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qnr Numbering and Sequence

In 2008 a group of investigators interested in qnr genes published a proposed numbering scheme to reduce the chaos that had developed from new sequences being given the same qnr number or having the number changed frequently in an attempt to avoid duplication (1). The following tables list those assignments. They can be downloaded as Excel files by clicking on the symbol next to the title. Application for new allele numbers should no longer be directed to gajacoby50@gmail.com but to https://www.ncbi.nlm.nih.gov/pathogens/submit-beta-lactamase. NCBI has taken over new qnr assignments.


  1. Jacoby, G., V. Cattoir, D. Hooper, L. Martínez-Martínez, P. Nordmann, A. Pascual, L. Poirel, and M. Wang. 2008. qnr gene nomenclature. Antimicrob. Agents Chemother. 52:2297-2299.

Qnr Allele Designations

Allele GenBank Accession No. - Nucleotide GenBank Accession No. - Protein Reference
QnrA1 AY070235 AAL60061 1
QnrA2 AY675584 AAT79355 2
QnrA3 DQ058661 AAZ04782 3
QnrA4 DQ058662 AAZ04783 3
QnrA5 DQ058663 AAZ04784 3
QnrA6 DQ151889 AAZ78355 4
QnrA7 GQ463707 ACV83303 26
QnrA8 KY554783 ATU31384 66
QnrB1 DQ351241 ABC86904 5
QnrB2 DQ351242 ABC86905 5
QnrB3 DQ303920 ABC17629 6
QnrB4 DQ303921 ABC17630 6
QnrB5 DQ303919 ABC17628 7
QnrB6 EF520349 ABP87778 8
QnrB7 EU043311 ABW03156 9
QnrB8 EU043312 ABW03157 9
QnrB9 EF526508 ABP88094 10
QnrB10 DQ631414 ABG56269 11
QnrB11 EF653270 ABS30107 12
QnrB12 AM774474 CAO82104 13
QnrB13 EU273755 ABX72042 14
QnrB14 EU273757 ABX72044 14
QnrB15 EU302865 ABX72227 14
QnrB16 EU136183 ABV66096 15
QnrB17 AM919398 CAP45902 16
QnrB18 AM919399 CAP45903 16
QnrB19 EU432277 ACA28712 17
QnrB20 AB379831 BAG55487 20
QnrB21 FJ611948 ACM50952 24
QnrB22 FJ981621 ACS71746 25
QnrB23 FJ981622 ACS71747 25
QnrB24 HM192542 ADI46626 27
QnrB25 HQ172108 ADN94685 28
QnrB26 HQ386846 AEH59666 29
QnrB27 HM439641 ADM52186 30
QnrB28 HM439643 ADM52188 30
QnrB29 HM439649 ADM52193 30
QnrB30 HM439650 ADM52194 30
QnrB31 HQ418999 ADQ43424 31
QnrB32 JN173054 AEL00450 32
QnrB33 JN173055 AEL00451 32
