Table 2.

Concordance between culture and sequencing results for each sample

	Culture Result				Number of Sequencing Reads				Concordance between Methods
Sample	MH	PM	HS	MB	MH	PM	HS	MB	MH	PM	HS	MB
1				+				8	MATCH	MATCH	MATCH	MATCH
2				+	6	1	2	10	Seq	Seq	Seq	MATCH
3		Few				9		5	MATCH	MATCH	MATCH	Seq
4						7			MATCH	Seq	MATCH	MATCH
5		1 +		+		49	11	344	MATCH	MATCH	Seq	MATCH
6		2 +			80	4,085	16	1	Seq	MATCH	Seq	Seq
7		1 +		+		1,436	3	1	MATCH	MATCH	Seq	MATCH
8		1 +		+		660		4	MATCH	MATCH	MATCH	MATCH
9		4 +		+	89	14,198	10	8	Seq	MATCH	Seq	MATCH
10		1 +		+		55		4	MATCH	MATCH	MATCH	MATCH
11		1 +		+		209	1		MATCH	MATCH	Seq	Cult
12		3 +		+	24	3,582	593		Seq	MATCH	Seq	Cult
13				+	3	255			Seq	Seq	MATCH	Cult
14		1 +		+		33			MATCH	MATCH	MATCH	Cult
15									MATCH	MATCH	MATCH	MATCH
16						2			MATCH	Seq	MATCH	MATCH
17	1 +				324	3	48		MATCH	Seq	Seq	MATCH
18		2 +				813			MATCH	MATCH	MATCH	MATCH
19		4 +			1	5,739	1	6	Seq	MATCH	Seq	Seq
20		1 +				1,339	1		MATCH	MATCH	Seq	MATCH
21					34	520	1		Seq	Seq	Seq	MATCH
22					65	67			Seq	Seq	MATCH	MATCH
23		1 +			381	2,306		4	Seq	MATCH	MATCH	Seq
24	1 +	1 +			7,926	10,712	9	15	MATCH	MATCH	Seq	Seq
25		1 +		+	27	1,222		5	Seq	MATCH	MATCH	MATCH

The columns under “culture result” indicate the semiquantitative abundance of each recovered isolate (MH Mannheimia haemolytica, PM Pasteurella multocida, HS Histophilus somni, MB Mycoplasma bovis). The columns under “Number of sequencing reads” indicate the number of metagenomic sequencing reads that were classified as each of the four target pathogens, regardless of length. The columns under “concordance between methods” indicates whether the two approaches yielded the same answer (“MATCH”), Sequencing detected the organism when culture did not (‘Seq”), or culture detected the organism when sequencing did not (“Cult”)