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Table 2 Comparison between genotypic AMR prediction by WGS and phenotypic expression based on MIC levels of AMR Salmonella isolates (n = 200)

From: Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

Antimicrobialsa

Resistant by phenotype

Susceptible by phenotype

Sensitivity (%)

Specificity (%)

PPVb (%)

NPVc (%)

WGS: AMR gene +

WGS: AMR gene -

WGS: AMR gene +

WGS: AMR gene -

AMP

36

7

4

153

83.72

97.45

90

95.63

AMC

8

2

4

186

80

97.89

66.67

98.94

CRO

9

1

3

187

90

98.42

75

99.47

FOX

6

1

3

187

90

98.42

75

99.47

XNL

6

1

3

187

90

98.42

75

99.47

GEN

24

4

5

167

85.71

97.09

82.76

97.66

KAN

37

9

9

145

80.43

94.16

80.43

94.08

STR

98

17

10

75

85.22

88.24

90.74

81.52

FIS

87

5

4

104

94.57

96.29

95.6

95.41

SXT

6

1

1

192

85.71

99.48

85.71

99.48

TET

93

9

8

90

91.18

91.84

94.9

88.24

CHL

7

2

1

190

77.78

99.48

87.5

98.96

Overall

    

87.61

97.13

88.35

96.93

  1. a ampicillin (AMP), amoxicillin/clavulanic acid (AMC), ceftriaxone (CRO), cefoxitin (FOX), Ceftiofur (XNL), gentamicin (GEN), kanamycin (KAN), streptomycin (STR), sulfisoxazole (FIS), trimethoprim/sulfamethoxazole (SXT), and tetracycline (TET), chloramphenicol (CHL)
  2. b positive predictive value (PPV)
  3. c negative predictive value (NPV)