Table 4 Long-read sequencing found AMR genes often near transposase genes and on the chromosome
Isolate No. | VN/DE | Spec | predictions short-read assembly | predictions based on ONT/hybrid assembly | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
plasmids contigs | plasmids circular | plasmids mobilization elements | plasmids conjugation elements | circular contigs | plasmid contigs | Point mutations and AMR genes on chromosome (in bold indicates location in proximity to transposase genes) | AMR genes on plasmid | |||
BfR-CA-15687 | DE | Cc | 1 (-) | 0 | 1 | 6 | 2 | 1 | blaOXA-489;tet(O);GyrA_T86I | tet(O) |
BfR-CA-15991 | VN | Cc | 0 | 0 | 0 | 0 | 1 | 0 | tet(O/M/O)-catA9-tnpIS1216 family-fexA-optrA-tnpIS1216family-tet(L);aac(6’)-Ie/aph(2’’)-Ia-aadE1-tet(O)xΔC−terminusblaOXA-193;23S_A2075G; 23S_A2075G; 23S_A2075G;GyrA_T86I |  |
BfR-CA-16040 | VN | Cc | 1 (-) | 0 | 0 | 0 | 1 | 0 | tnpISCco2 family-catA13-aph(3’)-IIIa-aad9;tet(O/M/O)-aad9-erm(B)-aadE1;aac(6’)-Ie/aph(2’‘)-Ia-aadE1-tet(O)xΔC−terminus; blaOXA-489;GyrA_T86I |  |
BfR-CA-16046 | VN | Cc | 2 (-) | 1 | 1 | 6 | 2 | 1 | tnpISCco2 family-catA13-aph(3’)-IIIa-aad9-aph(2’‘)-If-blaOXA-193;tet(O/M/O)-aad9-erm(B)-aadE1;aadE-Cc;GyrA_T86I |  |
BfR-CA-16077 | VN | Cj | 1 (-) | 0 | 0 | 0 | 1 | 0 | tnpISCco2 family-catA13-aph(3’)-IIIa-aad9-aph(2’‘)-If;tet(O/M/O)-aadE1-tet(O)xΔN−terminus;aph(3’)-IIIa-tnpISCaje6 family;blaOXA-184 family; tnpISCco2 family-lnu(C);GyrA_T86I |  |
BfR-CA-16088 | VN | Cj | 1 (-) | 0 | 0 | 0 | 1 | 0 | tnpISCco2 family-catA13-aph(3’)-IIIa-aad9-aph(2’‘)-If;tet(O/M/O)-aadE1-tet(O)xΔN−terminus;aph(3’)-IIIa-tnpISCaje6 family;blaOXA-184 family; tnpISCco2 family-lnu(C);GyrA_T86I;23S_A2075G;23S_A2075G;23S_A2075G |  |
BfR-CA-16110 | VN | Cc | 0 | 0 | 0 | 0 | 1 | 0 | tet(O)-aad9-erm(B)-aadE1;blaOXA-193;GyrA_T86I | Â |
BfR-CA-16201 | VN | Cc | 0 | 0 | 0 | 0 | 2 | 1 | tet(O)-aad9-erm(B)-aadE1; tnpISCco2 family-catA13-aph(3’)-IIIa-aad9-aph(2’‘)If-blaOXA-193;tet(O);GyrA_T86I |  |
BfR-CA-16258 | VN | Cc | 1 (+) | 1 | 0 | 0 | 2 | 1 | tet(O)-aad9-erm(B)-aadE1;tet(O);blaOXA-193;GyrA_T86I | Â |
BfR-CA-16297 | VN | Cc | 0 | 0 | 0 | 0 | 1 | 0 | tet(O/M/O)-aad9-erm(B)-aadE1;aph(2’‘)-If-aph(3’)IIIa-tnpISCaje6 family; aac(6’)-Ie/aph(2’’)-Ia-aadE1-tet(O)xΔC−terminus;tet(O)-tnpIS607 family;blaOXA-193;GyrA_T86I |  |
BfR-CA-16737 | DE | Cj | 2 (+) | 0 | 1 | 6 | 2 | 1 | blaOXA-185 like;tet(O);GyrA_T86I | tet(O/32/O)-aadE2_Δ1-415-sat4-aph(3’)-IIIa |
BfR-CA-18842 | VN | Cc | 0 | 0 | 0 | 0 | 1 | 0 | aac(6’)-Ie/aph(2’’)-Ia-aadE1-tet(O)xΔC−terminus; tet(O/M/O);blaOXA-193;GyrA_T86I |  |
BfR-CA-19087 | DE | Cc | 3 (+) | 0 | 0 | 0 | 2 | 1 | tnpIS607 family-tet(O/32/O)-aph(2’‘)-li1-aph(3’)-IIIa-aad9-aadE1-tet(O)xΔN−terminus;tet(O/32/O);aadE-Cc;GyrA_T86I |  |
BfR-CA-19301 | VN | Cj | 0 | 0 | 0 | 0 | 1 | 0 | aadE3-sat4-aph(3’)IIIa-tnpIS1216 family;tet(O/32/O);blaOXA-193; GyrA_T86I |  |