Table S4. Qpcr Assays Results, Shown As Average Delta Threshold Cycle ( CT) Values For

Table S4. qPCR assays results, shown as average delta threshold cycle (∆CT) values for the four field replicates calculated according to

Schmittgen and Livak (1). The CT is the difference of the 16S rRNA CT and each resistance gene CT. A value closer to zero corresponds to higher relative copy number. Forward primer sequences are provided as a signature to compare results between data tables. The first entry, “16S rRNA

(CT)”, signifies at this row contains the CT values for the 16S rRNA gene assay which is the reference gene, opposed to ∆CT values as are listed in all other rows.

Forward Gene BM BC BS JC JS PS Primer GGGTT 16S rRNA 10.2 GCGCTCG

(CT) 8.73 10.50 11.21 2 11.58 11.19 TTGC CCCTGC GTTGTGG aac 15.40 CTATGT CGTCGC CGAGCAA aac(6')-Ib 6.23 12.35 14.90 8.11 12.19 9.57 CTTG GTTTGA GAGGCAA GGTACCG aac(6')-Ib 6.20 12.88 15.09 9.37 13.28 11.71 TAA AGAAG CACGCCC aac(6')-Ib 6.31 12.23 14.18 8.87 12.18 9.01 GACACTT CGACC CGACTCC aac(6')-II 12.51 10.97 15.34 9.64 11.31 9.07 GAACAA CGTCAC TTATTCG ATGCCCT aacC 15.01 12.13 TAC aacC1 17.38 14.60 GGTCGT 1 GAGTTCG GAGACGT A ACGGC ATTCTCG 13.1 ATTGCTT aacC2 13.31 12.30 14.46 7 14.99 13.30 T CGGCG 12.2 TGGGACA aacC4 5.90 14.96 0 14.40 CGAT GTTCTT GCTCTTG CTCGCAT aadA5 6.85 10.09 12.43 6.20 11.91 8.53 T ATCAC GATCTTG CGATTTT aadA5 7.11 10.31 12.63 6.54 11.99 9.22 GCT CGAGA TTCTCCG aadA 4.01 7.36 10.27 4.53 10.73 7.14 CGCTGTA GTTGTG CACGACG ACATCAT aadA 3.75 7.18 10.14 4.76 10.01 13.35 T AGCTA AGCGCGA ACTGCAA aadA1 3.82 7.50 10.65 5.64 10.44 6.55 T CAATG ACATTCT TGCGGGT aadA2 3.60 7.25 9.67 3.71 9.08 5.64 ATC CTTGTC GTGCATG ACGACAT aadA2 4.87 9.23 11.53 4.79 8.84 6.34 C aadA2 4.54 9.25 10.78 4.79 9.37 11.77 ACGGC TCCGCAG 2 TGGAT GGATG CACGCTT aadA9 6.57 10.74 13.59 6.97 12.71 12.56 GGATGAA CGCGG CAAGCCT aadA9 6.35 11.37 14.26 6.85 13.33 12.82 ATCTTG CCGAC AACATTT 10.3 CTACCAT aadD 6.24 13.18 2 14.69 13.60 CCTT CGGAA TTGAAAA 12.0 AACTGAT aphA3 2.35 12.77 14.46 0 13.83 13.31 CGAA AAAAG CCCGAAG AGGAACT aphA3 2.81 14.31 14.71 8.38 10.97 13.79 TG TGAGC AGTATCA TAAGTTG AGTGAAA aph(2')-Id AG TGAAC AAGTCTG GAAAGAA aphA1 3.67 13.67 9.30 13.20 10.31 ATGCA CCGGT GGCATTT 10.7 GAGAAAA strA 8.74 15.19 9 12.96 A GCTCG GTCGTGA GAACAAT strB 3.39 9.36 12.42 5.06 11.96 6.74 CT bla1 15.21 GCAAG TTGAAGC 3 GAAAGAA AAGA GCGAT AACGTGG CGATGAA blaCTX-M T GGAGG CGTGACG blaCTX-M 17.12 GCTTTT GCAAT GTGCTCA ACGTTCA blaGES AG CGTTCA GGCGGCA blaOXY 15.16 14.10 13.21 GGTT TTGTGA CCTATTC 13.3 CCCTGTA blaPSE 8.98 14.81 7 15.19 12.26 ATAGAA GCAAA GGCATGA blaROB 17.39 CGATTGC TCCCAT GATGAGC ACCTTTA blaSHV 17.31 15.20 14.65 14.95 AA AGCAT CTTACGG 13.1 ATGGCAT blaTEM 8.31 14.28 13.23 0 12.01 9.20 GA ACACTT TGCCATT GCTGTTT blaTLA 12.72 ATGT CCCGAT GCAAAGC blaVEB GTTATG

