Table S1. Primer Sets Used in This Study and Their Target Classification. Quantitative

Table S1. Primer sets used in this study and their target classification. Quantitative PCR primer sets, assay target, and gene classification by target drug and mechanism of resistance. Target gene designations were found by BLAST on the ARDB or National

Center for Biotechnology Information (NCBI) databases. FCA = fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol resistance genes. MLSB = Macrolide-Lincosamide-Streptogramin B resistance. IS = Insertion sequence.

Resistance Gene Name Forward Primer Reverse Primer Gene Classification Mechanism ATGGYTGTCGTC 16S rRNA GGGTTGCGCTCGTTGC AGCTCGTG 16S rRNA NA AGAGCCGATCCA catB3 GCACTCGATGCCTTCCAAAA AACGTCAT FCA deactivate AAAATGACTCCC cfr GCAAAATTCAGAGCAAGTTACGAA AACCTGCTTTAT FCA deactivate CCGCGATGTCGT floR ATTGTCTTCACGGTGTCCGTTA CGAACT FCA efflux CTTCCCGGCAAA yidY/mdtL GCAGTTGCATATCGCCTTCTC CAGCAT FCA efflux CAGGCGCGACG yidY/mdtL TGCTGATCGGGATTCTGATTG AACATAAT FCA efflux CAGACCGAGCA cmlA1 TAGGAAGCATCGGAACGTTGAT CGACTGTTG FCA efflux ACAGACCGAGC cmlA1 AGGAAGCATCGGAACGTTGA ACGACTGTTG FCA efflux TCGACACGGAGC cmx(A) GCGATCGCCATCCTCTGT CTTGGT FCA efflux CACCTTGTCGCC catA1 GGGTGAGTTTCACCAGTTTTGATT TTGCGTATA FCA deactivate AGCTCGACGTAC mexE GGTCAGCACCGACAAGGTCTAC TTGAGGAACAC FCA efflux TTGAGTTCGGCG mexF CCGCGAGAAGGCCAAGA GTGATGA FCA efflux emrB/qacA CTTTTCTCTAACCGTACATTATCTACGATAAA AGAACGTAGCG FCA efflux 1 ACTGATAAAATG CT GCAGAGCCTGAT pmrA TTTGCAGGTTTTGTTCCTAATGC TTCTCCTTTG FCA efflux CCGCTTTCAATG qnrA AGGATTTCTCACGCCAGGATT AAACTGCAA FCA unknown CAAGGAAACGA acrB AGTCGGTGTTCGCCGTTAAC ACGCAATACC FCA efflux GGCAACGTAATC acrB TGGTAGTGGGCGTCATTAACAC CGAAATATCC FCA efflux TACGCTCTTCCC acrF GCGGCCAGGCACAAAA ACGGTTTC FCA efflux CGCCCTGACCGA adeA CAGTTCGAGCGCCTATTTCTG CCAAT FCA efflux AGCAGGGTAAG TAAAACTAAGTG cmeA GCAGCAAAGAAGAAGCACCAA GTAAATCT FCA efflux TGGCGATGCCAC acrA CAACGATCGGACGGGTTTC CGTACT FCA efflux GCGCGCACGAA acrA GGTCTATCACCCTACGCGCTATC CATACC FCA efflux CCGGAAAGGGC mexA AGGACAACGCTATGCAACGAA CGAAAT FCA efflux CACTGCGGAGA mexD TTGCCACTGGCTTTCATGAG ACTGTCTGTAGA FCA efflux AAGGCGATCTCG oprJ ACGAGAGTGGCGTCGACAA TTGAGGAA FCA efflux CGACAATTTCGC acrA CAGACCCGCATCGCATATT GCTCATG FCA efflux CGTGCGCGAACG acrA TACTTTGCGCGCCATCTTC AACAT FCA efflux ACTTTGCGCGCC acrA CGTGCGCGAACGAACA ATCTTC FCA efflux TTGGCCACGCCA aac CCCTGCGTTGTGGCTATGT ATCC Aminoglycoside deactivate GCAAGTTCCCGA aacC1 GGTCGTGAGTTCGGAGACGTA GGTAATCG Aminoglycoside deactivate CCGAGCTTCACG aacC2 ACGGCATTCTCGATTGCTTT TAAGCATTT Aminoglycoside deactivate AGGGAACCTTTG aacC4 CGGCGTGGGACACGAT CCATCAACT Aminoglycoside deactivate aac(6')I1 GACCGGATTAAGGCCGATG CTTGCCTTGATA Aminoglycoside deactivate TTCAGTTTTTAT

