1 IS26-R ATTCGGCAAGTTTTTGCTGT Tn21 and Tn7           tnpM of Tn21 TnpM-F TCAACCTGACGGCGGCGA 55 348 AF071413 TnpM-R GGAGGTGGTAGCCGAGG tnpR of Tn21 TnpR-F GTC AGC AGC TTC GAC CAG AA 62 500 NC 002134.1 TnpR-R GAG GTA CTG GTA GAG GGT TT tnpA of Tn21 TnpA21-F TGC GCT CCG GCG ACA TCT GG 62 1200 NC 002134.1 TnpA21-R TCA GCC CGG CAT GCA CGC G tnpA of Tn7 TnA7-F CCCAGCAATAAAAGAGCTCATTGAGCAAGC 55 738 FJ914220.1 TnA7-R TATCTAGAAACAGAGTGTCTTG (fluoro)quinolone resistance genes CYC202 purchase         qnrA

qnrA-F TTCAGCAAGAGGATTTCTCA 55 627 AY070235 qnrA-R GGCAGCACTATTACTCCCAA qnrB qnrB-F CCTGAGCGGCACTGAATTTAT 60 408 DQ351241 qnrB-R GTTTGCTGCTCGCCAGTCGA qnrS qnrS-F CAATCATACATATCGGCACC 60 641 AB187515 qnrS-R TCAGGATAAACAACAATACCC aac(6′)-Ib-cr aac(6′)-Ib-cr-F TTGCGATGCTCTATGAGTGGCTA 55 482 AAL93141.1 aac(6′)-Ib-cr-R CTCGAATGCCTGGCGTGTTT aac(6′)-Ib-cr (sequencing) CGTCACTCCATACATTGCAA   bla genes           blaTEM TEM-F ATGAGTATTCAACAT

TTC CG 55 840 EF125012 TEM-R CCAATGCTTAATCAG TGA GG blaSHV SHV-F TTCGCCTGTGTATTATCTCCCTG 50 854 AF148850 SHV-R TTAGCGTTGCCAGTGYTCG blaCTX-M CTX-M-F ATGTGCAGYACCAGTAARGTKATGGC PS-341 mouse 60 593 Y10278 CTX-m-R TGGGTRAARTARGTSACCAGAAYCAGCGG blaCMY CMY-F ATGATGAAAAAATCGTTATGC 55 1200 U77414 CMY-R TTGCAGCTTTTCAAGAATGCGC blaOXA-1 OXA-1 F ATGAAAAACACAATACATATCAACTTCGC 62 820 JO2967 OXA-1R GTGTGTTTAGAATGGTGATCGCATT blaOXA-2 OXA-2 F ACGATAGTTGTGGCAGACGAAC 62 602 AF300985   OXA-2R ATYCTGTTTGGCGTATCRATATTC       Primers used for screening various genetic elements and for interrogating physical linkages learn more between different genetic elements and between such elements and Aldol condensation bla genes or (fluoro)quinolone resistance genes. Y = T or C, R = G or A, S = G or C, K = G or T. Detection of aac(6’)-lb-cr and qnr genes Screening for aac(6′)-Ib-cr gene that confers cross-resistance to fluoroquinolones and aminoglycoside was done using a combination of PCR, RFLP and

sequencing as described by Park et al.[41]. The isolates were also screened for genes conferring resistance to quinolones: – qnrA, qnrB and qnrS using PCR and sequencing strategies previously described by Wu et al.[42]. Interrogation for physical linkages between genetic elements and resistance genes Physical linkages between integron and the transposons were determined using a combination of published primers targeting 5’-conserved sequences (5’-CS) of class 1 integrons and those targeting the tnpM of Tn2 or those specific for tnpA7 of Tn7, Figure 1 . A combination of primers targeting IS elements and those targeting the 5’-CS or the 3’-termini of integrons were used for interrogation for physical linkages between integrons and IS elements.