4 GGAGA TAAAGTA ACAAATC CAGTTAG blaZ 12.26 ATATGA TCATTC CTCGTTC AAGTTTT cfxA 15.30 CAGA GGCGA ACTTCTA ATTAATC Pbp5 18.14 CTATCCA AGACG GTAACGT ATAACTT TTTGAAA penA 15.62 15.09 14.28 GA CACCG GGTTACC 14.6 AGCTGAA bla-L1 16.10 14.78 15.56 8 10.76 14.72 G GCGAG 16.2 CTGCACA cphA 15.37 1 14.94 14.09 AGCTGAT CAGCC GCTGATG AAAAAAT ampC 15.63 ATG TGGCGT ATCGGGT ampC 17.65 CAATGT CTGTTC GAGCTGG GTTCTAT ampC 18.01 AAGTAAA ampC 10.18 AACAA AAGATCC 5 CCGGTAT GG GCAGC ACGCCCC ampC 10.60 14.26 GTAA CCGCTC AAGCTGG ampC 17.80 15.69 14.99 ACCATAC TGGCC ampC/ GCAGCAG blaDHA AAAGA GCGAG CAGCCTG blaCMY2 15.44 AAGCA AAAGC CTCAT GGGTGCA blaCMY2 15.59 TAAA CTATGT CAATGTG blaMOX/ CCGAAGC blaCMY 15.36 15.35 A CGCCGT 13.9 ACAACCG blaPAO 18.00 6 14.12 GTGAT GGTTTG CCGCTGC fox5 14.82 14.91 AGTTC CGGAT GGTTTGA blaOXA1/ AGGGTTT blaOXA30 ATTAT CGCAA TTATCGG 14.6 CCTAGAA blaOXA10 9.36 6 13.22 ACT blaOXA10 9.70 15.65 14.7 15.36 12.96 CGCAA 4 TTATCGG CCTAGAA 6 ACT TAGGA AGCATCG GAACGTT cmlA1 6.78 11.94 13.94 5.71 13.63 8.44 GAT AGGAA GCATCGG AACGTTG cmlA1 12.69 11.66 15.04 6.59 14.57 8.71 A GCGAT CGCCATC cmx(A) 2.96 10.30 12.94 6.62 10.01 7.85 CTCTGT TAGTA GGCAAGC 15.0 TCGGTGT matA/mel 9.26 12.83 15.51 0 13.93 TGA CTGCTA ACACAAG TACGATT msrA CCAAAT CCCGG 11.1 AGTCGAT oleC 13.64 14.55 3 14.36 14.88 GTTCGA CGAGT ATTGTGG AAAGCAG vgaA 14.60 CTAGTT TAAAA GAGAATA AGGCGCA vgaB AGGA GGCGG ACCGACT erm(36) 10.05 11.81 9.48 13.26 TGCAT TTGAG AAGGGAT TTGCGAA ermA 15.80 AAG 7 ACATTT TACCAAG ermA/ GAACTTG ermTR 13.82 TGGAA TAAAG GGCATTT AACGACG ermB AAACT TTTGAA ATCGGCT CAGGAAA ermC 16.66 A GTTTGA TATTGGC ATTGTCA ermK GAGAAA CTCGG GTACCAA 15.1 GGTCTGC ermX 5.13 10.29 0 15.07 12.95 TT GCTCA 15.8 GTGGTCC ermX 4.54 13.98 7 15.15 12.11 CCATGGT TTGTCT TTGAAAG TGAAGCA ermY 16.26 ACAGT TCGTGG GCCAGGT pikR2 GAAGA CCTGTG GTACGGA GAATTCA ereA 13.03 16.25 13.95 14.59 TGT AGGGA GGGTATC CATGCAG vgb 15.86 AT

