Table 2.

Oligonucleotides used in the study

Target	Oligonucleotide	Sequence 5′–3′	References
IncW	TrwAB1	AGCGTATGAAGCCCGTGAAGGG	[3]
	TrwAB2	AAAGATAAGCGGCAGGACAATAACG	[3]
IncP	TrfA2 1	CGAAATTCATATGGGAGAAGTA	[3]
	TrfA2 2	CGTTTGCAATGCACCAGGTC	[3]
IncN	KikA1	ACTTACCTTTATCAACATTCTGGCG	[3]
	KikA2	CGACTGGTTACTTCCACCTTCGC	[3]
IncF	REPA	GGAGCGATTTGCATTCCG	[3]
	REPC	AAATGAGCCTGTTTGAG	[3]
IncA/C	CA1	ATGTCGCAGACAGAAAATGC	[3]
	OR1	CCTTGCAGTTTAATGTGAATAA	[3]
IS26	IS26F	GCTGGCTGAACGCGGAG	[9]
	IS26R	ATACCTTTGATGGTGGC	[9]
IS440	IS440F	CTCACTGTTCGCGACT	[9]
	IS440R	GGCATGCGCAGTGAGCGG	[9]
Tn1331	Tn1331NF	GAATTGCCTCGTGATACGCCTATTT	[15]
	Tn1331NR	GCGGCCGCGATAGTTTGGCTGTGAGC AATT	[15]
Tn3	Tn3F	AAGTTCATCGGGTTCGC	[9]
	201L	ACTACGATACGGGAGGGCT	[9]
tnsA	TnsAF	CTCCATATTCACTACTTGGCT	[5, 14]
	TnsAR	GCTAACAGTACAAGAAGTTCC	[5, 14]
tnsB	TnsBF	CATGTGGTCCAAGAACATAAG	[5, 14]
	TnsBR	GAGCAAGCATTTACAAAAGC	[5, 14]
tnsC	TnsCF	GTTTATCGTGATACGGGGG	[5, 14]
	TnsCR	GCTATCCCAGTCGCTGGG	[5, 14]
tnsD	TnsDF	GGGATTGTTAGTCCTAAGC	[5, 14]
	TnsDR	CCGTCTAATTTGATAATCTTC	[5, 14]
tnsE	TnsEF	TTGCTCTCTAACCACTCT	[5, 14]
	TnsER	TCGATTTGCTGCTTTTGATG	[5, 14]
aac(6′)-Ib	aac(6)’ibF	TGTGACGGAATCGTTGC	[13]
	aac(6)’IbR	CAGTGACGGTTATTCCGC	[13]
intI1	Inti1F	CGAGGCATAGACTGTAC	[12]
	Inti1R	TTCGAATGTCGTAACCGC	[12]
intI2	Inti2F	GCAAATGAAGTGCAACGC	[12]
	Inti2R	ACACGCTTGCTAACGATG	[12]
5′CS	Sulpro	GCCTGACGATGCGTGGA	[12]
3′CS	3′CS	AAGCAGACTTGACCTGATAG	[12]
sat	SatF	TGAGCAGGTGGCGGAAAC	[12]
	SatR	TCATCCTGTGCTCCCGAG	[12]
aadA1	aadA1r	TCATTGCGCTGCCATTC	[12]
	aadA1	TCGATGACGCCAACTAC	[12]
dfrA1	Dhfr1r	CCTGAAATCCCCAGCAA	[12]
	dhfrA1	AGCTGTTCACCTTTGGC	[12]
bla OXA-2	Oxa2F	GAAGAAACGCTACTCGC	[12]
	Oxa2R	TACCCACCAACCCATAC	[12]
dfrA16	Dhfr16F	CAAAGGCGAGCAACTTC	This study
	Dhfr16R	CACCCTCATCATTCGTA	This study