2 AACCA TTGATCCATACC ATAGACTATCTC aacA/aphD AGAGCCTTGGGAAGATGAAGTTT ATCA Aminoglycoside deactivate GGAGAACAAAA ATACCTTCAAGG aac(6')-Iy GCTTTGCGGATGCCTCAAT AAA Aminoglycoside deactivate GCACGAATCCTG aac(6')-II CGACCCGACTCCGAACAA CCTTCTCA Aminoglycoside deactivate GTCGGGCGCGGC aacC CGTCACTTATTCGATGCCCTTAC ATA Aminoglycoside deactivate GAATGCCTGGCG aac(6')-Ib GTTTGAGAGGCAAGGTACCGTAA TGTTTGA Aminoglycoside deactivate CGGTACCTTGCC aac(6')-Ib CGTCGCCGAGCAACTTG TCTCAAACC Aminoglycoside deactivate CTGCGGATGGGC aadA5 ATCACGATCTTGCGATTTTGCT CTAGAAG Aminoglycoside deactivate GATGCTCGGCAG aadA5 GTTCTTGCTCTTGCTCGCATT GCAAAC Aminoglycoside deactivate GCTCTCCATTCA aac(6')-Ib AGAAGCACGCCCGACACTT GCATTGCA Aminoglycoside deactivate TGGCTCGAAGAT aadA1 AGCTAAGCGCGAACTGCAAT ACCTGCAA Aminoglycoside deactivate GGCCACAGTAAC aadA2 ACGGCTCCGCAGTGGAT CAACAAATCA Aminoglycoside deactivate GGCTCGAAGATA aadA GTTGTGCACGACGACATCATT CCTGCAAGAA Aminoglycoside deactivate TCGAAGATACCC aadA2 CTTGTCGTGCATGACGACATC GCAAGAATG Aminoglycoside deactivate ACCGAAGCGCTC aadD CCGACAACATTTCTACCATCCTT GTCGTATA Aminoglycoside deactivate GACCTACCAAGG aadA2 CAATGACATTCTTGCGGGTATC CAACGCTATG Aminoglycoside deactivate CAAATCAGCGAC aadA9 CGCGGCAAGCCTATCTTG CGCAGACT Aminoglycoside deactivate GCTGCCATTCTC aadA CGAGATTCTCCGCGCTGTA CAAATTGC Aminoglycoside deactivate CCTCTAGCGGCC aadA9 GGATGCACGCTTGGATGAA GGAGTATT Aminoglycoside deactivate GGAACTATGTCC CTTTTAATTCTA aadE TACCTTATTGCCCTTGGAAGAGTTA CAATCT Aminoglycoside deactivate 3 TCCAGTGGTAGT spcN AAAAGTTCGATGAAACACGCCTAT CCCCGAATC Aminoglycoside deactivate CGCAGACACGCC spcN CAGAATCTTCCTGAAAAGTTTGATGAA GAATC Aminoglycoside deactivate CATCTTTCACAA AGATGTTGCTGT aphA3 AAAAGCCCGAAGAGGAACTTG CT Aminoglycoside deactivate GCCACCGCTTCT aph6ia CCCATCCCATGTGTAAGGAAA GCTGTAC Aminoglycoside deactivate GACAGAACAAT CAATCTCTATGG aph(2')-Id TGAGCAGTATCATAAGTTGAGTGAAAAG AATG Aminoglycoside deactivate TTTAATCCCTCT TCATACCAATCC aph(2')-Id TAAGGATATACCGACAGTTTTGGAAA ATA Aminoglycoside deactivate CCAAGCTGTTTC aph TTTCAGCAAGTGGATCATGTTAAAAT CACTGTTTTTC Aminoglycoside deactivate CCTATTAATTTC CCCTCGTCAAAA aphA1 TGAACAAGTCTGGAAAGAAATGCA A Aminoglycoside deactivate ATACCGGCTGTC aphA3 CGGAATTGAAAAAACTGATCGAA CGTCATTT Aminoglycoside deactivate AATCAAAACCCC TATTAAAGCCAA str AATGAGTTTTGGAGTGTCTCAACGTA T Aminoglycoside deactivate GTGGCTCAACCT strA CCGGTGGCATTTGAGAAAAA GCGAAAAG Aminoglycoside deactivate CAATTTCGGTCG strB GCTCGGTCGTGAGAACAATCT CCTGGTAGT Aminoglycoside deactivate TTCGTCACCGGC blaSHV TCCCATGATGAGCACCTTTAAA ATCCA Beta Lactamase deactivate GAAAGATTCCCT TTATCTATCTCA blaVEB CCCGATGCAAAGCGTTATG GACAA Beta Lactamase deactivate TACCAGTATCAA TCGCATATACAC bla1 GCAAGTTGAAGCGAAAGAAAAGA CTAA Beta Lactamase deactivate GGTGACGTTGTC blaOKP GCCGCCATCACCATGAG ACCGATCTG Beta Lactamase deactivate CGCGCTGTTGTC blaROB GCAAAGGCATGACGATTGC GCTAAA Beta Lactamase deactivate GCCGCGATATAA blaOXY CGTTCAGGCGGCAGGTT GATTTGAGAATT Beta Lactamase deactivate

