Table 2.

Organism-specific prevalence and quantification of load in cases and controls from nasopharyngeal samples

	Prevalence of organism			Quantification of organism (median [IQR]; log10copies per mL)
	Case (N=284)	Control (N=412)	Odds ratio (95% CI)	Case	Control
Bacteria
Bordetella pertussis	6 (2%)	1 (0%)	11·08 (1·33–92·54)	7·38 (4·95–9·84)	8·36 (8·36–8·36)
Haemophilus influenzae type b	4 (1%)	5 (1%)	1·08 (0·28–4·10)	5·32 (4·18–6·14)	5·87 (5·26–6·22)
Mycoplasma pneumoniae	10 (4%)	14 (3%)	1·20 (0·54–2·78)	4·61 (3·73–5·16)	5·22 (4·21–6·61)
Staphylococcus aureus	81 (28%)	142 (35%)	0·70 (0·48–1·02)	4·59 (3·47–5·57)	5·12 (3·71–6·42)
H influenzae	152 (54%)	164 (40%)	1·67 (1·20–2·30)	6·57 (5·53–7·31)	6·53 (5·75–7·26)
Streptococcus pneumoniae	168 (60%)	237 (58%)	1·07 (0·76–1·48)	6·07 (5·31–6·62)	6·03 (5·08–6·65)
Moraxella catarrhalis	214 (75%)	292 (71%)	1·19 (0·82–1·74)	6·58 (5·79–7·20)	7·03 (6·40–7·50)
Viruses
Respiratory syncytial virus	66 (23%)	17 (4%)	8·05 (4·21–15·38)	6·77 (5·75–7·68)	4·37 (3·55–5·05)
Influenza (types A, B, and C)	32 (11%)	11 (3%)	4·13 (2·06–8·26)	3·84 (2·62–5·29)	4·38 (2·73–6·34)
Parainfluenza (types 1, 2, 3, and 4)	35 (12%)	26 (6%)	2·03 (1·20–3·42)	5·44 (3·86–7·08)	4·29 (3·44–5·37)
Adenovirus	53 (19%)	41 (10%)	2·15 (1·31–3·53)	5·38 (3·54–6·70)	5·16 (4·06–5·74)
Metapneumovirus	29 (10%)	44 (11%)	1·12 (0·67–1·88)	5·57 (4·56–6·50)	4·98 (4·33–5·72)
Bocavirus	37 (13%)	32 (8%)	2·29 (1·25–4·17)	4·34 (3·79–5·22)	4·23 (3·43–5·27)
Cytomegalovirus	151 (53%)	177 (43%)	1·57 (1·11–2·21)	4·98 (4·10–5·62)	4·99 (4·41–5·60)
Coronavirus (NL63,229E, OC43, and HKU1)	33 (12%)	43 (10%)	1·20 (0·75–1·97)	6·58 (4·22–7·74)	5·38 (4·07–7·21)
Enterovirus	37 (13%)	57 (14%)	0·93 (0·58–1·49)	3·75 (2·98–5·31)	4·02 (3·45–5·27)
Rhinovirus	100 (35%)	161 (39%)	0·87 (0·63–1·20)	4·12 (3·43–4·91)	4·38 (3·59–5·13)
Fungi
Pneumocystis jirovecii	44 (16%)	122 (30%)	0·35 (0·22–0·55)	4·10 (3·69–4·78)	4·08 (3·69–4·78)