Table 3 Co-occurrence of dfrB and dfrA gene fragments with signatures of other antibiotic resistance genes on one and the same read (see Table 1 for average read lengths).

From: Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene

   

dfrB gene variant

Target

Linked ARG

Origin

1

3

4

5

7

10

Aminoglyc.

aac

WWTP infl.

8/5

   

2/2

 

Aminoglyc.

aac

WWTP effl.

1/1

     

Aminoglyc.

ant

WWTP infl.

8/7

 

7/2

 

3/3

2/1

Aminoglyc.

ant

WWTP effl.

 

16/7

    

Aminoglyc.

ant

River water

  

3/1

   

Ansamycin

ARR

WWTP infl.

2/2

  

?

  

Ansamycin

ARR

WWTP effl.

 

?

    

Beta-lactam

blaGES

WWTP infl.

   

?

  

Beta-lactam

blaOXA

WWTP infl.

2/2

?

  

1/1

 

Beta-lactam

blaOXA

WWTP effl.

  

?

   

Phenicol

catB

WWTP infl.

  

1/1

   

Phenicol

catB

WWTP effl.

?

 

2/1

   

Phenicol

catB

River water

  

1/1

   
   

dfrA gene variant

Target

Linked ARG

Origin

1

5

7

12

13

14

15

16

17

21

22

27

32

Aminoglyc.

aac

WWTP infl.

  

2/2

5/4

?

   

2/2

 

?

  

Aminoglyc.

aac

River water

   

1/1

 

3/2

      

?

Aminoglyc.

aac

River sedim.

   

1/1

         

Aminoglyc.

aadA

WWTP infl.

5/5

  

2/2

 

48/31

?

 

3/3

    

Aminoglyc.

aadA

WWTP effl.

1/1

    

108/9

       

Aminoglyc.

aadA

River water

        

1/1

    

Aminoglyc.

ant

WWTP infl.

32/14

10/7

4/4

8/7

?

38/23

 

5/4

3/3

2/2

   

Aminoglyc.

ant

WWTP effl.

14/5

 

1/1

1/1

 

2/2

4/3

5/4

  

1/1

  

Aminoglyc.

ant

River water

 

2/2

1/1

2/1

    

1/1

 

1/1

?

5/5

Aminoglyc.

aph

WWTP infl.

     

4/3

       

Ansamycin

ARR

WWTP infl.

14/8

          

2/2

 

Ansamycin

ARR

WWTP effl.

6/4

            

Beta-lactam

blaGES

WWTP infl.

     

?

   

?

   

Beta-lactam

blaOXA

WWTP infl.

?

    

?

       

Beta-lactam

blaOXA

River water

2/2

            

Macrolide

ere

WWTP infl.

?

?

           

Phenicol

cmlA

WWTP infl.

     

4/2

       

Quinolone

qnrVC

WWTP infl.

     

3/2

       
  1. Both dfr and the linked gene(s) fulfilled the criterion of at least 95% sequence identity. The first integer represents the number of double-positive reads, the integer after the slash indicates the number of distinct samples in which those reads were found. If a particular gene combination was observed only once across the entire data set, numbers were replaced by a question mark to indicate uncertainty associated with those singletons.
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