QnrB34 JN173056 AEL00452 32
QnrB35 JN173057 AEL00456 32
QnrB36 JN173058 AEL00458 32
QnrB37 JN173059 AEL00459 32
QnrB38 JN173060 AEL00461 32
QnrB39 NZ_ABWL02000005 ZP_06352683 32
QnrB40 JN166689 AEL31271 33
QnrB41 JN166690 AEL31272 33
QnrB42 JN680743 AEQ94272 28
QnrB43 JQ349151 AFA52643 36
QnrB44 JQ349153 AFA52645 37
QnrB45 JQ349152 AFA52644 38
QnrB46 JQ349154 AFA52646 39
QnrB47 JQ349155 AFA52647 40
QnrB48 JQ762640 AFH88686 41
QnrB49 JQ582718 AFD54601 42
QnrB50 JX440357 AFU25656 43
QnrB51 JX440358 AFU25658 43
QnrB52 EF488762 ABO93588 45
QnrB53 HQ704413 ADW54092 31
QnrB54 HE820727 CCI51002 46
QnrB55 KF730650 AHE41343 47
QnrB56 JX259317 AFR46587 48
QnrB57 JX259318 AFR46588 48
QnrB58 JX259319 AFR46589 48
QnrB59 JX259320 AFR46590 48
QnrB60 AB734055 BAN04743 49
QnrB61 AB734053 BAN04737 49
QnrB62 JX987101 AFY16910 50
QnrB63 51
QnrB64 KC580653 AGL43625 51
QnrB65 KC580654 AGL43626 51
QnrB66 KC580655 AGL43627 51
QnrB67 KC580656 AGL43628 51
QnrB68 KC580657 AGL43629 51
QnrB69 KC580658 AGL43630 51
QnrB70 KC580659 AGL43631 51
QnrB71 KC580660 AGL43632 51
QnrB72 KC741443 AGN92479 52
QnrB73 KF443075 AGT59159 58
QnrB74 KJ415247 AHX97725 60
QnrB75 KP207591 AKI82195 63
QnrB76 KM985469 AKO62868 63
QnrB77 KM985470 AKO62869 63
QnrB78 KM985471 AKO62870 63
QnrB79 KM985472 AKO62871 63
QnrB80 KM985473 AKO62872 63
QnrB81 KX372671 AOE23833 64
QnrB82 KX372672 AOE23835 64
QnrB83 64
QnrB84 64
QnrB85 64
QnrB86 64
QnrB87 64
QnrB90 69
QnrB91 70
QnrB92 71
QnrB93 71
QnrB94 71
QnrC EU917444 ACK75961 22
QnrD1 FJ228229 ACG70184 23
QnrD2 KF055448 AHW56805 53
QnrD3 KX130945 AND62509 72
QnrE1 KY073238 APC93960 68
QnrS1 AB187515 BAD88776 18
QnrS2 DQ485530 ABF47470 7
QnrS3 EU077611 ABU52984 19
QnrS4 FJ418153 ACJ24509 21
QnrS5 HQ631377 AEG74319 34
QnrS6 HQ631376 AEG74318 34
QnrS7 KF730651 AHE41344 47
QnrS8 KF730652 AHE41345 47
QnrS9 KF732714 AHF20043 59
QnrVC1 EU436855 ACC54440 54
QnrVC3 HM015626 ADI81040 55
QnrVC4 GQ891757 ADI55014 56
QnrVC5 JN408080 AEM62764 57
QnrVC6 KC202804 AGH08253 61
QnrVC7 KM555152 AJA36815 62
QnrVC8 MH181806 AXA19787 73
QnrVC9 MH181807 AXA19788 73
QnrVC10 74