4 TGCGAAGCACGC blaPSE TTGTGACCTATTCCCCTGTAATAGAA ATCATC Beta Lactamase deactivate TGCAGCACCAAG cfxA TCATTCCTCGTTCAAGTTTTCAGA AGGAGATGT Beta Lactamase deactivate TCGTATCTTGCC cepA AGTTGCGCAGAACAGTCCTCTT CGTCGATAAT Beta Lactamase deactivate TTCAGTGCGATC blaCTX-M GGAGGCGTGACGGCTTTT CAGACGAA Beta Lactamase deactivate ATCGGATTATAG TTAACCAGGTCA blaCTX-M GCCGCGGTGCTGAAGA GATTT Beta Lactamase deactivate GCATTGCCCAAC blaCTX-M CGATACCACCACGCCGTTA GTCAGATT Beta Lactamase deactivate CGTTCATCGGCA blaCTX-M CTTGGCGTTGCGCTGAT CGGTAGA Beta Lactamase deactivate GTGCCTGAGTCA blaGES GCAATGTGCTCAACGTTCAAG ATTCTTTCAAAG Beta Lactamase deactivate GGGCCGCCAAG blaSFO CCGCCGCCATCCAGTA ATGCT Beta Lactamase deactivate TGCAAATTTCGG blaTLA ACACTTTGCCATTGCTGTTTATGT CAATAATCTTT Beta Lactamase deactivate TGCTTAATTTTC CATTTGCGATAA blaZ GGAGATAAAGTAACAAATCCAGTTAGATATGA G Beta Lactamase deactivate CGCCGATGACAT Pbp5 GGCGAACTTCTAATTAATCCTATCCA TCTTCTTATCTT Beta Lactamase protection AAAATAGCCGCC pbp CCGGTGCCATTGGTTTAGA CCAAGATT Beta Lactamase protection GTCGAGACGGA blaCTX-M GCGATAACGTGGCGATGAAT ACGTTTCGT Beta Lactamase deactivate TCCTGCTGGCGA blaSHV CTTTCCCATGATGAGCACCTTT TAGTGGAT Beta Lactamase deactivate TCCTCCGATCGT blaTEM AGCATCTTACGGATGGCATGA TGTCAGAAGT Beta Lactamase deactivate CTCCGCTGCCGG blaCTX-M CACAGTTGGTGACGTGGCTTAA TTTTATC Beta Lactamase deactivate GCGTGTAGCCGG penA AGACGGTAACGTATAACTTTTTGAAAGA CAATG Beta Lactamase protection CCAAAGGAAAC TTGCTTGAGATT pbp2x TTTCATAAGTATCTGGACATGGAAGAA AG Beta Lactamase protection CCTGCGCAATGA blaPER TGCTGGTTGCTGTTTTTGTGA TAGCTTCAT Beta Lactamase deactivate 5 GTTCGGGATAAA cfiA GCAGCGTTGCTGGACACA CGTGGTGACT Beta Lactamase deactivate CGGCCCAGTCGC cphA GCGAGCTGCACAAGCTGAT TCTTC Beta Lactamase deactivate GGTGTGGTAGTT cphA GTGCTGATGGCGAGTTTCTG GGTGTTGATCAC Beta Lactamase deactivate GCGAAGCTGCGC bla-L1 CACCGGGTTACCAGCTGAAG TTGTAGTC Beta Lactamase deactivate CGACGGTGATGC blaVIM GCACTTCTCGCGGAGATTG GTACGTT Beta Lactamase deactivate GCGCTCCACAAA blaIMP AACACGGTTTGGTGGTTCTTGTA CCAATTG Beta Lactamase deactivate GGATAGATCGA GAATTAAGCCAC blaIMP AAGGCAGCATTTCCTCTCATTTT TCT Beta Lactamase deactivate AATAAACGCGAT bla-ACC-1 CACACAGCTGATGGCTTATCTAAAA GGGTTCCA Beta Lactamase deactivate CTCCACGGGCCA ampC TGGCGTATCGGGTCAATGT GTTGAG Beta Lactamase deactivate TGTACCCATGAT ampC GCAGCACGCCCCGTAA GCGCGTACT Beta Lactamase deactivate ACGCCCGTAAAT ampC AACAAAAGATCCCCGGTATGG GTTTTGCT Beta Lactamase deactivate GCCACTGTTTGC blaCMY CCGCGGCGAAATTAAGC CTGTCAGTT Beta Lactamase deactivate CAGCACGCCGGT ampC TCCGGTGACGCGACAGA GAAAGT Beta Lactamase deactivate GGCTTGTCCTCT blaMOX/blaCMY CTATGTCAATGTGCCGAAGCA TTCGAATAGC Beta Lactamase deactivate TTTTCTGCTCGG blaOCH GGCGACTTGCGCCGTAT CCATGAG Beta Lactamase deactivate GAAGTAATGCG blaPAO CGCCGTACAACCGGTGAT GTTCTCCTTTCA Beta Lactamase deactivate ATAGCTTTTGTT blaCMY2 AAAGCCTCAT GGGTGCATAAA TGCCAGCATCA Beta Lactamase deactivate CAGTATCTGGTC ampC CTGTTCGAGCTGGGTTCTATAAGTAAA ACCGGATCGT Beta Lactamase deactivate CCATATCCTGCA ampC CCGCTCAAGCTGGACCATAC CGTTGGTTT Beta Lactamase deactivate CGGATGGGCTTG blaCMY2 GCGAGCAGCCTGAAGCA TCCTCTT Beta Lactamase deactivate CCGTTTTATGCA ampC/blaDHA TGGCCGCAGCAGAAAGA CCCAGGAA Beta Lactamase deactivate

