Table 4 Results of routine microbiology AST and AMR genes identified by CMg from wound swab samples

01

E. cloacae:

Amoxicillin resistant

fosA

100

23.75

Phosphonic acid

blaACT-23

100

32.11

Penam, cephamycin, cephalosporin, carbapenem

02

No growth reported: AST not carried out.

None identified

N/A

N/A

N/A

03

S. aureus:

Sensitive (Levofloxacin intermediate)

None identified

N/A

N/A

N/A

04

P. multocida:

Sensitive

None identified

N/A

N/A

N/A

S. aureus:

Sensitive (Levofloxacin intermediate)

05

Mixed colonising organisms: AST not carried out.

blaCMY-2

100

1

Penam, cephamycin, cephalosporin, carbapenem

vgaA

100.25

2.05

Streptogramin, pleuromutilin, lincosamide

emrD

103.04

1.47

Phenicol

qacR

105.47

1.58

Fluoroquinolone

dfrS1

100

1

Diaminopyrimidines

blaZ

104.26

1.52

Penam

aac(6′)Ie

104.1

1.82

Aminoglycoside

blaZ

102.36

1.84

Penam

lsaA

100

59.89

Streptogramin, lincosamide, pleuromutilin

vgaB

98.07

1.64

Streptogramin, pleuromutilin

06

Mixed colonising organisms: AST not carried out.

None identified

N/A

N/A

N/A

07

S. oralis:

Sensitive

mefA

100.08

5.33

Streptogramin, macrolide

msrD

101.5

2.6

Streptogramin, macrolide

tetM

100.16

1.79

Tetracycline

E. cloacae:

Amoxicillin resistant

tetL

99.71

3.84

Tetracycline

ermF

100

5.19

Streptogramin, macrolide, lincosamide

blaCFXA3

100.21

2.81

Cephamycin

08

E. coli: Sensitive

ermX

100.23

3.68

Streptogramin, macrolide, lincosamide

tetD

101.35

1.8

Tetracycline

kdeA

99.59

2.36

Multidrug resistance

acrF

100

8.96

Fluoroquinolone, penam, cephamycin, cephalosporin

K. pneumoniae: Amoxicillin resistant

ermA

102.73

1.81

Streptogramin, macrolide, lincosamide

aph(3')-IIIa

100.25

2.72

Aminoglycoside

ermB

100.95

2.01

Streptogramin, macrolide, lincosamide

oqxA

100.43

2.88

Tetracycline, diaminopyrimidine, glycylcycline, nitrofuran, fluoroquinolone

blaCFXA

95.34

1.6

Oxacephem, cephamycin

Enterococcus species: AST not carried out.

emrE

100

9.96

Multidrug resistance

blaEC

100.09

5.63

Cephalosporin

fosA2

101.41

2.01

Phosphonic acid

blaACT

100.17

3.03

Carbapenem, cephalosporin, cephamycin, penam

emrD

99.16

2.55

Phenicol

09

Mixed colonising organisms: AST not carried out.

None identified

N/A

N/A

N/A

10

S. aureus:

Sensitive

tet38

100.23

3.68

Tetracycline

blaZ

101.35

1.8

Penam

11

S. aureus:

Sensitive

None identified

N/A

N/A

N/A

Coagulase negative Staphylococcus: AST not carried out

Group D Streptococcus: AST not carried out

12

Coliform:

Amoxicillin resistant

blaCKO

100

8.46

Penam

13

Group A Streptococci: Tetracycline resistant

tetM

100

3.73

Tetracycline

cepA

100

7.61

Cephalosporin

14

S. aureus:

Levofloxacin resistant

mepA

100.07

4.69

Tetracycline, glycylcycline

blaZ

100

25.67

Penam

blaR1

100

31.91

Penam

tet38

100

5.47

Tetracycline

lmrS

100

55.75

Aminoglycoside, macrolide, phenicol, diaminopyrimidine, oxazolidinone

15

S. aureus:

Levofloxacin resistant

mepA

100

9.77

Tetracycline, glycylcycline

blaZ

100

29.72

Penam

blaR1

100

28.4

Penam

tet38

100

8.48

Tetracycline

lmrS

103.19

3.82

Aminoglycoside, macrolide, phenicol, diaminopyrimidine, oxazolidinone

16

S. aureus:

Levofloxacin resistant

fosB

100.95

2.01

Phosphonic acid

17

AST not carried out.