Amino acid alterations in qnrB alleles

Allele 2 4 6 7 8 11 13 14 17 18 20 21 22 23 27 29 31 33 35 36 55 37 45 48 54 59 60 62 64 69 74 75 79 80 83 87 88 94 106 107 115 118 119 129 130 142 144 146 147 149 150 151 156 157 161 162 163 168 169 171 183 185 186 188 198 199 200 202 204 205 212 213
QnrB1 A A V G E D N R G E I E N S N D S A L S N G F R C A M K A C A D S S G R H A T T Y N T V V I A V L A T F L S F S T A A F D D I G N Y Q S L M V I
QnrB2 N A M R I
QnrB3 K M
QnrB4 T V N I N S M T S V S L M
QnrB5 T V V M T S I
QnrB6 A M
QnrB7 A M T I
QnrB8 T V I V A M T L S T A
QnrB9 A M I
QnrB10 T V V M T
QnrB11 T A V I V S M T S V S I L M
QnrB12 T A V I V S M T S V S I L
QnrB13 A M R I
QnrB14 D A M T I
QnrB15 S A N M I
QnrB16 A M T I
QnrB17 M
QnrB18 D A M
QnrB19 T V V M T S
QnrB20 N A M R
QnrB21 T V I V A M T L S T S A
QnrB22 T V C N I N S M T S V V S L M
QnrB23 Y A M I
QnrB24 M V A M
QnrB25 V I V S A M T L S T S A I
QnrB26 V G A M
QnrB27 T S V A S M T A A S A
QnrB28 T S V V S M T A A S A
QnrB29 V A M
QnrB30 S A M
QnrB31 L A S M R I
QnrB32 A S M I
QnrB33 T S V S A S M T A A S A
QnrB34 T A V I G V S M T S V S I L
QnrB35 I A V I V A M T M L S T S A
QnrB36 T V T V M T
QnrB37 T V I V S M T S V V S I L
QnrB38 I V I V A M T L S T S A
QnrB39 T V V T I A S M T S V S I L
QnrB40 T V R V M T T
QnrB41 D M
QnrB42 V C I
QnrB43 A M A
QnrB44 A M T
QnrB45 T A M
QnrB46 T V R V M T T
QnrB47 T V R V M T
QnrB48 A M G I
QnrB49 A M T R I
QnrB50 T K V V M T
QnrB51 T V R V M T
QnrB52 N A S M R I
QnrB53 T V R V M T T
QnrB54 S G A M T I
QnrB55 T V L N I N S M T S V S L M
QnrB56 T V V M T G S I
QnrB57 A M N I
QnrB58 D A M I
QnrB59 T S V V M T I
QnrB60 I V I V A M T L S T S V
QnrB61 T S V V M T
QnrB62 T V V M T I
QnrB63 I A I
QnrB64 D A M R I
QnrB65 T V N I N M T S V S L
QnrB66 N M
QnrB67 T C V V M T
QnrB68 T V V M T
QnrB69 T V I V S M T S V S I L
QnrB70 T V V V M T
QnrB71 T A V V M T
QnrB72 T C V V M M T
QnrB73 S S V V S M T A A S A I
QnrB74 I F F
QnrB75 K G M
QnrB76 A M Y R I
QnrB77 T M
QnrB78 A M S I
QnrB79 X A M S I
QnrB80 A D M T I
QnrB81 T V V M T S R
QnrB82 T V V T M T S R
QnrB83 T V I N Q S M T S V S D L M
QnrB84 T V I V S L T S V S I L
QnrB85 S A M R I
QnrB86 T V N I N S F M T S V V S L M
QnrB87 T V N I N I M T S V S D L M
QnrB90 T V I V M T N
QnrB91 N A C M R I
QnrB92 A M A I
QnrB93 N A M R I
QnrB94 A M L I
QnrB53 and QnrB46 are identical, QneB51 is the same as QnrB47, QnrB76 is QnrB9, and QnrB79 and QnrB78 are identical. A Qnr differing in 30 amino acids from QnrB1 was found in K. pneumoniae and initially assigned QnrB88 (GenBank ANI75684) but subsequently redesignated as QnrE1 (GenBank APC93960). A Qnr differing in 22 amino acids from QnrB1, with 8 of the substitutions at novel positions, has been found in Citrobacter sp. and provisionally assigned QnrB89

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Amino acid alterations in QnrA alleles

Allele 39 54 108 116 127 130 156 161 213
QnrA1 Q V V S T S G R V
QnrA2 R A A I
QnrA3 R I A
QnrA4 R I A N
QnrA5 R I A C
QnrA6 R I I A H
QnrA7 R I A H
QnrA8 R I A D

Amino Acid alterations in QnrS alleles

Allele 5 11 12 16 20 21 28 31 41 44 61 65 89 91 100 102 106 120 123 136 140 148 201 206 207 216
QnrS1 N H N K D L F S T V V R F A S T H S N K F N A L I Y
QnrS2 R S Q I C A I L E A N T H S Q L F
QnrS3 R
QnrS4 A
QnrS5 R A T T R H Q L F
QnrS6 R S Q I C A I L E A N T Y H S Q L F
QnrS7 H
QnrS8 L
QnrS9 F

Amino Acid Alterations in QnrD Alleles

Allele 52 94 180 189 202
QnrD1 E A A I L
QnrD2 T F
QnrD3 V V V T

QNR4 References

1. