symptoms in the clusters was assessed by enrichment analysis. The dominating bacterial families in the clusters are as follows. B1: Moraxellaceae; B2: “Others”; B3: Streptococcaceae.
Supplementary Material
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Supplementary methods 00066-2018_Supplementary_methods
Supplementary table S1 00066-2018_Table_S1
Supplementary table S2 00066-2018_Table_S2
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Supplementary table S10 00066-2018_Table_S10
