Table 2.

Comparison of respiratory pathogen yields in nasopharyngeal/oropharyngeal (NP/OP) vs sputum specimens, March 2014–July 2015.

Pathogens	Positive		p-value	NP/OP & Sputum Positive	NP/OP & Sputum Negative	% Agreement Rate
	NP/OP	Sputum
	n (%)	n (%)
Any pathogen	200 (68)	170 (58)	<0.01	133	57	65
Any Bacterial pathogen	141 (48)	141 (48)	1	97	109	70
Any Viral pathogen	115 (39)	45 (15)	<0.01	38	172	71
Bacterial pathogens
Streptococcus pneumoniae	76 (26)	61 (21)	0.02	49	206	87
Haemophilus influenzae- All	55 (19)	47 (16)	0.27	31	223	86
Staphylococcus aureus	41 (14)	28 (10)	0.07	12	237	85
Moraxella catarrhalis	35 (12)	22 (7)	0.01	17	254	92
Pseudomonas aeroginosa	18 (6)	19 (6)	1	3	260	89
Klebsiella pneumoniae	13 (4)	27 (9)	0.01	6	260	90
Haemophilus influenzae B 1	4 (1)	3 (1)	1	2	289	99
Haemophilus influenzae B 2	3 (1)	4 (1)	1	3	290	100
Streptococcus pyogenes	1 (0)	2 (1)	1	1	292	100
Mycoplasma pneumoniae	1 (0)	0		0	293	100
Chlamydia pneumoniae	1 (0)	0		0	293	100
Bordetella pertussis	0	0		0	294	100
Legionella spp.	0	0		0	294	100
Viral pathogens
Rhinovirus	63 (21)	23 (8)	<0.01	21	229	85
Enterovirus	10 (3)	0		0	284	97
Influenza A	12 (4)	7 (2)	0.13	6	281	98
Influenza B	3 (1)	4 (1)	1	3	290	100
Resp. syncytial virus (RSV)	11 (4)	2 (1)	0.01	1	282	96
HCoV 2 (NL63)	9 (3)	1 (0)	0.01	1	285	97
HCoV 3 (OC43)	6 (2)	1 (0)	0.06	1	288	98
HCoV 4 (HKU1)	3 (1)	0		0	291	99
HCoV 1 (229E)	0	0		0	294	100
Para-influenza 3	5 (2)	2 (1)	0.25	2	289	99
Para-influenza 2	5 (2)	1 (0)	0.13	1	289	99
Para-influenza 4	2 (1)	0		0	292	99
Para-influenza 1	1 (0)	0		0	293	100
Human metapneumovirus	5 (2)	2 (1)	0.25	2	289	99
Adenovirus	1 (0)	4 (1)	0.38	0	289	98
Mycobacteria
Mycobacterium tuberclosis	3 (1)	16 (5)	<0.01	2	277	95
Fungi
Pneumocystis jirovecii	0	0		0	294	100

^*Threshold cycle (C_T) value of <35 considered positive, except for Legionella spp. where C_T > 30 for legionellae spp. were disregarded.