Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

Charalampous, Themoula; Alcolea-Medina, Adela; Snell, Luke B.; Williams, Tom G. S.; Batra, Rahul; Alder, Christopher; Telatin, Andrea; Camporota, Luigi; Meadows, Christopher I. S.; Wyncoll, Duncan; Barrett, Nicholas A.; Hemsley, Carolyn J.; Bryan, Lisa; Newsholme, William; Boyd, Sara E.; Green, Anna; Mahadeva, Ula; Patel, Amita; Cliff, Penelope R.; Page, Andrew J.; O’Grady, Justin; Edgeworth, Jonathan D.

doi:10.1186/s13073-021-00991-y

Table 2 Comparison of pathogens reported by routine culture with metagenomics sequencing in respiratory samples

From: Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

Patient ID	Sample ID	Semi-quantitative routine culture report^a	Pathogens identified by metagenomic sequencing	Pathogen reads^b identified by metagenomic sequencing	Microbial reads^b identified by metagenomic sequencing
26	S35	Acinetobacter spp. (L)	A. baumannii	99	853
100	S39	C.koseri (H)	C. koseri K. pneumoniae	23,870 284	26,251
121	S37	P.mirabilis (M) M.morganii (M)	P. mirabilis M morgannii K. pneumoniae	397 28,300 876	45,395
177	S36	S. aureus (H)	S. aureus	109,767	119,881
196	S42	B. cenocepacia (L)	Burkholderia spp.	34,347	51,551
400	S49	K. pneumoniae (M)	K. pneumoniae	594	2202
408	S20	S. aureus (M)	S. aureus	36,281	38,708
441	S21	E. cloacae (M)	E. cloacae	62,314	75,866
441	S51	S. aureus (L) C. koseri (L)	S. aureus C. koseri	5203 2262	8582
550	S10	K. pneumoniae (M)	K. pneumoniae	69,029	75,350
563	S28	Aspergillus (S)	A. fumigatus S. aureus	2649 3165	44,684
613	S18	Negative	Negative	0	22,776
618	S45	K. aerogenes (S)	–	104	1228
677	S52	K. aerogenes (L)	K. aerogenes	5277	38,854
	S54	Negative	Negative	1758	3015
	S63	K. pneumoniae (M)	K. pneumoniae	17,034	147,379
727	S53	Negative	Negative	0	0
740	S30	Negative	Negative	0	759
740	S59	K. pneumoniae (M)	K. pneumoniae	99,186	119,458
749	S40	Negative	Negative	0	1157
749	S62	K. aerogenes (L)	K. aerogenes	184	1021
815	S25	Negative	Negative	0	1413
815	S46	C. koseri (M)	C. koseri	237	462
855	S41	Negative	S. aureus	1365	31,067
872	S11	K. pneumoniae (H)	K. pneumoniae	16,828	35,668
872	S61	P. mirabilis (H) K. pneumoniae (M)	P. mirabilis K. pneumoniae C. koseri	29,797 14,118 815	47,924
1033	S8	A. fumigatus (S)	A. fumigatus K. oxytoca	77 44	1399
1036	S5	Negative	Negative	0	0
1054	S31	K. pneumoniae (L)	K. pneumoniae	28,056	31,800
1065	S16	Negative	S. aureus	1768	43,692
1065	S19	Negative	Negative	0	10,371
1069	S17	P. aeruginosa (M)	P. aeruginosa	1457	1905
1082	S14	Negative	Negative	0	205
1092	S27	Negative	Negative	0	1413
1262	S29	Negative	Negative	0	759
1292	S44	S. marcescens (L) K. aerogenes (S)	S. marcescens C. freundii	53,082 6082	65,078
1346	S56	A. fumigatus (S) P. mirabilis (L)	A. fumigatus P. mirabilis	79 11,323	36,658
1440	S33	Negative	Negative	0	1176
1457	S64	Negative	Negative	0	24,484
1457	S65	Negative	Negative	0	45,990
1503	S1	K. aerogenes (L)	K. aerogenes	138,626	145,195
1512	S34	K. pneumoniae (L)	K. pneumoniae	38,758	82,796
1538	S55	Negative	A. fumigatus	16	9146

^aReported growth by culture for each pathogen. H= heavy growth, M = moderate growth, L = light growth, S scanty growth
^bCriteria for reporting organisms was ≥ 1% of microbial-classified reads and with a centrifuge score ≥ 2504 and > 9 reads for A. fumigatus only

Back to article page

ISSN: 1756-994X

Contact us

Submission enquiries: editorial@genomemedicine.com
General enquiries: info@biomedcentral.com

Genome Medicine

Contact us