8 GCGCG TTGACGA erm(34) CGATTT CCGTA GCATTGG 11.9 AACAGCT mefA 6.48 11.86 13.14 7 13.41 13.15 TTT CTGAC 14.6 GCGCTCC mphA 11.25 14.67 7 13.44 GTGTT TGATG 16.0 ACCCTGC mphA 11.38 16.16 8 15.09 CATCGA CGCAG CGCTTGA TCTTGTA mphB 14.20 G TGACG CTCAACA CACTCAA lnuA AAA CGGAA ATTGGGA ACGATGT vatC T GACCG TCCTACC AGGCGTA vatE 7.65 15.32 A GGTGC CATTATC GGAGCAA vatE 16.30 14.97 AT GCGGC GTACTGG TGAAGCT marR 18.18 A sdeB 15.43 15.19 14.3 12.25 11.97 CACTAC 9 CGCTTCC GCACTTA 5 A ATCGGT CGCTCTT mepA 15.40 CGTTCAC CTCAGC AGTATGG TGGTAAG emrD 14.50 CATT ATTGTC TTCACGG TGTCCGT floR 4.04 9.95 11.10 5.73 9.41 5.00 TA ATACA GCAGTGG ATATTGG TTTAATT mdetl1 GT TGACG CATCGCG rarD 10.06 15.64 TGATCT TGGCA CAAAATA TCTGGCA yceE/ mdtG 10.34 GTT CGCGT GAAACCT TAAGTGC yceL/ mdtH 9.98 TT CTGCCG TTAAATG GATGTAT yceL/ mdtH 9.87 15.76 GC TGCTGA TCGGGAT TCTGATT yidY/ mdtL 9.84 G