6 GCGGCCAGGTG fox5 GGTTTGCCGCTGCAGTTC ACCAA Beta Lactamase deactivate GCTCGACTTCAC ampC CCGCCCAGAGCAAGGACTA GCCGTAAG Beta Lactamase deactivate AGATCCGTGGCC ampC GCAGCGAAGCGTCAGTCA GCATAA Beta Lactamase deactivate CAGCGAGCCCAC ampC CAGCCGCTGATGAAAAAATATG TTCGA Beta Lactamase deactivate TTGGCTTTCCGT blaOXA10 CGCAATTATCGGCCTAGAAACT CCCATTT Beta Lactamase deactivate TTGGCTTTCCGT blaOXA10 CGCAATTATCGGCCTAGAAACT CCCATTT Beta Lactamase deactivate TCTTGGCTTTTA TGCTTGATGTTA blaOXA1/blaOXA30 CGGATGGTTTGAAGGGTTTATTAT A Beta Lactamase deactivate TGTCTTTTAATA AGTGAGGTGCGT mecA GGTTACGGACAAGGTGAAATACTGAT TAATA Beta Lactamase protection CCTATTTTTTGG AGTCTTCTCTCT msrC TCAGACCGGATCGGTTGTC AATGTT MLSB efflux CCTGTGCTATTT TAAGCCTTGTTT matA/mel TAGTAGGCAAGCTCGGTGTTGA CT MLSB efflux TCAAGTAAAGTT GTCTTACCTACA msrA CTGCTAACACAAGTACGATTCCAAAT CCATT MLSB efflux CGTACACAACGG msrC GAATCACTTGTCCGCAGTTTGTT TTTCGTCAGA MLSB efflux CCCGTACCGTTA vgaA CGAGTATTGTGGAAAGCAGCTAGTT GAGCCGATA MLSB efflux TGTTTAGTAGCA TGTTGCATTTTC vgaB TAAAAGAGAATAAGGCGCAAGGA C MLSB efflux CGTGACTACCCA lmrA TCGACGTGACCGTAGTGAACA GGTGAGTTGA MLSB efflux ATTCGTGTTTCC vgaB GAATGATTAAGCCCCCTTCAAAA AACGATTTCG MLSB efflux TTTCCTGTACCA TTAGATCCGATA vgaA GACGGGTATTGTGGAAAGCAA ATT MLSB efflux vgbB CAGCCGGATTCTGGTCCTT TACGATCTCCAT MLSB efflux

7 TCAATTGGGTAA A CAACCGTGCCTT msrA AACGAAATCAAGCGCAACAA TTTCTTTTG MLSB efflux GCCGAAGACGT oleC CCCGGAGTCGATGTTCGA ACACGAACAG MLSB efflux ATCGGCGAAAC carB GGAGTGAGGCTGACCGTAGAAG GCACAAA MLSB efflux ACCATTGCCGAG ermK GTTTGATATTGGCATTGTCAGAGAAA TCCACTTT MLSB protection CCCCGAAACGCA ermJ/ermD GGACTCGGCAATGGTCAGAA ATATAATGTT MLSB protection GTGTTTCATTTG ermK GAGCCGCAAGCCCCTTT ACGCGGAGTAA MLSB protection TCTATAATCACA ACTAACCACTTG erm(35) TTGAAAACGATGTTGCATTAAGTCA AACGT MLSB protection AAATTCCTAAAA TCACAACCGACA ermF CAGCTTTGGTTGAACATTTACGAA A MLSB protection TCTGCGTTGACG erm(36) GGCGGACCGACTTGCAT ACGGTTAC MLSB protection TTTATACCTCTG TTTGTTAGGGAA ermB TAAAGGGCATTTAACGACGAAACT TTGAA MLSB protection GAAGGGTGTCTT TTTAATACAATT ermT GTTCACTAGCACTATTTTTAATGACAGAAGT AACGA MLSB protection ATCCCCCCGTCA ermX GCTCAGTGGTCCCCATGGT ACGTTT MLSB protection TGAGTGATATTT TTGAAGGGTGTC ermT GTAAAATCCCTAGAGAATACTTTCATCCA TT MLSB protection TAACGCTAGAGA ACGATTTGTATT ermY TTGTCTTTGAAAGTGAAGCAACAGT GAG MLSB protection ATATCCATCTCC ACCATTAATAGT ermA TTGAGAAGGGATTTGCGAAAAG AAACC MLSB protection ATGGTCTATTTC AATGGCAGTTAC ermC TTTGAAATCGGCTCAGGAAAA G MLSB protection ermA/ermTR ACATTTTACCAAGGAACTTGTGGAA GTGGCATGACATMLSB protection

8 AAACCTTCATCA CCGCGAATTAGG pikR1 TCGACATGCGTGACGAGATT CCAGAA MLSB protection TTCCCCTTGCCG pikR2 TCGTGGGCCAGGTGAAGA GTGAA MLSB protection ACCGCATTCGCT ereA CCTGTGGTACGGAGAATTCATGT TTGCTT MLSB deactivate ACCAAATGCGCC vgb AGGGAGGGTATCCATGCAGAT CGTTT MLSB deactivate GGCCATGCAGG vgb CCACGATGGCTGCCTTTG ACGGATAT MLSB deactivate TGTGAACCACAG vgbB ATACGAGCTGCCTAATAAAGGATCTT GGCATTATCA MLSB deactivate TTCACCTGTTTC mdtA CCTAACGGGCGTGACTTCA AAGGGTCAAA MLSB efflux TGGTCATACTCG erm(34) GCGCGTTGACGACGATTT ACGGCTAGAAC MLSB protection ATAATCGGGAAC ATAATGAGCATA lmrA TTCAGATGCAATGGCGTTTG ACTAC MLSB efflux AAACGGAGTAT AAGAGTGCTGCA mefA CCGTAGCATTGGAACAGCTTTT A MLSB efflux GGTGGTGCATGG mphA CTGACGCGCTCCGTGTT