Supplementary material 9.
Resistance testing as determined by NGS with the ResFinder Software.
| ID and species | Phenotypic resistance by Vitek II (acronyms of antibiotics that were not tested sensitive) | Genotypic detection of resistance genes by NGS with low coverage* | Phenotypic resistance without detected genotypic correlate | Genotypic resistance without detected phenotypic correlate |
|---|---|---|---|---|
| 1 Acinetobacter baumannii | PRL, TZP, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | execution failed | ||
| 2 Citrobacter freundii | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC | execution failed | ||
| 3 Enterobacter cloacae ssp. cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF, COT | strA, aadB, aph(3’)-Ic, blaOXA-23, blaOXA-64, blaADC-25, sul2 | fluoroquinolone, tetracycline, trimethoprim | none |
| 4 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, COT | execution failed | ||
| 5 Pseudomonas aeruginosa | PRL, TZP, CAZ, ATM, CIP, COT | execution failed | ||
| 6. Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, COT | aadA2, aadA1, blaSHV-12, blaTEM-135, sul3, sul2, dfrA12 | none | aminoglycoside |
| 7 Pseudomonas aeruginosa | PRL, TZP, CAZ, FEP, ATM, AK, GC, NN, CIP, COT | aph(3’)-XV, strA, aph(3’)-Ic, aacA4, strB, aadA6, aph(3’)-IIb, blaPAO, blaGES-1, blaOXA-50, aac(6’)lb-cr, fosA, catB7, sul1, tet(G) | none | fosfomycin (not tested phenotypically) |
| 8 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, NF | execution failed | ||
| 9 Acinetobacter baumannii | PRL, TZP, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | execution failed | ||
| 10 Enterobacter cloacae ssp. cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF, COT | execution failed | ||
| 11 Pseudomonas aeruginosa | PRL, TZP, CAZ, FEP, ATM, AK, GC, NN, CIP, COT | execution failed | ||
| 12 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, IPM, MEM, GC, CIP, LEV, NF, COT | execution failed | ||
| 13 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, IPM, MEM, GC, CIP, LEV, TGC, NF | execution failed | ||
| 14 Enterobacter cloacae ssp. cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD. CTX, CAZ, GC, CIP, LEV, TGC, NF, COT | execution failed | ||
| 15 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, TGC, NF, COT | execution failed | ||
| 16 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF | execution failed | ||
| 17 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, COT | execution failed | ||
| 18 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CN, CIP, LEV, TGC, NF, COT | execution failed | ||
| 19 Pseudomonas aeruginosa | ATM, COT | execution failed | ||
| 20 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, IMP, MEM, GC, CIP, LEV, TGC, NF, COT | execution failed | ||
| 21 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV | no sequence data | ||
| 26 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, IMP, MEM, GC, CIP, LEV, TGC, FOS, NF, COT | execution failed | ||
| 27 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF | no sequence data | ||
| 28 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF | execution failed | ||
| 29 Pseudomonas aeruginosa | ATM, COT | aadB, aac(6’)lb-cr, aac(3)-lla, strA, strB, aadA2, blaTEM-1B, blaCMY-4, blaCTX-M-15, blaSHV-33, blaOXA-1, oqxA, aac(6’)lb-cr, oqxB, QnrA1, fosA, mph(E), msr(E), catB3, floR, sul1, sul2, tet(A) | trimethoprim | aminoglycoside, beta-lactam, fluoroquinolone, fosfomycin (not tested phenotypically) |
| 30 Pseudomonas putida | PRL, MEM, CIP, LEV, | execution failed | ||
| 31 Acinetobacter baumannii | PRL, TZP, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | execution failed | ||
| 32 Enterobacter cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, FOS, NF, COT | execution failed | ||
| 33 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ | execution failed | ||
| 36 Morganella morganii ssp. morganii | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, TGC, FOS, NF, COT | aac(3)-lld, aadA5, blaDHA-1, mph(A), catA2, sul1, tet(B), dfrA17 | fosfomycin, fluoroquinolone, nitrofurantoin | none |
| 37 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV | execution failed | ||
| 38 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, COT | execution failed | ||
| 39 Proteus mirabilis | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, TGC, NF | execution failed | ||
| 40 Pseudomonas aeruginosa | PRL, PZP, ATM, COT | aph(3’)-llb, blaPAO, blaOXA-50, fosA, catB7 | sulfonamide, trimethoprim | aminoglycoside, fosfomycin |
| 41 Morganella morganii | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, TGC, FOS, NF, COT | strA, aac(6’)lb-cr, aph(3’)-la, aadA5, strB, aadA1, blaTEM-1B, blaDHA-1, blaCTX-M-15, blaOXA-1, aac(6’)lb-cr, catB3, catA2, catA1, sul1, sul2, tet(B), dfrA17, dfrA1 | fosfomycin | aminoglycoside |
