Table 2.

List of all used primer systems with their corresponding target gene, expected amplicon size, accuracy, and efficiency of the used calibration curves.

Organism	Target gene	Primer	Sequence	Amplicon (bp)	Accuracy (R2)	Efficiency [%]	References
ANTIBIOTIC RESISTANCE GENES
E. coli	mcr-1	mcr1FP	GGGCCTGCGTATTTTAAGCG	183	0.999	97.6	this study
		mcr1RP	CATAGGCATTGCTGTGCGTC
E. coli	CTX-M	S_CTX-MuF	CGCTTTGCGATGTGCAG	551	1.0	92.9	Paterson et al., 2003
		S_CTX-MuR	ACCGCGATATCGTTGGT
E. coli pNorm	CTX-M-32	ctxm32-F	CGTCACGCTGTTGTTAGGAA	155	1.0	92.5	Stalder et al., 2014
		ctxm32-R	CGCTCATCAGCACGATAAAG
K. pneumoniae	CMY-2	CMY-2 RT-F	CGTTAATCGCACCATCACC	172	0.998	89.9	Kurpiel and Hanson, 2011
		CMY-2 RT-R	CGTCTTACTAACCGATCCTAGC
S. hyointestinales	ermB	ermB-F	TGAATCGAGACTTGAGTGTGCAA	71	1.0	99.7	Alexander et al., 2015
		ermB-R	GGATTCTACAAGCGTACCTT
E. coli pNorm	blaTEM	qblaTEM-F	TTCCTGTTTTTGCTCACCCAG	112	0.999	100.8	Stalder et al., 2014
		qblaTEM-R	CTCAAGGATCTTACCGCTGTTG
E. coli	tetM	S_tetM-F	GGTTTCTCTTGGATACTTAAATCAATCR	88	0.998	95.9	Peak et al., 2007
		S_tetM-R	CCAACCATAYAATCCTTGTTCRC
TAXONOMY GENES
E. coli	yccT	yccTFP	GCATCGTGACCACCTTGA	59	0.994	98.4	Clifford et al., 2012
		yccTRP	CAGCGTGGTGGCAAAA
K. pneumoniae	gltA	gltAFP	ACGGCCGAATATGACGAATTC	68	0.998	97.4	Clifford et al., 2012
		gltARP	AGAGTGATCTGCTCATGAA
E. coli pNorm	16S rRNA	331FP	TCCTACGGGAGGCAGCAGT	195	1.0	96.6	Stalder et al., 2014
		518RP	ATTACCGCGGCTGCTGG
A. baumannii	secE	secEFP	GTTGTGGCTTTAGGTTTATTATACG	94	1.0	97.6	Clifford et al., 2012
		secERP	AAGTTACTCGACGCAATTCG