Table 1. Details of the primers used.

Multiplex PCR	Gene	Primer sequence (5’–3’)	PCR product (bp)	Annealing temperature (°C)	Reference
Aminoglycoside adenylyl transferases	AadA (aadA1 or aadA2)	GCTCTTCAGCAATATCACGG GCAGCGCAATGACATTCTTG	282	60	[52]
SNP Detection
DNA gyrase	GyrA	CTCCTCCCAGACCAAAGACA TCACGACCGATACCACAGCC-	447	60	[35, 36]
DNA topoisomerase IV	ParC	AAACCTGTTCAGCGCCGCATT GTGGTGCCGTTAAGCAAA	395	54	[35, 36]
Antibiotic Resistance Genes
Tetracycline	TetA-F TetA-R	GTAATTCTGAGCACTGTCGC CTGCCTGGACAACATTGCTT	937	62	[53]
Sulphonamides	Sul1-F Sul2-R	TGGTGACGGTGTTCGGCATTC GCGAGGGTTTCCGAGAAGGTG	789	63	[22]
Gentamicin	AacC1-F AacC1-R	ACCTACTCCCAACATCAGCC ATATAGATCTCACTACGCGC	169	60	[54]
Tetracycline	TetB-F TetB-R	CTCAGTATTCCAAGCCTTTG CTAAGCACTTGTCTCCTGTT	416		[54]
Tetracycline	TetC-F TetC-R	TCTAACAATGCGCTCATCGT GGTTGAAGGCTCTCAAGGGC	570		[54]
ESBL	TEM	AGTGCTGCCATAACCATGAGG CTGACTCCCCGTCGTGTAGATA	431		[55]
	SHV	GATGAACGCTTTCCCATGATG CGCTGTTATCGCTCATGGTAA	214
	OXA	ATTATCTACAGCAGCGCCAGTG TGCATCCACGTCTTTGGTG	296
	CTX-M	GACAAAGAGAGTGCAACGGATG TCAGTGCGATCCAGACGAAA	501
MBL	blaNDM-1	ATTAGCCGCTGCATTGAT CATGTCGAGATAGGAAGTG	154	55	[56]
	blaIMP	TTGACACTCCATTTACAG GATTGAGAATTAAGCCACTCT	139		[57]
	blaVIM	GATGGTGTTTGGTCGCATA CGAATGCGCAGCACCAG	390
ABL	CMY	GCTGCTCAAGGAGCACAGGAT CACATTGACATAGGTGTGGTGC	520	60	[58]
	DHA	AACTTTCACAGGTGTGCTGGGT CCGTACGCATACTGGCTTTGC	405
	ACT-1	TCGGTAAAG CCGATGTTG CGG CTT CCA CTG CGG CTG CCA GTT	302
Reference gene	16SrRNA	CCCCCTGGACGAAGACTGAC ACCGCTGGCAACAAAGGATA	401		[49]