| 42 Klebsiella pneumoniae ssp. pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, TGC, NF, COT | aac(6’)lb-cr, strB, strA, blaSHV-83, blaCTX-M-15, blaTEM-1B, blaOXA-1, aac(6’)lb-cr, oqxB, oqxA, QnrB66, fosA, catB3, sul2, dfrA14 | tetracycline | aminoglycoside, fosfomycin |
| 44 Acinetobacter radioresistens | no EUCAST breakpoints for VITEK available | blaOXA-133 | ||
| 45 Citrobacter freundii | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, COT | execution failed | ||
| 46 Stenotrophomonas maltophila | no EUCAST breakpoints for VITEK available | sph, blaL1 | ||
| 47 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | aacA4, strB, strA, aadA2, aadB, aph(3’)-Vla, blaADC-25, blaGES-11, blaOXA-89, aac(6’)lb-cr, cmlA1, dfrA7 | sulphonamide | none |
| 48 Enterobacter cloacae ssp. cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, FOS, COT | aac(6’)lb-cr, strA, aadA1, strB, blaTEM-1B, blaACT-16, blaCTX-M-15, blaOXA-1, aac(6’)lb-cr, QnrB1, fosA, catB3, catA1, sul2, tet(A), dfrA14 | none | tetracycline |
| 49 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | aph(3’)-Vla, aadB, blaADC-25, blaOXA-71, tet(A) | fluoroquinolone, sulphonamide, trimethoprim | tetracycline (not tested phenotypically) |
| 50 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | strB, aph(3’)-lc, strA, armA, blaADC-25, blaTEM-1D, blaOXA-23, blaOXA-66, msr(E), mph(E), tet(B) | sulphonamide, trimethoprim, fluoroquinolone | tetracycline (not tested phenotypically) |
| 51 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, COT | aac(3)-lld, strA, strB, blaTEM-1B, blaCTX-M-15, QnrS1, sul2, dfrA14 | ||
| 52 Raoultella planticola | AMP, SAM, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, FOS | aac(3)-lla, aac(6’)lb-cr, blaPLA1a, blaCTX-M-15, blaOXA-1, fosA, catB3, tet(B) | none | tetracycline |
| 54 Enterobacter cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, COT | execution failed | ||
| 55 Citrobacter freundii | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, COT | aac(6’)-lb-cr, aadA2, blaTEM, blaCTX-M-15, blaCMY-84, blaOXA-1, QnrS2, mph(A), catB3, ARR-3, sul1, dfrA12 | ||
| 56 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, CIP | aph(3’)-lc, strA, strB, blaOXA-23, blaOXA-66, blaADC-25, blaTEM-1D, tet(B) | fluoroquinolone | aminoglycoside, tetracycline (not tested phenotypically) |
| 57 Enterobacter cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, TGC, FOS, NF, COT | execution failed | ||
| 59 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF | no resistance genes found | ||
| 60 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, COT | no resistance genes found | ||
| 61 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, COT | aadA5, strB, strA, blaCTX-M-15, blaTEM-1B, mph(A), sul1, sul2, tet(A), dfrA17 | none | aminoglycoside, tetracycline |
| 62 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP, COT | aacA4, aadA2, aadB, strB, aph(3’)-Vla, strA, blaOXA-23, blaGES-11, blaOXA-66, blaOXA-117, blaTEM-1D, aac(6’)lb-cr, cmlA1, sul1, sul2, dfrA7 | ||
| 63 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP | no resistance genes found | ||
| 64 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP | execution failed | ||
| 65 Citrobacter freundii | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ | qnrS1 | beta-lactam | fluoroquinolone |
| 66 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC | aac(3’)-lla, aadA1, aadB, blaCTX-M-15, mph(A), cmlA1, tet(B), dfrA17 | none | tetracycline |
| 68 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV | strA, strB, blaTEM-1B | fluoroquinolone | aminoglycoside |
| 69 Proteus mirabilis | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF, COT | execution failed | ||
| 70 Enterobacter cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, IPM, MEM, CIP, LEV, TGC, FOS, COT | no resistance genes found | ||
| 71 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, CIP, LEV, NF | execution failed | ||
| 72 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, COT | execution failed | ||
| 73 Acinetobacter baumannii | PRL, CTX, CAZ, FEP, ATM, IPM, MEM, GC, NN, CIP | execution failed | ||
| 74 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ | execution failed | ||
| 75 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, COT | execution failed | ||
| 76 Escherichia coli | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV | execution failed | ||
| 77 Enterobacter cloacae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, NF, COT | execution failed | ||
| 78 Klebsiella pneumoniae | AMP, SAM, TZP, CXM, CXMAX, CPD, CTX, CAZ, GC, CIP, LEV, TGC, NF | execution failed |