Table 2.

Bacterial Organisms Identified by Targeted Metagenomic Sequencing (tMGS) or Conventional Cultures in Clinically Infected Patients (n=14) and Clinically Uninfected Patients (n=6), With a Brief Description of the Clinical Context and Antibiotics at the Time of Thoracentesis

tMGS	Cycle threshold (Ct) value	Culture	Clinical background/Intervention	Initial Antibiotic Regimen
Clinical evidence of pleural space infection with positive tMGS and/or conventional culture (n=14)
Staphylococcus aureus complex Enterobacteriaceae	35.06	Staphylococcus aureus	Mediastinal S. aureus surgical site infection complicated by empyema; pigtail catheter placed. No lytic therapy.	Cefepime + vancomycin + metronidazole
S. aureus complex	34.61	S. aureus	Postobstructive pneumonia and metastatic renal cell carcinoma with recurrent effusion. Indwelling pleural catheter removed days before study sample collection; no pigtail catheter placed.	Cefepime + vancomycin + metronidazole
S. aureus complex Streptococcus mitis group	35.21	S. aureus	Hepatic hydrothorax in setting of alcoholic cirrhosis; no pigtail catheter placed.	Ceftriaxone
Staphylococcus epidermidis	No Ct	S. epidermidis	Chronic empyema; pigtail catheter placed. No lytic therapy.	Cefepime + vancomycin + metronidazole
Streptococcus intermedius/constellatus	19.06	Streptococcus intermedius	Community-acquired pneumonia (CAP) with empyema; pigtail catheter placed. Lytic therapy.	Piperacillin/tazobactam + vancomycin
S. intermedius/constellatus	23.86	Streptococcus anginosus group	Hospital-acquired pneumonia with empyema; pigtail catheter placed. Lytic therapy.	Piperacillin/tazobactam + vancomycin
Streptococcus anginosus Fusobacterium nucleatum	25.70	S. anginosus group	Empyema in setting of long-term alcohol use; pigtail catheter placed. Lytic therapy.	Ceftriaxone + metronidazole
F. nucleatum	37.00	Negative	Recurrent aspiration pneumonia with empyema; Head and neck cancer resected; pigtail catheter placed. Lytic therapy.	Piperacillin/tazobactam + vancomycin
S. intermedius/constellatus	30.78	Negative	Lung abscess; pigtail catheter placed. Lytic therapy.	Piperacillin/tazobactam + vancomycin
S. intermedius/constellatus Dialister invisus Prevotella denticola	27.15	Negative	CAP; pigtail catheter placed. Lytic therapy.	Piperacillin/tazobactam + levofloxacin
Haemophilus influenzae	26.6	Negative	CAP; pigtail catheter placed. Lytic therapy.	Levofloxacin
S. aureus complex	34.62	Negative	Methicillin resistant S. aureus–pneumonia with complicated parapneumonic effusion; pigtail catheter placed. No lytic therapy.	Vancomycin
S. intermedius/constellatus Fusobacterium nucleatum	18.63	Negative	Bronchopleural fistula complicated by empyema; pigtail catheter placed. Lytic therapy.	Ceftriaxone
S. mitis group	35.18	Negative	Parapneumonic effusion; pigtail catheter placed. No lytic therapy.	Ceftriaxone + levofloxacin
No clinical evidence of pleural space infection with positive tMGS (n=6).
Enterobacteriaceae	34.77	Not done	Pleural effusion following mitral/tricuspid valve operation. No evidence of subsequent infection.	None
Capnocytophaga granulosa	35.01	Not done	Malignant effusion due to marginal zone lymphoma. Pleural space instrumentation before study sample collection. No evidence of subsequent infection.	None
S. mitis group	36.23	Not done	Malignant effusion due to metastatic colon cancer. Pleural space instrumentation before study sample collection. No evidence of subsequent infection.	None
Enterobacteriaceae Corynebacterium freneyi	35.88	Not done	Malignant effusion due to breast cancer. Pleural space instrumentation before study sample collection. Subsequent admission with concern for infection; received antibiotics.	None
S. mitis group	34.40	Not done	Malignant effusion due to lung adenocarcinoma. No evidence of subsequent infection.	None
Enterobacteriaceae	34.08	Negative	Malignant effusion due to anaplastic thyroid carcinoma. Initial concern for neutropenic fever. Suspicion for infected pleural effusion was low. No evidence of subsequent infection.	Cefepime + vancomycin