Table 2.
ABR genes whose relative frequency in plasmids (Pls) and chromosomes (Chr) differs among the three tested genera. The table shows ABR gene occurrence on plasmids and chromosomes in the three genera. The ABR gene frequency on both replicons was compared using Fisher's exact test (the p-value is reported in addition to adjusted p-value for multiple comparisons using false discovery rate (FDR)). Chromosome- and plasmid-exclusive genes and genes absent from any of the genera were excluded from this analysis (a total of 98 ABR genes were tested). Genes discussed in the Results §§3(c)–3(e) are highlighted in italics.
| resistance mechanism |
Escherichia |
Salmonella |
Klebsiella |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|
| ARO | gene | Chr | Pls | Chr | Pls | Chr | Pls | p | padj | |
| 3003922 | oqxA | antibiotic efflux | 2 | 45 | 2 | 36 | 728 | 1 | 1.02 × 10−105 | 1.00 × 10−103 |
| 3003923 | oqxB | antibiotic efflux | 2 | 31 | 2 | 19 | 162 | 0 | 5.51 × 10−45 | 2.70 × 10−43 |
| 3000165 | tetA | antibiotic efflux | 62 | 283 | 20 | 165 | 13 | 232 | 1.02 × 10−5 | 7.71 × 10−5 |
| 3000166 | tetB | antibiotic efflux | 69 | 100 | 39 | 58 | 3 | 6 | 9.47 × 10−1 | 1.00 × 10−1 |
| 3005010 | qacEΔ1 | antibiotic efflux | 55 | 291 | 68 | 137 | 116 | 371 | 1.73 × 10−5 | 1.21 × 10−4 |
| 3000873 | blaTEM-1 | antibiotic inactivation | 65 | 333 | 53 | 133 | 9 | 404 | 6.65 × 10−22 | 2.17 × 10−20 |
| 3004290 | ampC | antibiotic inactivation | 1119 | 1 | 2 | 0 | 0 | 0 | — | — |
| 3003689 | mcr-1 | antibiotic target alteration | 13 | 95 | 0 | 26 | 0 | 8 | 1.10 × 10−1 | 2.83 × 10−1 |
| 3002790 | qnrS1 | antibiotic target protection | 8 | 105 | 1 | 41 | 2 | 132 | 6.61 × 10−2 | 2.06 × 10−1 |
| 3000412 | sul2 | antibiotic target replacement | 90 | 287 | 55 | 187 | 21 | 272 | 2.00 × 10−9 | 2.79 × 10−8 |
| 3002705 | floR | antibiotic efflux | 33 | 143 | 33 | 121 | 2 | 63 | 9.17 × 10−4 | 4.99 × 10−3 |
| 3000168 | tetD | antibiotic efflux | 6 | 1 | 1 | 4 | 2 | 50 | 3.69 × 10−6 | 3.28 × 10−5 |
| 3002660 | aph(6)-Id | antibiotic inactivation | 82 | 270 | 60 | 173 | 17 | 249 | 1.70 × 10−10 | 4.16 × 10−9 |
| 3002639 | aph(3″)-Ib | antibiotic inactivation | 82 | 263 | 59 | 167 | 18 | 245 | 4.26 × 10−10 | 8.34 × 10−9 |
| 3001059 | blaSHV-1 | antibiotic inactivation | 0 | 2 | 0 | 1 | 144 | 7 | 2.01 × 10−4 | 1.23 × 10−3 |
| 3002601 | aadA | antibiotic inactivation | 43 | 130 | 10 | 76 | 3 | 133 | 8.62 × 10−9 | 1.06 × 10−7 |
| 3001877 | blaCTX-M-14 | antibiotic inactivation | 23 | 43 | 2 | 13 | 7 | 51 | 7.64 × 10−3 | 3.57 × 10−2 |
| 3002013 | blaCMY-2 | antibiotic inactivation | 22 | 42 | 6 | 70 | 0 | 7 | 1.81 × 10−4 | 1.18 × 10−3 |
| 3002539 | aac(3)-IV | antibiotic inactivation | 5 | 37 | 4 | 45 | 12 | 21 | 4.48 × 10−3 | 2.20 × 10−2 |
| 3002603 | aadA3 | antibiotic inactivation | 5 | 29 | 27 | 29 | 97 | 44 | 1.70 × 10−8 | 1.85 × 10−7 |
| 3002683 | catI | antibiotic inactivation | 35 | 27 | 26 | 35 | 9 | 81 | 5.23 × 10−1 | 8.54 × 10−9 |
| 3001926 | blaCTX-M-65 | antibiotic inactivation | 4 | 13 | 1 | 20 | 0 | 76 | 5.21 × 10−4 | 3.00 × 10−3 |
| 3004656 | catII | antibiotic inactivation | 0 | 7 | 4 | 19 | 1 | 88 | 8.84 × 10−3 | 3.94 × 10−2 |
| 3002240 | blaCARB-1 | antibiotic inactivation | 0 | 4 | 25 | 0 | 0 | 2 | 1.36 × 10−6 | 1.33 × 10−5 |
| 3001397 | blaOXA-2 | antibiotic inactivation | 3 | 0 | 0 | 1 | 0 | 0 | 2.75 × 10−3 | 1.42 × 10−2 |
| 3000410 | sul1 | antibiotic target replacement | 53 | 286 | 66 | 140 | 76 | 371 | 8.05 × 10−6 | 6.58 × 10−5 |
| 3002862 | dfrA7 | antibiotic target replacement | 13 | 2 | 21 | 23 | 0 | 1 | 9.83 × 10−3 | 4.19 × 10−2 |