Development of a clinical metagenomics workflow for the diagnosis of wound infections

Halford, Carl; Le Viet, Thanh; Edge, Katie; Russell, Paul; Moore, Nathan; Trim, Fiona; Moragues-Solanas, Lluis; Lukaszewski, Roman; Weller, Simon A.; Gilmour, Matthew

doi:10.1186/s12920-024-02044-w

BMC Medical Genomics

Table 2 Results of routine microbiology testing and CMg analysis of wound swab samples

From: Development of a clinical metagenomics workflow for the diagnosis of wound infections

Sample Number	Routine microbiology report	Corresponding species identified by CMg	Reads (% classified microbial reads)	Sequencing Depth (×)	Additional reportable wound pathogens identified by CMg (≥1% classified microbial reads)	Reads (% classified microbial reads)	Sequencing Depth (×)
01	Enterobacter cloacae^a	Enterobacter hormaechei	111837 (70.84)	29.76	Enterobacter sp. DSM 30060	21481 (13.61)	7.16
					Enterobacter roggenkampii	7014 (4.44)	1.04
					E. cloacae complex sp. ECL414	6398 (4.05)	0.22
					Klebsiella pneumoniae	1707 (1.08)	0.33
02	No growth reported	N/A	N/A	N/A	None identified	N/A	N/A
03	S. aureus	S. aureus	1555 (64.85)	0.39	Finegoldia magna^C	231 (9.63)	0.06
04	Pasteurella multocida	P. multocida	2708 (31.25)	0.62	None identified	N/A	N/A
05	Mixed colonising organisms^b	N/A	N/A	N/A	None identified	N/A	N/A
	Enterococci	Enterococcus faecalis	232570 (93.93)	93.48
	Coliform^b	Klebsiella aerogenes	8879 (3.59)	2.46
06	Mixed colonising organisms^b	N/A	N/A	N/A	None identified	N/A	N/A
07	Streptococcus oralis	S. oralis	3482 (22.49)	1.81	Streptococcus constellatus^C	1030 (6.66)	0.45
	E. cloacae	Not identified	N/A	N/A	Streptococcus milleri^C	716 (4.63)	0.54
					Streptococcus anginosus^C	166 (1.07)	0.02
08	E. coli	E. coli	20441 (44.77)	5.19	E. hormaechei	9940 (21.81)	2.69
	Klebsiella pneumoniae	K. pneumoniae	4423 (9.70)	1.13	E. cloacae	1810 (3.97)	0.77
	Enterococci	E. faecalis	1839 (4.04)	0.67	Citrobacter portucalensis	954 (2.07)	495.75
	Enterococci	E. faecalis	1839 (4.04)	0.67	F. magna^C	953 (2.07)	0.44
09	No growth reported	N/A	N/A	N/A	None identified	N/A	N/A
10	S. aureus	S. aureus	1126 (41.17)	0.39	S. pyogenes	1542 (56.31)	0.89
11	S. aureus	Not identified	N/A	N/A	None identified	N/A	N/A
	Coagulase negative Staphylococcus	Not identified	N/A	N/A
	Group D Streptococcus	Not identified	N/A	N/A
12	Coliform^b	Citrobacter koseri	29984 (95.49)	6.89	None identified	N/A	N/A
13	Anaerobes^b	Bacteroides fragilis	15092 (65.22)	2.29	Streptococcus dysgalactiae	2830 (12.23)	0.08
	Group A Streptococci	S. pyogenes	138 (0.60)	0.05	F. magna^C	561 (2.42)	0.11
	Enterococci	E. faecalis	110 (0.48)	0.03
	Coliform^b	C. koseri	50 (0.22)	0.01
14	S. aureus	S. aureus	23082 (99.84)	7.11	None identified	N/A	N/A
15	S. aureus	S. aureus	15365 (99.81)	4.92	None identified	N/A	N/A
16	S. aureus	S. aureus	1933 (33.40)	0.39	F. magna^C	1880 (32.49)	0.46