CGATCT MLSB deactivate TTACTGCATCCA mphB CGCAGCGCTTGATCTTGTAG TACGCTGCTT MLSB deactivate TTCGCGAGCCCC mphA TGATGACCCTGCCATCGA TCTTC MLSB deactivate GCTGCGGGTTTG mphC CGTTTGAAGTACCGAATTGGAAA CCTGTA MLSB deactivate TAATTGCCCTGT TTCATCGTAAAT lnuB TGAACATAATCCCCTCGTTTAAAGAT AA MLSB deactivate GGAGCTACGTCA lnuB AAAGGAGAAGGTGACCAATACTCTGA AACAACCAGTT MLSB deactivate TGTTTTATTTCGT TAGCAGGATTTC vatD TGCAATAGTAGCTGCTAATTCTGTTGTT C MLSB deactivate TTGGATTGCCAC vatE GGTGCCATTATCGGAGCAAAT CGACAAT MLSB deactivate vatB GGAAAAAGCAACTCCATCTCTTGA TCCTGGCATAAC MLSB deactivate 9 AGTAACATTCTG A GCAATAATAGCC vatC CGGAAATTGGGAACGATGTT CCGTTTCCTA MLSB deactivate TTCATGCTTAAG TTCCATACGTGA lnuA TGACGCTCAACACACTCAAAAA A MLSB deactivate TTGGATTGCCAC vatE GACCGTCCTACCAGGCGTAA CGACAATT MLSB deactivate CAATCCACACAT vatB TTGGGAAAAAGCAACTCCATCT CATTTCCAACA MLSB deactivate GCTGCAATAATA vatC CGATGTTTGGATTGGACGAGAT GCCCCGTTT MLSB deactivate AAGGTGGCAATT lnuA AGAATGAAAAAGAAGCTGAGCTTCTT ACGTTTTTCAAA MLSB deactivate CACCCCAGCCAC lnuC TGGTCAATATAACAGATGTAAACCAGATTT CATCAA MLSB deactivate TCACCAAACTGT TTATGGAGTCGT tnpA AATTGATGCGGACGGCTTAA T IS6 Group transposase TTCAGCACATAC IS613 AGGTTCGGACTCAATGCAACA CGCCTTGAT IS613 transposase GTCGGAGATGTG tnpA CATCATCGGACGGACAGAATT GGTGTAGAAAGTIS21 Group transposase GGCTCGCATGAC tnpA CCGATCACGGAAAGCTCAAG TTCGAATC IS6 Group transposase CAGCACCGTTTG tnpA GAAACCGATGCTACAATATCCAATTT CAGTGTAAG ISEcp1B transposase GCGGGATCTGCC tnpA GCCGCACTGTCGATTTTTATC ACTTCTT IS6 Group transposase CATCCATGCGCT Tp614 GGAAATCAACGGCATCCAGTT TTTGTCTCT Tp614 transposase GTGGGCGGGATC tnpA GGGCGGGTCGATTGAAA TGCTT IS4 Group transposase TCGGTTCATCAA tnpA TGCAGATGGTTTAACCTTGGATATTT ACTGCTTCAC IS6 Group transposase TGCCCTGGTCGT marR GCGGCGTACTGGTGAAGCTA TGATGA other/efflux efflux GTGCAAAGGCTG marR TCTGGCGTTAGCTTCACCAGTAC GATCGAA other/efflux efflux CCGAGCCTATCC catB8 CACTCGACGCCTTCCAAAG AGACATCATT other/efflux deactivate dfrA1 GGAATGGCCCTGATATTCCA AGTCTTGCGTCC other/efflux deactivate

10 AACCAACAG GCGACAGCGTTG dfrA12 CCTCTACCGAACCGTCACACA AAACAACTAC other/efflux deactivate CCCAGTCATCCG folA CGAGCAGTTCCTGCCAAAG GTTCATAATC other/efflux deactivate TGATTGATGGTT bexA GCGGATCTCTGGTCAGCAA CCCCGTACA other/efflux efflux CGGTTCCGAAAA cmr CGGCATCGTCAGTGGAATT AGATGGAA other/efflux efflux TGAAAAAACGG sdeB CACTACCGCTTCCGCACTTAA GAAAAGTCCAT other/efflux efflux TTTTAAATGCCA ereB GCTTTATTTCAGGAGGCGGAAT CAGCACAGAATCother/efflux deactivate TCTCCTTCCATA fosX GATTAAGCCATATCACTTTAATTGTGAAAG ATGCAAATCCA other/efflux deactivate ATAAATAGGATC mepA ATCGGTCGCTCTTCGTTCAC GAGCTGCTGGATother/efflux efflux ACCAGGCGCCG emrD CTCAGCAGTATGGTGGTAAGCATT AAGAAC other/efflux efflux TGCATAAGGTGA mdetl1 ATACAGCAGTGGATATTGGTTTAATTGT ATGTTCCATGA other/efflux efflux TTGTGTGGCGAT yceE/mdtG TGGCACAAAATATCTGGCAGTT AAGAGCATTAG other/efflux efflux GCGTGGTGACAA yceE/mdtG TTATCTGTTTTCTGCTCACCTTCTTTT ACAGGCTTA other/efflux efflux CGATAACCGAGC yceL/mdtH TCGGGATGGTGGGCAAT CGATGTAGA other/efflux efflux AGACGGCTAAA yceL/mdtH CGCGTGAAACCTTAAGTGCTT CCCCATATAGCT