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).
| 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 | ||||||||||||
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.