Table 2 Abundance of sequence reads per Kilobase per million reads (RPKM) of ARGs associated with different drug classes and mechanisms of action in fecal samples from gilts (n = 12) Raised in an organic breeding operation. TP1: Arrival/quarantine start, TP2: introduction to training pen, TP3: introduction to breeding pen, TP4: breeding pen 3 d, TP5: breeding pen 7 d, TP6: breeding pen 10 d, TP7: artificial insemination (AI), TP8: AI plus 3 d, TP9: AI plus 7 d, TP10: AI plus 10 d.
TP1 | TP2 | TP3 | TP4 | TP5 | TP6 | TP7 | TP8 | TP9 | TP10 | SEM Min | SEM Max | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Tetracyclines | ||||||||||||
Resistance ribosomal protection proteins | 1027.0 | 826.4 | 787.4 | 662.7 | 634.2 | 617.4 | 620.7 | 583.7 | 564.0 | 545.2 | 14.2 | 65.3 |
Resistance MFS efflux pumps | 171.4 | 112.5 | 109.5 | 72.3 | 50.5 | 34.3 | 34.0 | 21.8 | 25.7 | 24.7 | 2.8 | 34.4 |
16 S ribosomal subunit protein | 1.0 | 1.5 | 1.1 | 1.1 | 1.1 | 0.9 | 0.8 | 0.7 | 0.9 | 1.3 | 0.1 | 0.3 |
Aminoglycosides | ||||||||||||
Aminoglycoside O-nucleotidyltransferases | 145.8 | 146.4 | 133.0 | 123.5 | 116.4 | 135.8 | 109.0 | 99.5 | 99.1 | 107.4 | 5.0 | 12.3 |
Aminoglycoside O-phosphotransferases | 116.5 | 99.3 | 93.8 | 103.3 | 73.5 | 86.2 | 76.1 | 73.6 | 62.6 | 61.9 | 2.5 | 15.3 |
Aminoglycoside-resistant 16 S ribosomal subunit protein | 27.7 | 21.7 | 22.1 | 27.0 | 32.5 | 27.2 | 29.7 | 14.7 | 27.3 | 25.5 | 2.1 | 4.9 |
Aminoglycoside efflux pumps | 6.3 | 3.5 | 2.9 | 5.1 | 5.0 | 2.7 | 1.7 | 0.8 | 2.5 | 1.0 | 0.5 | 1.4 |
Aminoglycoside N-acetyltransferases | 5.2 | 4.9 | 4.6 | 4.1 | 3.3 | 3.6 | 2.6 | 2.8 | 2.6 | 2.8 | 0.4 | 0.7 |
MLS | ||||||||||||
Lincosamide nucleotidyltransferases | 105.1 | 112.8 | 105.8 | 97.3 | 92.3 | 106.7 | 90.8 | 89.5 | 92.4 | 85.2 | 6.1 | 12.0 |
23 S rRNA methyltransferases | 41.6 | 55.1 | 58.9 | 44.9 | 46.0 | 46.9 | 35.2 | 27.9 | 32.8 | 35.2 | 2.8 | 8.3 |
MFS efflux pumps | 37.1 | 36.3 | 34.0 | 23.3 | 30.4 | 34.5 | 29.6 | 28.7 | 28.4 | 27.9 | 1.4 | 4.0 |
Macrolide-resistant 23 S rRNA mutation | 21.3 | 16.5 | 14.4 | 17.3 | 18.8 | 17.1 | 14.1 | 10.0 | 15.9 | 12.8 | 1.3 | 2.6 |
ABC efflux pumps | 14.3 | 12.0 | 11.5 | 10.9 | 11.5 | 11.4 | 8.2 | 5.4 | 7.0 | 8.2 | 0.6 | 2.1 |
Macrolide phosphotransferases | 4.0 | 2.7 | 2.5 | 3.9 | 5.2 | 3.5 | 2.0 | 2.2 | 3.0 | 1.2 | 0.4 | 1.1 |
Nucleosides | ||||||||||||
Streptothricin acetyltransferase | 42.6 | 38.6 | 35.7 | 38.2 | 30.2 | 36.7 | 33.0 | 31.5 | 26.0 | 27.2 | 1.3 | 5.2 |
Betalactams | ||||||||||||
Class A betalactamases | 24.2 | 32.2 | 18.4 | 13.2 | 25.0 | 22.8 | 21.8 | 23.3 | 24.8 | 18.5 | 2.0 | 4.0 |
Penicillin binding protein | 9.1 | 1.6 | 4.2 | 8.8 | 10.0 | 2.9 | 2.2 | 0.7 | 4.8 | 1.2 | 0.7 | 10.0 |
Class C betalactamase regulator | 2.0 | 1.1 | 1.4 | 2.8 | 2.1 | 1.0 | 0.5 | 0.5 | 0.9 | 0.2 | 0.2 | 2.8 |
Multi-drug resistance | ||||||||||||
ABC efflux pumps | 11.7 | 9.3 | 9.0 | 10.2 | 11.0 | 8.0 | 6.0 | 3.2 | 5.9 | 4.6 | 0.8 | 2.0 |
RND efflux pumps | 2.7 | 1.9 | 1.5 | 3.0 | 2.8 | 1.9 | 0.2 | 0.3 | 1.8 | 0.7 | 0.2 | 1.0 |
RND efflux regulator | 2.6 | 0.6 | 1.4 | 2.6 | 3.1 | 0.7 | 0.7 | 0.2 | 1.5 | 0.4 | 0.2 | 1.1 |
Elfamycins | ||||||||||||
EF-Tu inhibition | 16.0 | 18.7 | 16.1 | 13.5 | 15.8 | 14.7 | 15.3 | 12.3 | 11.3 | 12.3 | 0.7 | 2.1 |
Rifampin | ||||||||||||
Beta-subunit of RNA polymerase rpoB | 4.3 | 28.3 | 22.6 | 20.5 | 28.6 | 15.8 | 14.8 | 15.5 | 15.7 | 17.3 | 1.8 | 4.3 |
Lipopeptides | ||||||||||||
Colistin-resistant mutant | 4.0 | 0.6 | 2.0 | 3.9 | 4.4 | 2.1 | 1.0 | 0.7 | 1.9 | 0.8 | 0.4 | 1.4 |
