Table 5.

Additional potential pathogens detected

Sample number	Sample type	Routine testing detections	Sequencing results after 2 h
			Microorganisms (Ct values)	Number of microbial reads	Percentage of bacterial reads
51	BAL	Agar culture negative S. pneumoniae urine Ag positive	S. pneumoniae	13	26.531
11	Sputum	Commensals	R. mucilaginosa S. mitis S. pneumoniae S. oralis SARSCov2 (Ct 20) P. histicola	29765 1014 835 549 413 395	87.446 2.979 2.453 1.613 N/A 1.16
20	BAL	Agar culture negative S. pneumoniae urine Ag positive PIV3	S. pneumoniae Parainfluenza virus 3 (Ct 31)	985 30	91.628 N/A
34	BAL	P. aeruginosa PCR not requested	P. aeruginosa Rhinovirus A (Ct 24)	52007 56	67.401 N/A
36	Sputum	Commensals	E. corrodens N. mucosa V. parvula R. mucilaginosa P. melaninogenica P. jejuni N. meningitidis N. cinerea E. coli K. denitrificans A. defectiva Influenza virus A (Ct 24)	195 164 39 37 31 21 20 13 12 7 7 2	32.939 27.703 6.588 6.25 5.236 3.547 3.378 2.196 2.027 1.182 1.182 N/A
37	Sputum	C. freundii	C. freundii Human gammaherpesvirus 4 Rhinovirus B (Ct25)	5660 44 15	70.119 N/A N/A
49	BAL	P. aeruginosa PCR not requested	P. aeruginosa SARSCov2 (Ct 19/21)	12016 3935	66.67 N/A
50	NTS	Negative	Influenza virus C	40	N/A

H high growth, L light growth, S scanty growth.