Table 1.

Primers used in the study.

Gene name	sequence 5΄-3΄ a) b)	Target	Ref.
341F1	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCCTACGGGNGGCWGCAG	16S rRNA gene	Herlemann et al. (2011)
341F2	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTgtCCTACGGGNGGCWGCAG	16S rRNA gene	Herlemann et al. (2011)
341F3	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTagagCCTACGGGNGGCWGCAG	16S rRNA gene	Herlemann et al. (2011)
341F4	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTtagtgtCCTACGGGNGGCWGCAG	16S rRNA gene	Herlemann et al. (2011)
785R1	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGACTACHVGGGTATCTAATCC	16S rRNA gene	Herlemann et al. (2011)
785R2	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaGACTACHVGGGTATCTAATCC	16S rRNA gene	Herlemann et al. (2011)
785R3	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTtctGACTACHVGGGTATCTAATCC	16S rRNA gene	Herlemann et al. (2011)
785R4	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTctgagtgGACTACHVGGGTATCTAATCC	16S rRNA gene	Herlemann et al. (2011)
tetM_F1	CATCATAGACACGCCAGGACA	tetM epic forward	Karkman et al. (2016)
tetM_R1_F2’	GWATTACCGCGGCKGCTGCTGTTTGATTACAATTTCCGC	tetM epic linker	Tamminen et al. (2011)
TetM_F3_TS	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGCAATTCTACTGATTTCTGC	tetM epic nested	Tamminen et al. (2011)
qacEΔ1_F1	TCGCAACATCCGCATTAAAA	qacEΔ1 epic forward	Eckert, Gautier and Arlet (,2006)
qacEΔ1_R1_F2’	GWATTACCGCGGCKGCTGATGGATTTCAGAACCAGAGAAAGAAA	qacEΔ1 epic linker	Karkman et al. (2016)
qacEΔ1_F1_TS	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGCAACATCCGCATTAAAA	qacEΔ1 epic nested	Karkman et al. (2016)
int1-a_F1	CGAAGTCGAGGCATTTCTGTC	int1 epic forward	Muziasari et al. (2014)
int1-a_R1_F2’	GWATTACCGCGGCKGCTGGCCTTCCAGAAAACCGAGGA	int1 epic linker	Muziasari et al. (2014)
int1-a_F1_TS	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCGAAGTCGAGGCATTTCTGTC	int1 epic nested	Muziasari et al. (2014)
blaOXA-58_F1	ACAGGCACTGTAGATGCTTG	bla OXA-58 epic forward	Karkman et al. (2016)
blaOXA-58_R1_F2’	GWATTACCGCGGCKGCTGTGTGCTGAGCATAGTATGAG	bla OXA-58 epic linker	Karkman et al. (2016)
blaOXA-58_F3_TS	ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGGTCTAAATGCGTGCCAT	bla OXA-58 epic nested	Karkman et al. (2016)
pH’	AAGGAGGTGATCCAGCCGCA	16S rRNA gene	Edwards et al. (1989)

^aLower case nucleotides in primers 341F and 785R are introduced for mixing in sequencing.

^bNucleotides in bold mark the 16S rRNA gene sequence (in R1_F2’) or the short Illumina TrueSeq adapter (in nested primers).