10 TCGCCC 16.7 TGGATGT ttgB 14.43 2 11.02 ACACCTT CAGAC CCGCATC acrA GCATATT GGTCTA TCACCCT ACGCGCT acrA 9.93 ATC CAACG ATCGGAC acrA 10.03 GGGTTTC CGTGC GCGAACG acrA 16.79 13.99 13.45 13.96 AACA TACTTT GCGCGCC acrA 16.37 14.53 12.94 14.15 ATCTTC AGTCG GTGTTCG CCGTTAA acrB 10.40 C GCGGC CAGGCAC acrF 9.70 AAAA GATGA TACCCCC TGCTGTG acrR 13.54 AGA CAGTTC GAGCGCC TATTTCT adeA G ATCAA CACGGAC CAGGACA ceoA 14.90 AG 11 CGTCG GCGCACT mdtE/ yhiU 9.89 CGTT AGGAC AACGCTA 13.5 TGCAACG mexA 0 15.70 AA GGTCA GCACCGA 13.1 CAAGGTC mexE 14.44 1 14.54 14.69 TAC CCGCG 10.1 AGAAGGC mexF 13.14 12.47 8.15 7 7.79 7.84 CAAGA GGTCG GCACGCT mtrD 17.84 15.47 CTTGTC ATGAA 15.6 GTGGAGC oprD 16.74 14.85 3 14.08 12.08 GCCATTG ACGAG 11.3 AGTGGCG oprJ 17.97 3 13.70 12.59 TCGACAA GCCAG GCAGAGA ACCTGAT tolC 17.00 G GGCCG AGAACCT tolC 10.45 GATGCA CAGGC AGAGAAC CTGATGC tolC 17.66 A ACGCC AATGCCA ttgA 12.11 AACGATT qacE∆1 TCGCA ACATCCG 12 CATTAAA A CCCCTT CCGCCGT qacE∆1 2.96 7.17 9.28 11.40 4.12 TGT CATCGT 16.3 GCTTGTG qacH 10.54 16.21 2 15.20 GCAGCTA GTGGC AGCTATC GCTTGGA qacH 8.24 14.12 15.55 7.92 15.28 13.43 T GCACTC GATGCCT catB3 7.20 13.20 15.60 8.55 14.77 10.48 TCCAAAA CACTCG 10.3 ACGCCTT catB8 9.52 14.83 15.51 0 14.38 11.56 CCAAAG GCAAA ATTCAGA GCAAGTT cfr 15.08 ACGAA AACCA CGCGTCT GTTGACT uidA 9.93 G GCTTTA TTTCAGG AGGCGGA ereB 16.38 15.74 AT TTCCAC GACACGA TTAAGTC bacA 9.91 ATTG GGGTG AGTTTCA CCAGTTT catA1 12.52 15.44 TGATT 13 GCAAT CGAGGCG pncA 17.89 14.45 14.56 13.95 GTGTTC AGGAT TTCTCAC GCCAGGA qnrA TT GAATG GGCAAAG CATAAAA sat4 ACTTG GGAAT GGCCCTG ATATTCC dfrA1 6.19 11.59 12.95 9.53 13.07 8.56 A CCTCTA CCGAACC 11.9 GTCACAC dfrA12 9.41 15.80 15.59 7 15.23 12.04 A CGAGC AGTTCCT folA 18.22 GCCAAAG CAGCG CTATGCG sul1 CTCAAG TCATCT GCCAAAC TCGTCGT sul2 2.64 8.23 7.70 4.27 6.88 4.05 TA ACCCC ATGACGT ACCTGTA tet(35) GAGA AAATTT GTTACCG 14.3 ACACGGA tetX 3.18 15.36 0 AGTT tet(32) 6.33 15.48 12.2 14.77 13.44 CCATTA 3 CTTCGGA 14 CAACGGT AGA AGAAT ACTCAGC AGAGGTC tet(36) 6.88 15.50 15.72 AGTTCCT TGCAG GAAAGAC 15.0 CTCCATT tet(36) 6.97 15.25 2 15.25 ACAG CATCAT AGACACG CCAGGAC tetM 3.80 14.29 ATAT TAATAT TGGAGTT TTAGCTC 10.1 ATGTTGA tetM 3.90 10.17 14.13 7 12.33 10.89 TG ATGTG GATACTA 10.0 CAACGCA tetO 6.20 14.19 8 13.78 14.16 TGAGATT ACACCT GGACACG CTGATTT tetPB T TGGGC GACAGTA GGCTTAG tetPB 14.43 AA CGCCTC AGAAGTA AGTTCAT 15.2 ACACTAA tetQ 3.29 7 15.48 G tetS TTAAG GACAAAC 15 TTTCTGA