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Table 2 Concordance between culture and sequencing results for each sample

From: Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle

 

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

  1. The columns under “culture result” indicate the semiquantitative abundance of each recovered isolate (MH Mannheimia haemolytica, PMPasteurella multocida, HSHistophilus somni, MBMycoplasma 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”)