Table 7.
Antimicrobial resistance determinants detected in four groups of calves in pre-and post-treatment pooled fecal samples from calves by metagenomic Hi-C.
| Antibiotic Class | Control | Low Dose Healthy | High Dose Healthy | High Dose BRD | ||||
|---|---|---|---|---|---|---|---|---|
| Pre (60 a, 9 b) |
Post (43, 5) |
Pre (80, 7) |
Post (118, 25) |
Pre (90, 22) |
Post (67, 18) |
Pre (39, 5) |
Post (123, 22) |
|
| Aminoglycoside | aph2(161 c,8 d), aph3(163,9), ant6(132,10), ant9(6,4), sat(72,5) | aph2(47,15), aph3(47,15), ant6(45,8), ant9(40,9), sat(22,8) | aph2(141,23), aph3(153,26), ant6(193,33), ant9(48,13), sat(141,23) | aph2(7,6), aph3(68,8), ant6(3,2), ant9(1,1) | aph2(515,21), aph3(516,22), ant6(65,15), ant9(67,13), sat(115,15) | aph2(99,16), aph3(101,18), ant6(159,14), ant9(150,11), sat(53,11) | aph2(79,11), aph3(79,11), ant6(17,6), ant9(20,8), sat(79,11) | aph2(44,17), aph3(41,15), ant6(42,18), ant9(30,12), sat(8,5) |
| Beta-lactam | aci(2,1), rob(2,1) | aci(2,1) | aci(17,3), cfx(1,1), rob(12,3) | pbp2(1,1), rob(63,4) | rob(1,1) | aci(1,1), oxa(162,4), rob(2,2) | cfX(2,1) | aci(1,1),cmX(7,2) |
| Macrolide | ermB(1,1), ermF(1,1), ermG(7,5), ermQ(2,2), mefE(445,4) | ermF(11,1), ermG(2,2), mefE(109,3) | ermB(4,4), ermF(783,12), ermG(36,4), ermQ(1,1), mefE(442,9) |
ermF(3,1), ermG(3,3), ermQ(3,2), mefE(86,2) |
ermB(2,2), ermG(7,5), ermQ(47,8), ermX(1,1), mefE(11350,51) |
ermF(2,2), ermG(63,2), ermQ(1,1), mefE(508,3) | ermG(4,3), ermQ(2,1), mefE(1752,5) |
ermB(2,1), ermF(1,1), ermG(3,3), ermQ(87,12), ermX(2,1), mefE(4693,45) |
| Phenicol | cfr(16,5) | cfr(42,12) | cfr(34,7) | cfr(3,2) | cfr(52,7), floR(1,1) | cfr(13,4) | cfr(9,5) | cfr(29,3) |
| Sulfonamide | NA e | NA | NA | NA | sulII(1,1) | NA | NA | NA |
| Tetracycline | tet32(1,1), tet40(118,19), tet44(2,2), tetBP(2,2), tetL(1,1), tetO(14,4), tetQ(457,8), tetW(294,25) | tet32(1,1), tet40(157,18), tetA(5,2), tetB(9,1), tetO(4,3), tetW(248, 23), tetX(1,1) | tet32(2,2), tet40(371,31), tetA(4,3), tetL(1,1), tetM(2,2), tetO(121,23), tetQ(1833,31), tetW(721,56) |
tet32(2,1), tet40(32,16), tet44(3,3), tetB(4,1), tetL(1,1), tetM(3,1), tetO(32,15), tetQ(67,4), tetW(186,36), tetX(2,1) | tet32(3,3), tet40(534,46), tet44(69,11), tetA(54,15), tetB(436,21), tetM(23,7), tetO(76,22), tetQ(647,27), tetW(718,49), tetX(1,1) | tet32(21,8), tet40(154,27), tetA(2,2), tetO(46,27), tetW(1371,79) | tet40(48,15), tetA(2,2),tetM(1,1),tetO(67,18), tetQ(27,3), tetW(185,30), tetX(1,1) | tet40(161,40), tet44(6,3), tetA(16,9), tetB(8,4), tetM(11,5), tetO(39,15), tetQ(414,17), tetW(440,63), tetX(1,1) |
a Number of total clusters in the pooled sampled, b number of clusters with ≥80% complete genome, c number of ARG hits detected in the pooled sample, and d number of clusters hosting the specified ARG. e Not available, no ARGs of this antibiotic were detected.