CGACATC CCATAT AGAGGTT CCACCAA tetT ATCC CAACA TTAACGG AAAGTTT 10.1 ATTGTAT tetW 5.99 14.95 4 10.93 12.16 ACCA ATGAA CATTCCC ACCGTTA tetW 4.55 11.96 14.32 9.60 12.53 10.95 TCTTT CTCACC AGCCTGA tetA 5.97 10.09 13.18 6.29 12.24 7.81 CCTCGAT GCCCA GTGCTGT TGTTGTC tetB 8.92 15.10 13.14 AT AGTGC GCTTTGG ATGCTGT tetB 9.23 15.39 14.81 A CATATC GCAATAC ATGCGAA tetC AAA ACTGGT AAGGTAA ACGCCAT tetC 10.08 15.48 13.92 TGTC TGTCAT CGCGCTG tetD 13.01 15.09 GTGATT tetD 13.20 14.90 TGCCGC GTTTGAT 16 TACACA TTGGCG CTGTATG tetE 15.33 CAATGAT CATCA GCGCCGG tetG 5.42 12.58 9.75 5.23 9.66 4.76 TCTTATG TCAACC ATTGCCG tetG 5.63 14.88 15.16 5.09 13.70 7.73 ATTCGA TTTGGG TCATCTT 15.4 ACCAGCA tetH 6.53 15.04 0 15.44 TTAA ATGGTT GTAGTTG CGCGCTA tetL 5.88 6.53 11.44 7.58 11.52 9.29 TAT CGCGA TGGAGCA AAAGTAC tetR 10.35 AT CGCGA TAGACGC tetR 6.96 12.19 15.42 7.93 10.36 10.25 CTTCGA GCGGG AACGACG ATGTATA tetV 15.60 14.86 TC GGAAA TCAACGG tp614, IS4 16.0 CATCCAG family 7.91 7 14.21 TT TGCAG ATGGTTT tnpA, IS6 10.7 AACCTTG group 3.17 11.80 13.66 0 13.13 10.18 GATATTT tnpA, IS21 10.70 15.97 14.21 14.9 14.77 10.98 CATCAT 17 CGGACGG ACAGAAT group 4 T GGGCG GGTCGAT tnpA, IS4 4.31 11.12 15.35 8.33 14.47 10.90 TGAAA GAAAC CGATGCT tnpA, 15.0 ACAATAT ISEcp1B 4.23 14.28 5 14.82 12.02 CCAATTT GCCGC ACTGTCG tnpA, IS6 ATTTTTA group 2.78 10.66 12.42 5.95 11.22 6.75 TC CCGATC tnpA, IS6 ACGGAAA group 2.11 3.86 8.05 1.73 7.49 5.11 GCTCAAG AATTG ATGCGGA tnpA, IS6 15.9 CGGCTTA group 6.07 15.63 6 15.21 14.59 A AGGTTC GGACTCA tnpA, IS613 11.6 ATGCAAC group 2.32 16.08 7 15.09 15.16 A CCCTTA CTCCCAC CGAGTTT vanRA 12.62 T CCACTC CGGCCTT vanRA 15.72 GTCATT CCGGTC GAGGAAC vanB GAAATC TTGTCG GCGAAGT vanB 17.84 GGATCA

18 GAGGT TTCCGAG vanHB 17.62 GCGACAA GCCCTG TCGGATG vanRB ACGAA GCGCG GCAAATG vanSB ACAAC CGGAC AAAGATA CCCCCTA vanWB TAAAG AGGCA CAAAATC GAAGATG vanXB CTT GGCTA AAGCGGA AGCAGAA vanYB A ACAGG GATTGGC TATGAAC vanC 17.91 15.00 CAT AAATC AATACTA TGCCGGG vanC 17.48 15.29 CTTT TTTGAC TGTCGGT vanC2/ GCTTGTG vanC3 17.73 14.82 A GCCATC AGCGAGT vanSC 17.88 15.02 CTGATGA vanTC 15.08 CACAC GCATTTT 19 TTCCCAT CTAG ACAGTT GCCGCTG vanTC 16.04 15.60 14.69 14.77 GTGAAG CAAAC GGAAGAG AGGTCAC vanYD TTACA AAGGC GATACCC TGACTGT vanYD 15.17 CA GTGGT GCCAAGG AAGTTGC vanTE 18.01 T CGTGTA GCCGTTC vanTG CGTTCTT ACATTT TCATTTT GGCAGCT vanWG TGTAC

1. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3(6):1101–1108.