other/efflux efflux ACTCCAGCGGGC yceL/mdtH CTGCCGTTAAATGGATGTATGC GATAGG other/efflux efflux AGCGTTGGGCCG rarD GCGGGTGTGGTCACTACGAT ATATACTG other/efflux efflux AAATTTTCTGTG rarD TGACGCATCGCGTGATCT GCGTCTGAATC other/efflux efflux CCGAATCCAAAT AAAACCCAATA qacA/qacB TTTAGGCAGCCTCGCTTCA A other/efflux efflux CAAGCATAAGA CCGCATAAATGA yyaR CCGTTGCAAGAAGATTATAGAAAAAA T other/efflux deactivate fosB TCACTGTAACTAATGAAGCATTAGACCAT CCATCTGGATCT other/efflux deactivate 11 GTAAAGTAAAG AGATC ACAATGCGATAC bacA CGGCTTCGTGACCTCGTT CAGGCAAAT other/efflux deactivate CGGCTCTTTCGG bacA TTCCACGACACGATTAAGTCATTG CTTCAG other/efflux deactivate GTCGTGAATTCG nimE TGCGCCAAGATAGGGCATA GCAGGTTTA other/efflux unknown CCCACGCGGTAC imiR CCGGACTAGAGCTTCATGTAAGC TCTTGTAAA other/efflux unknown AGCCACTCGTTA nisB GGGAGAGTTGCCGATGTTGTA AAGGGCAAT other/efflux unknown ACCATTGCCGAC ttgB TCGCCCTGGATGTACACCTT ATCAACAAC other/efflux efflux GATTGTCATCAT TCGTTTATCACC putative multidrug AATTTTGCCGATTATTGCTGAAA AA other/efflux efflux TTGCCGCAGCCA pica GCAATCGAGGCGGTGTTC ATTCA other/efflux unknown AAGGCATCTTTT fabK TTTCAGCTCAGCACTTTGGTCAT TCAGCCAGTTC other/efflux deactivate GGAAAGTCCGCT ceoA ATCAACACGGACCAGGACAAG CACGATGA other/efflux efflux TCCAGACGTTGT mdtE/yhiU CGTCGGCGCACTCGTT ACGGTAACCA other/efflux efflux GCCTTGCTGCGA acrR GCGCTGGAGACACGACAAC GAACAAA other/efflux efflux ACCAAACAAGA acrR GATGATACCCCCTGCTGTGAGA AGCGCAAGAA other/efflux efflux CGTTCCAATTTC mtrD TGCGCGTAGTCGTTCATCTC CTGATGATTG other/efflux efflux CCTGCACCATGA mtrE CGATGTGTCGTTTTGGAAGGT TTCCTCAATA other/efflux efflux TGAAGAATTTGC mtrD GGTCGGCACGCTCTTGTC GCACCACTAC other/efflux efflux GGCCGGGTTGCC mtrD CCGCCAAGCCGATATAGACA AAA other/efflux efflux GGCCACGGCGA oprD ATGAAGTGGAGCGCCATTG ACTGA other/efflux efflux GTCACGGCGCAG ttgA ACGCCAATGCCAAACGATT CTTGA other/efflux efflux CGTAGCGTTCCG mtrC GGACGGGAAGATGGTCCAA GTTCGAT other/efflux efflux

12 ATCGTCGGCAAG mtrC CGGAGTCCATCGACCATTTG GAGAATCA other/efflux efflux AGACTTACGCAA tolC GGCCGAGAACCTGATGCA TTCCGGGTTA other/efflux efflux CGCAATTCCGGG tolC CAGGCAGAGAACCTGATGCA TTGCT other/efflux efflux CGCAATTCCGGG tolC GCCAGGCAGAGAACCTGATG TTGCT other/efflux efflux CCAACGAACGCC qacH GTGGCAGCTATCGCTTGGAT CACAA other/efflux efflux TGAACGCCCAGA qacH CATCGTGCTTGTGGCAGCTA AGTCTAGTTTT other/efflux efflux ATGGATTTCAGA ACCAGAGAAAG qacE∆1 TCGCAACATCCGCATTAAAA AAA other/efflux efflux CGACCAGACTGC qacE∆1 CCCCTTCCGCCGTTGT ATAAGCAACA other/efflux efflux AATAAGTGTTCC TAGTGTTGGCCA qac CAATAATAACCGAAATAATAGGGACAAGTT TAG other/efflux efflux AAGGTAACACTA TTTTCGGTCCAA qacA TGGCAATAGGAGCTATGGTGTTT ATC other/efflux efflux CCGATTTTGAAA CCACAATTATGA sat4 GAATGGGCAAAGCATAAAAACTTG TA other/efflux deactivate CAGGGTCACCCT speA GCAAGAGGTATTTGCTCAACAAGA CATAAAGAAAA other/efflux unknown GTCAAAGAACG sul2 TCATCTGCCAAACTCGTCGTTA CCGCAATGT Sulfonamide protection ATCCCGCTGCGC sul1 CAGCGCTATGCGCTCAAG TGAGT Sulfonamide protection CTTTCCTTGCGA sulA/folP CAGGCTCGTAAATTGATAGCAGAAG ATCGCTTT Sulfonamide protection CACATGGGCCAT sulA/folP GCGATTCGCAAGGAAAGTGA