None identified

N/A

N/A

N/A

18

E. coli:

Amoxicillin, CoTrimoxazole, Ceftriaxone, CoAmoxiclav, Cefpodoxime, Gentamicin resistant

dfrA17

100

24.01

Diaminopyrimidine

Sul1

100

14.14

Sulfonamide

vgaA

100.25

1.45

Streptogramin, pleuromutilin, lincosamide

acrF

99.97

18.44

Fluoroquinolone, penam, cephamycin, cephalosporin

mdtM

98.95

14.4

Nucleoside, fluoroquinolone, phenicol, lincosamide

blaTEM

100

14.55

Penam, monobactam, cephalosporin, penem

mphA

100

25.32

Macrolide

aph(6)-Id

100

26.15

Aminoglycoside

aadA5

100

16.61

Aminoglycoside

aac(3)-IId

100

30.91

Aminoglycoside

tetW

100.21

4.53

Tetracycline

tetA

100

21.1

Tetracycline

sul2

100

26.14

Sulfonamide

blaCTX-M

100

5.88

Cephalosporin

emrE

100

27.67

Multidrug resistance

ermX

100

2.48

Streptogramin, macrolide, lincosamide

aph(3'')-Ib

99.88

26.74

Aminoglycoside

blaEC

100

16.08

Cephalosporin

emrD

100

17.66

Phenicol

19

AST not carried out.

sul1

103.5

2.03

Sulfonamide

ermX

100

3

Streptogramin, macrolide, lincosamide

20

S. aureus:

Erythromycin, Clindamycin resistant

ermX

99.88

6.46

Streptogramin, macrolide, lincosamide

tetW

100

114.6

Tetracycline

qacR

101.59

2.01

Fluoroquinolone

dfrS1

103.7

1.96

Diaminopyrimidines

sul1

100

71.52

Sulfonamide

ant(2'')-Ia

100

133.1

Aminoglycoside

aph(6)-Id

101.91

2.02

Aminoglycoside

tetK

100

16.92

Tetracycline

ermC

100.14

3.62

Streptogramin, macrolide, lincosamide

tet33

100

128.19

Tetracycline

ermX

100

25.8

Streptogramin, macrolide, lincosamide

ermX

100.13

256.3

Streptogramin, macrolide, lincosamide

21

Group B Streptococcus:

Sensitive

tetM

99.69

1.19

Tetracycline

blaMAL-1

100

34.79

Carbapenem

tetK

100

22.67

Tetracycline

S. aureus:

Sensitive

ermC

100

35.48

Streptogramin, macrolide, lincosamide

spd

100

52.6

Aminoglycoside

fosA7.3

100

13.21

Phosphonic acid

22

AST not carried out.

blaDHA-5

100

27.76

Cephamycin, cephalosporin

mefA

101.07

2.01

Streptogramin, macrolide

ermA

100

4.45

Streptogramin, macrolide, lincosamide

catA2

99.84

24.59

Phenicol

ant(6)-Ia

101.87

1.94

Aminoglycoside

23

S. aureus:

Doxycycline, Erythromycin, Clindamycin, Fusidic acid, Norfloxacin resistant

tetK

100

7.64

Tetracycline

tetW

100

67.76

Tetracycline

ermA

107.1

2.06

Streptogramin, macrolide, lincosamide

Group G Streptococcus:

Doxycycline resistant

ermX

100.13

16.3

Streptogramin, macrolide, lincosamide

aac(3)-XI

100

6

Aminoglycoside

24

AST not carried out.

dfrC

100

9.28

Diaminopyrimidine

sul1

100.71

2.01

Sulfonamide

tet(W)

100

4.74

Tetracycline

ermC

100

5.04

Streptogramin, macrolide, lincosamide

aac(6')-Ie

100.07

6.17

Aminoglycoside

ermB

100.41

2.79

Streptogramin, macrolide, lincosamide

25

AST not carried out.

dfrC

100

2

Diaminopyrimidine

sat4

100

8.83

Nucleoside

blaZ

100

11.2

Penam

ermB

100

4.8

Streptogramin, macrolide, lincosamide

blaR1

100.06

6.36

Penam

aph(3')-IIIa

100

4.29

Aminoglycoside

ant(6)-Ia

100

6.18

Aminoglycoside

blaZ

100

5.8

Penam

26

S. aureus:

Norfloxacin resistant

blaTEM

100

3

Penam, monobactam, cephalosporin, penem

Group A Streptococcus:

Doxycycline resistant

tetM

100

6.12

Tetracycline

27

S. aureus:

Doxycycline, Erythromycin, Clindamycin resistant

ermX

100

11.97

Streptogramin, macrolide, lincosamide

blaTEM

102.67

1.84

Penam, monobactam, cephalosporin, penem

ermA

100

5.73

Streptogramin, macrolide, lincosamide

Group G Streptococcus:

Doxycycline resistant

ermX

100.13

109.45

Streptogramin, macrolide, lincosamide

tetW

100

46.8

Tetracycline

28

AST not carried out.

ermX

100

7

Streptogramin, macrolide, lincosamide

iri

100

2

Rifamycin

tetM

100.16

4.14

Tetracycline

sat4

100.18

6.01

Nucleoside

tetW

100

33.01

Tetracycline

ermA

100

25.91

Streptogramin, macrolide, lincosamide

aph(3')-IIIa

100

5.81

Aminoglycoside

ant(6)-Ia

100

2.89

Aminoglycoside

cmx

102.47

2.34

Phenicol

ermX

100.13

15.15

Streptogramin, macrolide, lincosamide

ermX

98.83

1.71

Streptogramin, macrolide, lincosamide

crpP

100.51

2.01

Fluoroquinolone

aac(3)-XI

100

6.78

Aminoglycoside

29

S. aureus:

Sensitive

None identified

N/A

N/A

N/A

30

AST not carried out.

