Table 2. Frequencies of acquired antimicrobial resistance genes identified using whole-genome sequence data from phenotypically resistant Escherichia coli isolates from wildlife, swine manure pits, and environmental sources in southern Ontario, Canada 2011−2013 (n = 200).
| Antimicrobial Group | Resistance Gene | Accession No.† | Wildlifea (n = 73) | Swine Manure Pit (n = 31) | Water (n = 20) | Other Environmentalb (n = 76) | Total (%) |
|---|---|---|---|---|---|---|---|
| Aminoglycoside | aac(3)-IId | EU022314 | 3 | 0 | 1 | 1 | 5 (2.5%) |
| aac(3)-IVa | NC_009838 | 4 | 0 | 1 | 3 | 8 (4.0%) | |
| aadA2 | JQ364967 | 4 | 1 | 1 | 3 | 9 (4.5%) | |
| aadA5 | AF137361 | 6 | 0 | 1 | 1 | 8 (4.0%) | |
| ant(3’’)-Ia | X02340 | 11 | 7 | 3 | 14 | 35 (17.5%) | |
| aph(3’)-Ia | V00359/EF015636 | 5 | 0 | 3 | 4 | 12 (6.0%) | |
| aph(3’)-IIa | V00618 | 0 | 1 | 0 | 0 | 1 (0.5%) | |
| aph(3")-Ib | AF321551/AF024602 | 24 | 13 | 11 | 29 | 77 (38.5%) | |
| aph(4)-Ia | V01499 | 0 | 0 | 1 | 0 | 1 (0.5%) | |
| aph(6)-Ic | X01702 | 0 | 1 | 0 | 0 | 1 (0.5%) | |
| aph(6)-Id | M28829 | 24 | 13 | 11 | 29 | 77 (38.5%) | |
| Beta-lactam | bla CMY-2 | X91840 | 7 | 0 | 1 | 2 | 10 (5.0%) |
| bla TEM-1 | AY458016/ HM749966/ FJ560503 | 28 | 7 | 11 | 17 | 63 (31.5%) | |
| bla TEM-35 | KP860986 | 1 | 0 | 0 | 0 | 1 (0.5%) | |
| bla CARB-2 | M69058 | 0 | 0 | 0 | 1 | 1 (0.5%) | |
| bla OXA-1 | HQ170510 | 0 | 0 | 1 | 0 | 1 (0.5%) | |
| Lincosamide | lnuC | AY928180 | 0 | 0 | 0 | 1 | 1 (0.5%) |
| lnuF | EU118119 | 0 | 0 | 0 | 1 | 1 (0.5%) | |
| Macrolide | mphA | U36578 | 3 | 0 | 1 | 0 | 4 (2.0%) |
| mphB | D85892 | 0 | 0 | 1 | 0 | 1 (0.5%) | |
| mef(B) | FJ196385 | 1 | 0 | 0 | 1 | 2 (1.0%) | |
| ereA | DQ157752 | 0 | 0 | 0 | 1 | 1 (0.5%) | |
| Folate pathway inhibitors | dfrA1 | AF203818/ X00926 | 2 | 1 | 1 | 5 | 9 (4.5%) |
| dfrA5 | X12868 | 1 | 1 | 3 | 4 | 9 (4.5%) | |
| dfrA8 | U10186 | 1 | 0 | 0 | 0 | 1 (0.5%) | |
| drfA12 | AM040708 | 3 | 0 | 0 | 1 | 4 (2.0%) | |
| dfrA14 | DQ388123 | 3 | 0 | 1 | 5 | 9 (4.5%) | |
| dfrA16 | AF174129 | 0 | 0 | 0 | 1 | 1 (0.5%) | |
| dfrA17 | FJ460238 | 6 | 0 | 1 | 1 | 8 (4.0%) | |
| dfrA23 | AJ746361 | 1 | 0 | 0 | 0 | 1 (0.5%) | |
| sul1 | EU780013 | 14 | 2 | 1 | 8 | 25 (12.5%) | |
| sul2 | HQ840942/ AY034138 | 18 | 1 | 10 | 16 | 45 (22.5%) | |
| sul3 | AJ459418 | 3 | 1 | 1 | 3 | 8 (4.0%) | |
| Phenicol | floR | AF118107 | 7 | 1 | 2 | 4 | 14 (7.0%) |
| catA1 | V00622 | 2 | 0 | 2 | 0 | 4 (2.0%) | |
| cmlA1 | M64556 | 2 | 1 | 1 | 2 | 6 (3.0%) | |
| Quinolone | QnrB19 | EU432277 | 0 | 0 | 1 | 0 | 1 (0.5%) |
| QnrS1 | AB187515 | 1 | 0 | 0 | 0 | 1 (0.5%) | |
| Fosfomycin | fosA7 | LAPJ01000014 | 1 | 0 | 0 | 3 | 4 (2.0%) |
| Tetracycline | tet(A) | AF534183 | 30 | 11 | 5 | 37 | 83 (41.5%) |
| tet(B) | AF326777/ AP000342 | 19 | 16 | 10 | 19 | 64 (32.0%) | |
| tet(C) | AY046276/ AF055345 | 0 | 0 | 0 | 3 | 3 (1.5%) | |
| tetM | X04388 | 0 | 0 | 0 | 1 | 1 (0.5%) |
† Values from Resfinder database.
a Includes fecal isolates from raccoons (n = 51), skunks (n = 4), opossums (n = 2), and paw swab samples from raccoons (n = 14), and one skunk.
b Includes soil (n = 73) and dumpster isolates (n = 3).