Table 2.
Details of class 1 integrons with blaVIM
| Integron number |
n | Gene cassettes | Promoter type (n) | Downstream of gene cassettes (n) | Accession number of the integron | |
|---|---|---|---|---|---|---|
| Major type | variant | |||||
| In87 | 5 | blaVIM-1-aacA27 | PcS (1), UD (4) | qacEΔ1-sul1-orf5-orf6-IS26 (1), UD (4) | AY648125 | |
| In110 | 6 | blaVIM-1-aacA4-aadA1 | PcH2 (6) | qacEΔ1-sul1-ISCR1 (2), qacEΔ1-sul1-orf5-orf6-IS6100 (1), qacEΔ1-sul1-orf5-ΔtniB-tniA-IRt (1), qacEΔ1-sul1-ISCR1-sapA-orf2-qnrB2-ΔqacEΔ1-sul1-orf5-orf6-IRt (1), UD (1) | LC169583 | |
| In237 | In237a | 2 | aacA4-blaVIM-1 | PcS (1), UD (1) | qacEΔ1-sul1-orf5-IS1326-ΔtniB-tniA-IRt (1), UD (1) | LC169571 |
| In238a | 1 | aacA4-blaVIM-4 | PcS (1) | qacEΔ1-sul1-orf5-orf6-IS6100 (1) | LC169580 | |
| In339 | 1 | blaVIM-2-aacA7 | UD (1) | UD (1) | FJ627181 | |
| In416 | In416 | 0b | blaVIM-4-aacA7-dfrA1-ΔaadA1-smr | PcS | ISPa21-like-arsR | AJ704863 |
| In4863 | 2 | blaVIM-19-aacA7-dfrA1-ΔaadA1-smr | PcH2 (1), UD (1) | ISPa21-like-arsR (2) | LC169563 | |
| In4873 | 1 | blaVIM-1-aacA7-dfrA1-ΔaadA1-smr | PcS (1) | ISPa21-like-qacEΔ1-sul1-orf5-ΔIS1326-IS1353-ΔIS1326-ΔtniB-ΔtniA-IS26 (1) | LC169572 | |
| In590 (In-e541) | In590 | 0b | blaVIM-1-aacA7-dfrA1-aadA1c | PcS | qacEΔ1-sul1-orf5-IS26 | AY339625 |
| In591 | 8 | blaVIM-1-aacA7-dfrA1-ΔaadA1 | PcS (8) | qacEΔ1-sul1-Δorf5-IS26 (6), qacEΔ1-sul1-orf5-ΔIS1326-ΔIS1353-IS26 (1), UD (1) | LC169574, LC169576, LC169577 | |
| In1157 | 2 | blaVIM-26-aacA7-dfrA1-ΔaadA1 | PcS (2) | qacEΔ1-sul1-Δorf5-IS26 (1), ΔqacEΔ1-IS10 (1) | LC169582 | |
| In1209 | 6 | blaVIM-1-aacA7-dfrA1-aadA1c | UD (6) | IS1R (5), IS1R-like (1) | LC169573 | |
| In1317 | 2 | blaVIM-33-aacA7-dfrA1-ΔaadA1 | PcS (2) | qacEΔ1-sul1-Δorf5-IS26 (2) | LC169581 | |
| In624 | 5 | blaVIM-1-aacA4-dfrB1-aadA1, catB2 | PcH1TTN-10 (2), UD (3) | qacEΔ1-sul1-orf5-ΔIS1326-IS26 (2), UD (3) | GQ422827 | |
| In669 | 1 | blaVIM-31-aacA4 | PcWTGN-10 (1) | qacEΔ1-sul1-orf5-Δorf6-IS6100 (1) | JN982330 | |
| In916 | 8 | blaVIM-1-aacA4-aphA15-aadA1-catB2 | PcS (1), UD (7) | qacEΔ1-sul1-orf5-ΔtniB-tniA-IS26 (2), qacEΔ1-sul1-Δorf5-chrA-padR-IS6100 (2), UD (4) | KF856617 | |
| In1315 | 1 | blaVIM-1-aacA7-smr | UD (1) | ISPa21-like-3′-CSd (1) | LC169570 | |
| In1316 | 1 | blaVIM-5-gcuD-aacA4-blaOXA-2-gcuD | PcWTGN-10 (1) | UD (1) | LC169578 | |
| In1318 | 1 | blaVIM-1, aadA1e | PcS (1) | qacEΔ1-sul1-orf5-IS26 (1) | LC169584 | |
| In1320 | 1 | blaVIM-23-gcu172-aacA7 | UD (1) | UD (1) | LC169586 | |
| In1322 | 1 | blaVIM-1-aadA7-ΔgcuDf | UD (1) | UD (1) | LC169574 | |
| In1323 | 3 | blaVIM-4-aacA27 | PcW-P2 (1), UD (2) | qacEΔ1-sul1-orf5-ΔtniB-tniA-IRt (1), qacEΔ1-sul1-orf5-ΔtniB-ΔtniA-IS26 (1), UD (1) | LC169579 | |
| In3103 | 1 | blaVIM-1-aacA4-dfrB1-aadA1 | UD (1) | UD (1) | LC169588 | |
UD, undetermined due to a contig break in 5′-CS or 3′-CS; IRt, inverted repeat of Tn402-like transposon.
These integrons lacked the duplication of the ΔblaVIM regions which was present in the original sequences of In237 (GenBank accession no. EF690695) and In238 (EU581706).
This type was not identified in this study, but is presented here for comparison.
In590 and In1209 have a different aadA1 allele (aadA1a and aadA1b, respectively).
Contig break in the nucleotide position 123 of 3′-CS.
Between blaVIM-1 and aadA1, putative group II intron reverse transcriptase, which has 93% nucleotide identity to the reverse transcriptase gene found in GenBank accession no. CP002811.1, was present disrupting the attC site.
C to A mutation at nucleotide position 279 created premature stop codon.