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Table 2 Concordance of swab types for culture and qPCR with culture and qPCR pattern of swabs

From: Does swab type matter? Comparing methods for Mannheimia haemolytica recovery and upper respiratory microbiome characterization in feedlot cattle

Concordance

Isolation pattern (DG, NS, PS)

Culture frequency

Culture percentage (%)

qPCR frequency

qPCR percentage (%)

Full

YYY

53

77.3

54

81.9

NNN

39

41

Two yes

YYN

3

10.9

2

12.1

YNY

5

1

NYY

5

11

Two no

NNY

4

11.8

1

6.0

NYN

4

5

YNN

6

1

 

Total

119*

100

116*

99.9

  1. Percentage is out of total swabs with results from all 3 swab types
  2. *Samples from 1 swab for culture (DG) and 4 swabs for qPCR (3 DG and 1 PS) were damaged in transport or failed DNA extraction so samples from these animals were not used in concordance analysis. DG double-guarded swab, NS nasal swab, PS proctology swab, Y culture/qPCR positive, N culture/qPCR negative
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Animal Microbiome

ISSN: 2524-4671