16S rRNA is a valuable tool in finding bacterial aetiology of community-acquired pleural empyema–a population-based observational study in South Sweden

Figures & data

Figure 1. Flow chart of steps of inclusion. *A complete list of bacterial species considered contaminants is displayed in Table A1.

Table 1. Bacterial aetiology in relation to blood cultures, length of stay and mortality.

	Patients	Age	Male sex	Length of stay (days)	Positive blood culture	30-day mortality	90-day mortality
	n (%)	Median (IQR)	n (%)	Mean (SD)	n (%)	n (%)	n (%)
Viridans streptococci^a	105 (36)	72 (64–84)	69 (66)	19 (14)	3 (3)	13 (12)	20 (19)
Streptococcus anginosus-group	84 (29)
Streptococcus pneumoniae	42 (14)	67 (56–74)	22 (52)	19 (13)	22 (52)	3 (7)	6 (14)
Anaerobic bacteria^b	34 (12)	63 (52–74)	24 (70)	21 (16)	2 (6)	2 (5,9)	3 (9)
Fusobacterium nucleatum	12 (4)
Viridans streptococci and anaerobic bacteria^c	26 (9)	59 (48–68)	16 (62)	19 (11)	0 (0)	1 (4)	2 (8)
Staphylococcus aureus	20 (7)	75 (56–85)	14 (70)	28 (15)	8 (40)	1 (5)	4 (20)
Other multi-flora	21 (7)	66 (55–83)	13 (62)	17 (11)	0 (0)	0 (0)	2 (10)
Enterobacterales	14 (5)	72 (62–80)	11 (79)	22 (20)	7 (50)	6 (43)	6 (43)
Other mono-flora	14 (5)	69 (62–78)	8 (57)	23 (36)	0 (0)	2 (14)	2 (14)
Group A streptococcus	11 (4)	40 (36–45)	5 (46)	19 (12)	2 (18)	0 (0)	0 (0)
Haemophilus influenzae	4 (1)	77 (71–85)	2 (50)	11 (6)	4 (100)	1 (25)	1 (25)
Total	291 (100)	69 (65–80)	183 (63)	20 (16)	48 (16)	29 (10)	46 (16)

^aThe majority belongs to the group Streptococcus anginosus, other species are S. mitis, oralis and parasanguinis.

^bThe majority is Fusobacterium nucleatum, other species are Prevotella spp., Parvimonas micra and other species of Fusobacteria.

^cMulti-flora of viridans streptococci and anaerobic bacteria.

Each patient has been allocated to one bacterial aetiology based on result of 16SrDNA and culturing.

Table 2. Data on patients, empirical and duration of treatment, fibrinolysis and surgery.

	n (%)	Median (IQR)
Sex
Women	107 (37)
Men	184 (63)
Age		69 (65–80)
Empirical antimicrobial treatment^a
No antimicrobial treatment	19 (7)
Cefotaxime	90 (31)
Cefotaxime+^b	39 (13)
Carbapenem	13 (5)
Imipenem	7 (2)
Meropenem	6 (2)
Clindamycin	14 (5)
Benzylpenicillin	48 (16)
Benzylpenicillin+^b	11 (4)
Piperacillin–tazobactam	25 (9)
Other mono treatment	11 (4)
Other combinational treatment	21 (7)
Outpatient antimicrobial treatment
No antimicrobial treatment	76 (26)
Amoxicillin	44 (15)
Amoxicillin+^b	10 (3)
Clindamycin	92 (32)
Clindamycin+^b	16 (6)
Phenoxymethylpenicillin	20 (7)
Quinolones	10 (3)
Other mono treatment	15 (5)
Other combinational treatment	8 (3)
Change in antibiotic treatment after culture result	150 (52)
Duration of antimicrobial treatment, days^c		26 (14.5–40.5)
Intrapleural fibrinolysis	87 (30)
Surgical decortication	23 (8)

^aAntimicrobial treatment given immediately after pleural sample was secured.

^bCombinational treatment including this treatment.

^cConsecutive days of antimicrobial treatment after pleural sample was secured.

Figure 2. The bacterial species found in this study.

Figure 3. Bacterial aetiology found with respect to culturing and 16S rRNA.

Table 3. Diagnostic method with respect to bacterial aetiology.

	Culture (%)^a	16srDNA (%)^b	Culture and 16srDNA^c (%)	Concordant result^d (%)	Discordant result^e (%)
Any Streptococci	125 (68)	112 (58)	66 (6)	48 (73)	18 (27)
Anaerobic bacteria	16 (9)	50 (26)	27 (25)	6 (22)	21 (78)
Any Gram-negative bacteria	20 (11)	18 (9)	7 (7)	4 (57)	3 (43)
Staphylococcus species	19 (10)	12 (6)	5 (5)	5 (100)	0 (0)
Miscellaneous	4 (2)	2 (1)	1 (1)	0 (0)	1 (100)

^aAll samples where only standard culturing method was performed. ^bAll samples where only 16srDNA was analysed. ^cAll samples where both culturing and 16SrDNA were performed. ^dIdentical species or group identified by culturing and 16SrDNA. ^e,dNot identical species or group identified by culturing and 16SrDNA.

Data availability statement

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.