blaPDC

100

2.28

Monobactam, carbapenem, cephalosporin

blaOXA-50

100

27.1

Penam, cephalosporin

mexA

100

46.28

Peptide, sulfonamide, diaminopyrimidine, phenicol, aminocoumarin, tetracycline, penam, cephalosporin, carbapenem, monobactam, fluoroquinolone, macrolide, penem, cephamycin

fosA

100

12.8

Phosphonic acid

catB7

100

19.85

Phenicol

aph(3')-IIb

100.12

3.9

Aminoglycoside

mexX

100

6.54

Aminoglycoside, phenicol, tetracycline, carbapenem, fluoroquinolone, macrolide, penam, cephamycin, cephalosporin

mexE

100

7.04

Diaminopyrimidine, phenicol, fluoroquinolone

31

Mixed colonising organisms: AST not carried out.

ermC

105.03

1.94

Streptogramin, macrolide, lincosamide

32

Group G Streptococcus:

Doxycycline resistant

tetM

99.69

2.64

Tetracycline

tetW

100

12.42

Tetracycline

ermX

100.13

8.34

Streptogramin, macrolide, lincosamide

33

Mixed colonising organisms: AST not carried out.

tetD

100

6.72

Tetracycline

blaDHA

100

7.49

Cephalosporin, cephamycin

sat4

100.37

2

Nucleoside

tetW

100

12.67

Tetracycline

tetM

100.16

3.63

Tetracycline

ermA

100.82

2.01

Streptogramin, macrolide, lincosamide

aph(3')-IIIa

100.5

2.01

Aminoglycoside

tetQ

100

14.38

Tetracycline

tetJ

100.33

1.96

Tetracycline

blaCFXA3

100

405.12

Cephamycin

cepA

100

27.96

Cephalosporin

ermX

100.13

12.35

Streptogramin, macrolide, lincosamide

aac(3)-XI

100

1

Aminoglycoside

34

Pseudomonas spp.: Sensitive (ciprofloxacin, ceftazidime, piperacillin-tazobactam, gentamicin intermediate)

tetW

100

15.68

Tetracycline

ermX

100.13

6.92

Streptogramin, macrolide, lincosamide

35

Group C Streptococcus: erythromycin, clindamycin resistant

qacB

101.94

1.41

Fluoroquinolone

dfrS1

100

5.51

Diaminopyrimidine

tetW

100

5.95

Tetracycline

blaZ

100

8.44

Penam

blaR1

101.37

2.67

Penam

qacC

100

11.83

Fluoroquinolone

S. aureus:

Sensitive (levofloxacin intermediate)

blaZ

100

8.12

Penam

bcrC

100

3

Peptide

bcrB

100

5

Peptide

ermX

100.13

10.37

Streptogramin, macrolide, lincosamide

aac(3)-XI

100

3

Aminoglycoside

36

Group C Streptococcus: erythromycin, clindamycin resistant

ermX

100.23

1.66

Streptogramin, macrolide, lincosamide

ermA

101.23

1.01

Streptogramin, macrolide, lincosamide

fosB

100.71

2

Phosphonic acid

S. aureus:

Sensitive (levofloxacin intermediate)

catB7

100.31

1.84

Aminoglycoside

mepA

101.18

2.33

Tetracycline, glycylcycline

37

Group C Streptococcus: erythromycin, clindamycin resistant

ermA

100.27

1.84

Streptogramin, macrolide, lincosamide

S. aureus:

Sensitive (levofloxacin intermediate)

38

Mixed colonising organisms: AST not carried out.

tetM

101.09

3.99

Tetracycline

blaOXY-1-7

101.35

9.84

Penam, cephalosporin, monobactam

tetW

99.96

2.02

Tetracycline

aph(3')-IIIa

100.68

1.8

Aminoglycoside

ant(6)-Ia

101.64

2.01

Aminoglycoside

aad9

100.99

15.95

Aminoglycoside

ermF

100

16.62

Streptogramin, macrolide, lincosamide

39

Mixed colonising organisms: AST not carried out.

ermA

100

5.74

Streptogramin, macrolide, lincosamide

ermC

100

14.53

Streptogramin, macrolide, lincosamide

qacC

100

41.27

Fluoroquinolone

ermX

100.7

2

Streptogramin, macrolide, lincosamide

qacG

100

1

Fluoroquinolone

tetM

100.52

2.75

Tetracycline

40

Mixed colonising organisms: AST not carried out.

ermX

100

20.74

Streptogramin, macrolide, lincosamide

tetM

100

5.49

Tetracycline

ermA

100

14.48

Streptogramin, macrolide, lincosamide

ermC

100

17.01

Streptogramin, macrolide, lincosamide

qacC

100

17.6

Fluoroquinolone

tet33

97.55

1.17

Tetracycline

qacG

100

2.98

Fluoroquinolone