TABLE 4.
Plasmid characteristics and plasmid-borne resistance genes in 25 transconjugants using Miseq/MinION sequencing platforms
| Plasmid ID | Resistance genes on the plasmidb,c | Farm/sample type | Inc groupd,e | Plasmid size (bp) | Predicted mobility | Predicted resistance phenotypef |
|---|---|---|---|---|---|---|
| pT82Aa | aac (6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 4/raw | Inc− | 104,812 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT101Aa | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 4/raw | Inc− | 104,812 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT159Aa | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 1/digested | Inc− | 104,812 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT209Aa | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 7/digested | Inc− | 104,864 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT267Aa | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 5/raw | Inc− | 104,864 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT270Aa | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 5/raw | Inc− | 104,864 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT221A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 7/digested | Inc− | ∼96,702 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT286A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 2/raw | Inc− | ∼96,702 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT496A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 5/raw | Inc− | ∼96,702 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT304A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 3/raw | Inc− | ∼96,702 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT306A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 3/raw | Inc− | ∼96,702 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT409A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 7/digested | Inc− | ∼96,702 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT478A | aac(6′)-Ib-cr, aph(3′')-Ib, aph(6)-Id, blaCTX-M-15, blaOXA-1, catB4, dfrA1, floR, lnu(G), sul2 | Farm 4/raw | Inc− | ∼96,650 | Conjugative | Cip Gen Str Kan Amp Axo Tmp Chl Lin Sxz |
| pT145A | blaCTX-M-15 | Farm 1/raw | IncI1 | ∼85,051 | Conjugative | Amp Axo |
| pT277A | blaCTX-M-15 | Farm 1/raw | IncI1 | ∼83, 223 | Conjugative | Amp Axo |
| pT308A | blaCTX-M-14 | Farm 3/raw | IncI1 | ∼94,724 | Conjugative | Amp Axo |
| pT247Aa | blaCTX-M-14 | Farm 2/raw | IncI1 | 91,905 | Conjugative | Amp Axo |
| pT199Aa | blaCTX-M-1 | Farm 7/raw | IncN | 42,578 | Conjugative | Amp Axo |
| pT257Aa | blaCTX-M-27 | Farm 2/digested | IncFIIA, IncFII | 66,581 | Conjugative | Amp Axo |
| pT455A | blaCTX-M-27 | Farm 2/digested | IncN | ∼41,970 | Conjugative | Amp Axo |
| pT295Aa | aph(3′')-Ib, aph(6)-Id, blaCTX-M-27, blaTEM-1B, dfrA14, sul2, tet(A) | Farm 2/digested | IncN, IncX1 | 77,311 | Conjugative | Str Kan Amp Axo Tmp Sxz Tet |
| pT476A | blaCTX-M-55, blaTEM-1B | Farm 7/digested | IncX1 | ∼40,307 | Conjugative | Amp Axo |
| pT224Aa | blaCTX-M-55, blaTEM-206, fosA3 | Farm 7/digested | IncFIIA, IncFII | 70,625 | Conjugative | Amp Axo Fos |
| pT156Aa | blaCTX-M-55, blaTEM-206 | Farm 1/digested | IncFIIA, IncFII | 61,659 | Conjugative | Amp Axo |
| pT413Aa | aadA2, blaPER-1, sul1g, tet(E), tet(X), mph(E), msr(E), aph(3′)-Ia, tet(C) | Farm 5/raw | IncC | 187,012 | Conjugative | Str Amp Axo Ery Azi |
a
Samples were sequenced on both Miseq and MinION platforms, followed by hybrid assembly. These plasmids had complete closed sequences of precise sizes.
b
Genes in bold were identified as ESBL genes.
c
Resistance genes were identified by starAMR tool.
d
Inc group, plasmid size, and predicted mobility were determined by whole-genome sequencing and the MOB-suite tool.
e
Inc−, plasmid with no detectable Inc type.
f
Cip, ciprofloxacin; Gen, gentamicin; Str, streptomycin; Amp, ampicillin; Axo, ceftriaxone; Tmp, trimethoprim; Chl, chloramphenicol; Lin, lincomycin; Sxz, sulfisoxazole; Ery, erythromycin; Azi, azithromycin; Tet, tetracycline; Fos, fosfomycin.
g
This plasmid had two copies of the sul1 gene.