TTTTTCATC Sulfonamide protection TGCCATCCTGTG sulA/folP CACGGCTTCGGCTCATGT ACTAGCTACGT Sulfonamide protection TGCGGGCTTGCA tetU GTGGCAAAGCAACGGATTG AAACTATC Tetracycline unknown ATGGTATCATTC AGTTTTCCGACA tetU AACAGCGGGTTAAGTGTGCAA AT Tetracycline unknown 13 CATAGCTGAAAA AATCCAGGACA tetX AAATTTGTTACCGACACGGAAGTT GTT Tetracycline unknown AACCAAGCCTGG tet(37) GAGAACGTTGAAAAGGTGGTGAA ATCAGTCTCA Tetracycline unknown CAACCCACACTG tet(35) ACCCCATGACGTACCTGTAGAGA GCTACCAGTT Tetracycline unknown CGGTGATACAGC tet(34) CTTAGCGCAAACAGCAATCAGT GCGTAAACT Tetracycline unknown TGGTAGGTCGAT tet(36) AGAATACTCAGCAGAGGTCAGTTCCT AACCCGAAAAT Tetracycline protection CAATCTCTGTGA tet(32) CCATTACTTCGGACAACGGTAGA GGGCATTTAACATetracycline protection TGCCTCCACATG tetO ATGTGGATACTACAACGCATGAGATT ATATTTTTCCT Tetracycline protection TCGTTCATGCGG ATATTATCAGAA tetQ CGCCTCAGAAGTAAGTTCATACACTAAG T Tetracycline protection CGCCATCTTTTG tetM CATCATAGACACGCCAGGACATAT CAGAAATCA Tetracycline protection ATATCGGCGGAG tetW ATGAACATTCCCACCGTTATCTTT AGCTTATCC Tetracycline protection TTGACGCTCCAA tetO CAACATTAACGGAAAGTTTATTGTATACCA ATTCATTGTATC Tetracycline protection CCTCTCTGACGT TCTAAAAGCGTA tetM TAATATTGGAGTTTTAGCTCATGTTGATG TTAT Tetracycline protection TGTCTCCCATTG tetS TTAAGGACAAACTTTCTGACGACATC TTCTGGTTCA Tetracycline protection ACCGTCTAGAAC tetPB ACACCTGGACACGCTGATTTT GCGGAATG Tetracycline protection CGTCCAAAACGC tetPB TGATACACCTGGACACGCTGAT GGAATG Tetracycline protection TGACCCTACTGA AACATTAGAAAT tetPB TGGGCGACAGTAGGCTTAGAA ATACCT Tetracycline protection TTTGTTCCTTCGT tetPB AGTGGTGCAAATACTGAAAAAGTTGT TTTGGACAGA Tetracycline protection CCCTCAACGGCA tetPB CTGAAGTGGAGCGATCATTCC GAAATAACTAA Tetracycline protection TGACCCTATTGG TAGTGGTTCTAT tetT CCATATAGAGGTTCCACCAAATCC TG Tetracycline protection

14 CTTTGTCCACAC TTCCACGTACTA tet(36) TGCAGGAAAGACCTCCATTACAG TG Tetracycline protection GGTTAAGTTCCT tetA GCTGTTTGTTCTGCCGGAAA TGAACGCAAACTTetracycline efflux TGCTACAAGTAC GAAAACAAAAC tetPA AGTTGCAGATGTGTATAGTCGTAAACTATCTATT TAGAA Tetracycline efflux CACCAGTGATCC tetD TGCCGCGTTTGATTACACA CGGAGATAA Tetracycline efflux GGTTGTGCGCGA tetR ATGAGTTCGGCCAGAATTTCC AATGATT Tetracycline efflux CACGTTGTTATA GAAGCCGCATA tetA CTCACCAGCCTGACCTCGAT G Tetracycline efflux AGCCCCAGTAGC tetB AGTGCGCTTTGGATGCTGTA TCCTGTGA Tetracycline efflux AAAGCCGCGGT tetC CATATCGCAATACATGCGAAAAA AAATAGCAA Tetracycline efflux TGGCCCGGCAAT tetG TCAACCATTGCCGATTCGA CATG Tetracycline efflux CCTTGTACTAAC CTACCAAAAATC tetK CAGCAGTCATTGGAAAATTATCTGATTATA AAAATA Tetracycline efflux TTGCGCATTATC tetH TTTGGGTCATCTTACCAGCATTAA ATCGACAGA Tetracycline efflux CATCCGCTTCCG tetD TGTCATCGCGCTGGTGATT GGAGAT Tetracycline efflux CCCCATGTAGCC tetG CATCAGCGCCGGTCTTATG GAACCA Tetracycline efflux TGAAAGCAAAC tetB GCCCAGTGCTGTTGTTGTCAT GGCCTAAATACATetracycline efflux CAAATGCTTTCC tetL AGCCCGATTTATTCAAGGAATTG CCCTGTTCT Tetracycline efflux ATCGCTGGACCG tetL ATGGTTGTAGTTGCGCGCTATAT ACTCCTT Tetracycline efflux TCCTGACAACGA tetR CGCGATAGACGCCTTCGA GCCTCCTT Tetracycline efflux AGTGAAAAACCT TGTTGGCATAAA tetR CGCGATGGAGCAAAAGTACAT A Tetracycline efflux tetC ACTGGTAAGGTAAACGCCATTGTC ATGCATAAACCATetracycline efflux