17	Coliform^b	Klebsiella oxytoca	68 (1.93)	0.01	Pseudomonas sp. NIBR-H-19	3127 (88.71)	0.76
	E. faecalis	Not identified	N/A	N/A
	Proteus overgrowth	Not identified	N/A	N/A
	Diptheroids^b	Corynebacterium striatum	86 (2.44)	0.04
18	E. coli	E. coli	35004 (66.03)	8.00	Candida albicans	3273 (6.17)	2.25
	Anaerobes^b	Lacticaseibacillus rhamnosus	8859 (16.71)	1.68
	Coagulase negative Staphylococcus	Staphylococcus epidermidis	537 (1.01)	0.18
	Diptheroids^b	C. striatum	2587 (4.88)	1.27
19	Scanty growth coagulase negative Staphylococcus	Not identified	N/A	N/A	None identified	N/A	N/A
19	Scanty growth Diptheroids^b	C. striatum	1396 (93.19)	0.65	None identified	N/A	N/A
20	S. aureus	S. aureus	186 (0.62)	0.05	None identified	N/A	N/A
	Enterococcus	E. faecium	161 (0.53)	0.05
	Non-lactose fermenting coliform^b	E. coli	23 (0.08)	0.00
21	Group B Streptococcus	Streptococcus agalactiae	323 (0.48)	0.14	C. koseri	59255 (88.09)	12.93
21	S. aureus	S. aureus	94 (0.14)	0.02	Citrobacter sp. TBCP-5362	3843 (5.71)	1.03
22	Alpha-haemolytic Streptococcus	Streptococcus gordonii	5522 (9.26)	3.43	Morganella morganii	45270 (75.88)	0.34
	Enterococci	E. faecalis	359 (0.60)	0.14
	Coliform^b	E. coli	73 (0.12)	0.02
	Oxidase negative non-lactose fermenter^b	Proteus mirabilis	18 (0.03)	0.00	F. magna^C	914 (1.53)	0.18
	Diptheroids^b	C. striatum	94 (0.16)	0.05	F. magna^C	914 (1.53)	0.18
23	Scanty growth Group C Streptococcus	S. dysgalactiae	280 (0.74)	0.02	None identified	N/A	N/A
	Scanty growth S. aureus	S. aureus	212 (0.56)	0.06
	Proteus	P. mirabilis	28 (0.07)	0.01
24	Yeasts^b	C. albicans	3288 (38.97)	1.90	E. faecalis	2495 (29.57)	0.64
24	Coagulase negative Staphylococcus	Staphylococcus haemolyticus	217 (2.57)	0.06	E. faecalis	2495 (29.57)	0.64
25	Coagulase negative Staphylococcus	S. epidermidis	85 (0.45)	0.02	None identified	N/A	N/A
26	Group A Streptococcus	S. pyogenes	6994 (82.97)	3.10	None identified	N/A	N/A
26	S. aureus	S. aureus	544 (6.45)	0.16	None identified	N/A	N/A
27	S. aureus	S. aureus	868 (7.93)	0.17	F. magna^C	1156 (10.56)	0.30
	Group G Streptococcus	S. dysgalactiae	6 (0.05)	0.00
	Diptheroids^b	C. striatum	5646 (51.55)	2.53
28	Pseudomonas	P. aeruginosa	1294 (3.06)	0.20	F. magna^C	1356 (3.21)	0.64
	Scanty Growth coagulase negative Staphylococcus	Staphylococcus equorum	14 (0.03)	0.00
	Proteus	P. mirabilis	11 (0.03)	0.00
	Diptheroids^b	C. striatum	30433 (71.95)	15.63
29	S. aureus	S. aureus	62 (65.26)	0.00	None identified	N/A	N/A
30	E. faecalis	E. faecalis	561 (0.46)	0.08	P. aeruginosa	101154 (82.80)	16.36
	Strenotrophomonas maltophilia	S. maltophilia	221 (0.18)	0.06	Pseudomonas putida	18103 (14.82)	3.87
	Diptheroids^b	Not identified	N/A	N/A
31	Mixed colonising organisms^b	N/A	N/A	N/A	None identified	N/A	N/A
32	Group G Streptococcus	S. dysgalactiae	4783 (28.95)	0.27	F. magna^C	320 (1.94)	0.14
	Enterococcus	E. faecalis	217 (1.31)	0.08
