TABLE 1.
Sources of the DNA fragments used to probe the Bacteroides isolates
| Target gene(s) | Source of DNA for the probea |
|---|---|
| Antibiotic resistance genes | |
| tet(Q) | The tetQ gene of CTnDOT cloned onto pNFD13-2 (28). A 1.55-kbp EcoRI-PvuII internal fragment was used as a probe. Primers Q for (GGC TTCT ACG ACA TCT ATT A) and Q rev (CAT CAA CAT TTA TCT CTC TG) were used to PCR amplify a 758-bp internal fragment (21). |
| tet(C) | HindIII- NruI fragment of pBR328 (tetC) |
| tet(L) | pMV158 (entire) (tetL) (20) |
| tet(M) | BamHI-KpnI tetM (Tn916) fragment from pFD310 (45) |
| tetB(P) | PstI-EcoRI internal fragment of tetB(P) from pJIR667 (43) |
| ermB | A 639-bp internal fragment of pTV1-OK (Tn 917) was used for sequencing and as a probe. Primers were B1 (GAA AAG GTA CTC AAC CAA ATA) and B2 (AGT AAC GGT ACT TAA ATT GTT TAC). The accession no. is X58285) (47). |
| ermF | A 0.85-kbp EcoRI fragment containing ermFS (accession no. M37699) of Tn4551 cloned in pFD214 (44) |
| ermG | PCR primers G for1 (ACA TTT CCT AGC CAC AAT C) and G rev1 (CGC TAT GTT TAA CAA GC) were used to obtain a 442-bp internal product (bp 465 to bp 907) (accession no. L42817) (8). |
| ermA, ermC, ermQ | PCR products or fragments of cloned genes. The primers and targets for ermA and ermC are described by Sutcliffe et al. (47). A 380-bp internal fragment of ermQ was isolated from pJIR745 (2). |
| Element probes | |
| CTnDOT joined ends | 1.1-kbp PCR product containing the CTnDOT joined ends; includes att site and part of the integrase gene (5) |
| NBU1–NBU2 shared region | prmN1 oriT mobN1 region of NBU1 (41) |
| IS4351 | 1.2-kbp EcoRI-HindIII fragment (accession no. M17124) of Tn4400 cloned onto pEG920 (31, 42) |
| tetQ-rteA-rteB and rteC region of CTnDOT | 7.7-kbp EcoRI fragment of CTnDOT isolated from a cosmid clone of CTnDOT (40, 46) |
| rteC alone | 1.1-kbp subclone from CTnDOT region on pLYL52 (23) (accession no. L02419) |
| rteB alone | 500-bp EcoRV-BsaI fragment of rteB from CTnDOT (accession no. M81439) |
a
Fragments of tet(C), tet(L), tet(M), and tetB(P) were isolated from plasmids and used as probes. See reference 22 for accession numbers.