TABLE 1.

Isolation and identification of organisms from urinary samples based on conventional methods, whole-genome sequencing of isolated bacteria, and direct sequencing

Sample no.	Culture result (CFU)	Conventional identification	WGS-based identification, strain	Direct sequencing identification		Chainmapper identification (%)a
				k-mer	MG-RAST (%)	Species	Genus
1				Clostridium sp.	Lactobacillus (42)	L. iners (3.5)	Lactobacillus (4.8)
3	≥105	Enterococcus spp.	E. faecalis, ST40	E. faecalis	Enterococcus (50)	E. faecalis (28)	Enterococcus (28)
4	104	Gram-positive rods	Clostridium	Clostridium sp.	Lactobacillus (78)	L. iners (33), Lactobacillus sp. (11.6)	Lactobacillus (45.8)
6	≥105	E. coli	E. coli, ST14	E. coli	E. coli (52)	E. coli (60), Escherichia sp. (10.8), Bifidobacterium breve (1.5)	Escherichia (71.3), Bifidobacterium (1.7), Shigella (1.2)
7				Clostridium sp.	G. vaginalis (15), Bifidobacterium (15)	G. vaginalis (3.78)	Gardnerella (3.78)
8				Clostridium sp.	Lactobacillus (53)	L. iners (6), Lactobacillus sp. (2.4)	Lactobacillus (8.7)
10	≥105	E. coli	E. coli, ST409	E. coli	E. coli (50)	E. coli (44), Escherichia sp. (15), Citrobacter freundii (5.5), Citrobacter sp. (5.2), Shigella sp. (3.3)	Escherichia (60), Citrobacter (12.2), Shigella (5.2)
12	≥105	E. coli	E. coli, ST95	E. coli	E. coli (38)	E. coli (23), Escherichia sp. (7), Bifidobacterium bifidum (1.6)	Escherichia (30), Bifidobacterium (1.6)
13				Clostridium sp.	Prevotella (22)	Prevotella timonensis (2)	Prevotella (4)
16	NCb	Proteus sp.	Proteus mirabilis	Clostridium sp.
19	≥105	E. coli	E. coli, ST127	P. mirabilis	Proteus (13)	P. mirabilis (2.9)	P. mirabilis (3)
20	≥105	E. coli	E. coli, ST1193	E. coli	E. coli (63)	E. coli (78), Escherichia sp. (13)	Escherichia (91)
21	NC	Proteus sp.	P. mirabilis	E. coli	E. coli (54)	E. coli (43), Escherichia sp. (10)	Escherichia (54)
	104	E. coli	E. coli, ST998
24	≥105	E. coli	E. coli, ST227	P. mirabilis	Proteus (18), E. coli (11)	P. mirabilis (26), Aerococcus urinae (19.45), E. coli (7.5)	Proteus (26), Aerococcus (19.47), Escherichia (8.8)
		E. coli	E. coli, ST227	E. coli
25	103	Enterococcus sp.	E. faecalis, ST16	E. coli	E. coli (57)	E. coli (51), Escherichia sp. (20), Shigella sp. (3)	Escherichia (73), Shigella (4.5)
26	103	E. coli	E. coli, ST597	E. faecalis	Enterococcus (48)	E. faecalis (25)	Enterococcus (26)
27	≥105	Staphylococcus sp.	S. lugdunensis	E. coli	E. coli (19)	E. coli (4)	Escherichia (5)
28	104	Mixed culture	NDc	S. lugdunensis	Staphylococcus (83)	S. lugdunensis (59)	Staphylococcus (60)
29	≥105	Enterococcus sp.	E. faecalis, ST19	E. coli	E. coli (26)	E. coli (23)	Escherichia (27.6)
31	≥105	Enterococcus sp.	Clostridium	E. faecalis	Enterococcus (48)	E. faecalis (17.4)	Enterococcus (17.5)
32	≥105	Enterococcus sp.	E. faecalis, ST41	Clostridium sp.	Enterococcus (29)	E. faecium (5.9)	Enterococcus (6.2)
33	≥105	Enterococcus sp.	E. faecalis, ST40	E. faecalis	Enterococcus (65)	E. faecalis (44)	Enterococcus (44)
34	≥105	Mixed culture	ND	E. faecalis	Enterococcus (40)	E. faecalis (13), E. coli (1.2)	Enterococcus (13), Escherichia (1.7)
35d				E. coli, E. faecalis	Enterococcus (12), E. coli (9)	E. faecalis (3), E. coli (2)	Enterococcus (3), Escherichia (2.6)

^aPercentages of the sequencing reads mapping to a given species when using Chainmapper are included in parentheses.

^bNC, not countable.

^cND, not determined.

^dPolymicrobial sample.