	Coagulase negative Staphylococcus	Not identified	N/A	N/A
33	Mixed colonising organisms^b	N/A	N/A	N/A	B. fragilis^C	70466 (73.74)	18.52
					M. morganii	10540 (11.03)	3.92
					Peptoniphilus sp. SAHP1^C	3211 (3.36)	2.55
					Bacteroides uniformis^C	2221 (2.32)	0.73
					P. mirabilis	1938 (2.03)	0.69
34	Pseudomonas spp.	P. aeruginosa	1224 (9.37)	0.17	None identified	N/A	N/A
35	Group C Streptococcus	S. dysgalactiae	1239 (6.86)	0.05	E. faecalis	1198 (6.63)	0.30
35	S. aureus	S. aureus	252 (1.39)	0.05	E. faecalis	1198 (6.63)	0.30
36	Group C Streptococcus	S. dysgalactiae	17990 (76.75)	0.69	S. pyogenes	631 (2.69)	0.10
	S. aureus	S. aureus	1377 (5.87)	0.32	S. agalactiae	547 (2.33)	0.10
					P. aeruginosa	314 (1.34)	0.05
37	Group C Streptococcus	S. dysgalactiae	20847 (76.04)	0.79	Prevotella corporis^C	2089 (7.62)	1.15
	Group C Streptococcus	S. dysgalactiae	20847 (76.04)	0.79	B. fragilis^C	1180 (4.30)	0.17
	S. aureus	S. aureus	23 (0.08)	0.01	S. pyogenes	722 (2.63)	0.12
					S. agalactiae	452 (1.65)	0.08
					F. magna^C	278 (1.01)	0.07
38	Mixed colonising organisms^b	N/A	N/A	N/A	Klebsiella michiganensis	12527 (38.66)	2.31
					S. anginosus^C	3261 (10.06)	1.02
					K. oxytoca	1667 (5.14)	0.14
					K. pneumoniae	1390 (4.29)	0.24
					Citrobacter freundii	1269 (3.91)	0.27
					E. faecalis	1182 (3.65)	0.30
					B. fragilis^C	757 (2.33)	0.13
					Klebsiella grimontii	731 (2.25)	1.63
					E. coli	576 (1.78)	0.14
					P. aeruginosa	463 (1.43)	0.07
					E. hormaechei	442 (1.36)	0.03
					M. morganii	329 (1.01)	0.08
39	Mixed colonising organisms^b	N/A	N/A	N/A	F. magna^C	2946 (37.15)	0.54
					Staphylococcus pettenkoferi^C	129 (1.63)	0.04
					S. pyogenes	103 (1.30)	0.03
					S. agalactiae^C	97 (1.22)	0.03
40	Mixed colonising organisms^b	N/A	N/A	N/A	F. magna^C	4110 (18.01)	0.97
40	Mixed colonising organisms^b	N/A	N/A	N/A	P. aeruginosa	518 (2.27)	0.07

Species identified by routine microbiology and the corresponding species identified by CMg at the highest classified microbial read proportion are reported. Additional reportable pathogens identified by CMg, as determined by a consultant microbiologist, identified ≥ 1% classified microbial reads are listed. % classified microbial reads = % of species reads over the total number of taxonomically classified microbial reads obtained. Sequencing depth was calculated by dividing the total bp assigned to a species by the total genome size
^aRoutine microbiology test reporting refers to a group of Enterobacter species as Enterobacter cloacae for routine reporting purposes This group includes Enterobacter hormaechei, listed as the corresponding organism in sample 01
^bMicrobial species or genus identification not provided by routine microbiology report
^cOrganism reported by routine microbiology if identified in pure culture only

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