Table 2.

Primers used for detection of selected antibiotic resistance genes

Determining resistance to	Target gene	Primer sequence (5′–3′)	Amplicon size (bp)	Annealing temperature (°C)	Reference
Tetracyclines	tetM	GTG GAC AAA GGT ACA ACG AG CGG TAA AGT TCG TCA CAC AC	406	60	[14]
	tetK	GAT CAA TTG TAG CTT TAG GTG AAG G TTT TGT TGA TTT ACC AGG TAC CAT T	155	60
	tetL	TGG TGG AAT GAT AGC CCA TT CAG GAA TGA CAG CAC GCT AA	229	60
	tetO	AAC TTA GGC ATT CTG GCT CAC TCC CAC TGT TCC ATA TCG TCA	515	60
	tetQ	TTA TAC TTC CTC CGG CAT CG ATC GGT TCG AGA ATG TCC AC	904	55	[64]
	tetW	GAG AGC CTG CTA TAT GCC AGC GGG CGT ATC CAC AAT GTT AAC	168	64	[65]
Macrolides	ermA	CCC GAA AAA TAC GCA AAA TTT CAT CCC TGT TTA CCC ATT TAT AAA CG	590	60	[14]
	ermB	TGG TAT TCC AAA TGC GTA ATG CTG TGG TAT GGC GGG TAA GT	745	60
	ermC	AAT CGT CAA TTC CTG CAT GT TAATCGTGGAATACGGGTTTG	299	58	[31]
	ermT	TAT TAT TGA GAT TGG TTC AGG G GGA TGA AAG TAT TCT CTA GGG ATT T	395	55	[33]
	msrA/B	GCA AAT GGT GTA GGT AAG ACA ACT ATC ATG TGA TGT AAA CAA AAT	399	54	[66]
	msrC	AAG GAA TCC TTC TCT CTC CG GTA AAC AAA ATC GTT CCC G	343	55	[67]
	mefA/E	CAA TAT GGG CAG GGC AAG AAG CTG TTC CAA TGC TAC GC	317	60	[14]
	lnuA	GGT GGC TGG GGG GTA GAT GTA TTA ACT GG GCT TCT TTT GAA ATA CAT GGT ATT TTT CGA TC	323	61	[32]
Aminoglicosides	aac(6’)-Ie-aph(2″)-Ia	CAG AGC CTT GGG AAG ATG AAG CCT CGT GTA ATT CAT GTT CTG GC	348	57	[15]
	aph3IIIa	GGC TAA AAT GAG AAT ATC ACC GG CTT TAA AAA ATC ATA CAG CTC GCG	523
	ant(4’)-Ia	CAA ACT GCT AAA TCG GTA GAA GCC GGA AAG TTG ACC AGA CAT TAC GAA CT	294
	aph(2″)-Ic	CCA CAA TGA TAA TGA CTC AGT TCC C CCA CAG CTT CCG ATA GCA AGA G	444
	aph(2″)-Id	GTG GTT TTT ACA GGA ATG CCA TC CCC TCT TCA TAC CAA TCC ATA TAA CC	641
	ant(6)-Ia	CGG GAG AAT GGG AGA CTT TG CTG TGG CTC CAC AAT CTG AT	563	56	[54]
	aac(6’)-Ii	TGGCCGGAAGAATATGGAGA GCATTTGGTAAGACACCTACG	410	55
	aadA	ATC CTT CGG CGC GAT TTT G GCA GCG CAA TGA CAT TCT TG	282	55	[47]
	aadE	ATG GAA TTA TTC CCA CCT GA TCA AAA CCC CTA TTA AAG CC	1100	51	[51]
Chloramphenicol	cat	TAA GGT TAT TGG GAT AAG TTA GCA TGR TAA CCA TCA CAW AC	~300	54	[18]
Tiamulin	cfr	TGA AGT ATA AAG CAG GTT GGG AGT CA ACC ATA TAA TTG ACC ACA AGC AGC	746	58	[68]
	lsaE	TGT CAA ATG GTG AGC AAA CG TGT AAA ACG GCT TCC TGA TG	496	54	[69]
	lsaC	GGC TAT GTA AAA CCT GTA TTT G ACT GAC AAT TTT TCT TCC GT	429	50	[70]
	vgaA	AGT GGT GGT GAA GTA ACA CG CTC TTG TTC TAA TTC TTC CG	1287	53	[70]
	vgaAv	CTC CGT GTT GAA GAT GTT TCG GGA TTC AAA CGC CTC TAT AGC C	459	56	[71]
Penicillins	blaZ	ACT TCA ACA CCT GCT GCT TTC TAG GTT CAG ATT GGC CCT TAG	240	60	[72]
	mecA	AGT TCT GCA GTA CCG GAT TTG C AAA ATC GAT GGT AAA GGT TGG C	533	55	[73]
	pbp5	AAC AAA ATG ACA AAC GGG TAT CCT TGG TTA TCA GGG	779	52	[74]
Many antibiotics	acrA	CTC TCA GGC AGC TTA GCC CTA A TGC AGA GGT TCA GTT TTG ACT GTT	107	58	[58]
	mdeA	CTT TCA GGT TAC CTT GTT GAA TAT TTA AAC ATC AAT AGG TAC TTT AAT TGT AGT TCC AAC	180	56	[75]
	norA	TTT GTT TTC AGT GTC AGA ATT TAT GTT TG GGC TTG GTG AAA TAT CAG CTA TTA AAC	140	56
	mepA	ATG GTA TAG GTT TCT TGT TTA CTG GTA TG AAT GAT AAT TGC ACC TTG TAA AAT GGC	150	57