15 GCCATTGAGTAA G CCGCTATCTCAC tetV GCGGGAACGACGATGTATATC GACCATGAT Tetracycline efflux TCGTCCAATGTA tetJ GGGTGCCGCATTAGATTACCT GAGCATCCATA Tetracycline efflux TTGCCTGGGAAA tet(38) TTAATGTGGCGGTATCTGTAGGTATT TTTAATGCTTT Tetracycline efflux CGACGACCTATG tetE TTGGCGCTGTATGCAATGAT CGATCTGA Tetracycline efflux CGGCCGTTATCT vanA AAAAGGCTCTGAAAACGCAGTTAT TGTAAAAACAT Vancomycin protection TTCGTCGCCCCA vanRA CCCTTACTCCCACCGAGTTTT TATCTCAT Vancomycin protection GCTAACCACATT vanRA CCACTCCGGCCTTGTCATT CCCCTTGTTTT Vancomycin protection TCCGCAGAAAGC vanSA CGCGTCATGCTTTCAAAATTC TCAATTTGTT Vancomycin protection TCAAAAGCGATT vanXA CGCTAAATATGCCACTTGGGATA CAGCCAACT Vancomycin protection AGCCTTTTTCCG vanB TTGTCGGCGAAGTGGATCA GCTCGTT Vancomycin protection TCCTCCTGCAAA vanB CCGGTCGAGGAACGAAATC AAAAGATCAAC Vancomycin protection CTCTCGGCGGCA vanHB GAGGTTTCCGAGGCGACAA GTCGTAT Vancomycin protection AAATAGTAAATT GCTCATCTGGCA vanWB CGGACAAAGATACCCCCTATAAAG CAT Vancomycin protection GGGTATGGCTCA vanXB AGGCACAAAATCGAAGATGCTT TCAATCAACTT Vancomycin protection TTACATAGTCGT vanRB GCCCTGTCGGATGACGAA CTGCCTCTGCAT Vancomycin protection TTTGCCATTTTA vanSB GCGCGGCAAATGACAAC TTCGCACTGT Vancomycin protection GATATCCACAGC vanYB GGCTAAAGCGGAAGCAGAAA AAGACCAAGCT Vancomycin protection TGACTGGCGATG vanC ACAGGGATTGGCTATGAACCAT ATTTGACTATG Vancomycin protection CGGCTTCATTCG vanC CCTGCCACAATCGATCGTT GCTTGATA Vancomycin protection CCGACCGCTGCC vanC AAATCAATACTATGCCGGGCTTT ATCA Vancomycin protection

16 CAGCCAACAGAT vanTC CACACGCATTTTTTCCCATCTAG CATCAAAACAA Vancomycin protection CAATCGTCAATT vanC1 AGGCGATAGCGGGTATTGAA GCTCATTTCC Vancomycin protection TCAATCGTTTCA vanC2/vanC3 TTTGACTGTCGGTGCTTGTGA GGCAATGG Vancomycin protection CCCCCCATACGG vanRC TGCGGGAAAAACTGAACGA TTTTGATTA Vancomycin protection TCCGGCAGCATC vanRC4 AGTGCTTTGGCTTATCTCGAAAA ACATCTAA Vancomycin protection TCCGCTGTTCCG vanSC ATCAACTGCGGGAGAAAAGTCT CTTCTT Vancomycin protection CAGCTGGGATCG vanSC GCCATCAGCGAGTCTGATGA TTTTTCCTT Vancomycin protection CGTGGCTGGTCG vanTC ACAGTTGCCGCTGGTGAAG ATCAAAA Vancomycin protection GCCGGATTTTGT vanD CAGAGGAACATAATGTTTCGATAAAATCT GATTCCAA Vancomycin protection CGCAGGTCATTC vanHD GTGGCCGATTATACCGTCATG AGGCAAT Vancomycin protection GCGATAGCCGTC vanXD TAAACCGTGTTATGGGAACGAA CCATAAGA Vancomycin protection CGTCTACATCCG vanRD TTATAATGGCAAGGATGCACTAAAGT GAAGCATGA Vancomycin protection ATTGCCGGACGG vanYD AAGGCGATACCCTGACTGTCA AAGCA Vancomycin protection CGGACGGTAATA vanYD CAAACGGAAGAGAGGTCACTTACA GGGACTGTTC Vancomycin protection CAATAATACTCG TCAAAGGAGTTC vanSE TGGCCGAAGAAGCAGGAA TCA Vancomycin protection CGTAGCCACCGC vanTE GTGGTGCCAAGGAAGTTGCT AAAAAAAT Vancomycin protection CCGCCATAAGAG vanWG ACATTTTCATTTTGGCAGCTTGTAC CCTACAATCT Vancomycin protection TGATTTGTCTTT GTCCATACATAA vanG ATTTGAATTGGCAGGTATACAGGTTA TGC Vancomycin protection CGGCATTACAGG vanTG CGTGTAGCCGTTCCGTTCTT TATATCTGGAAA Vancomycin protection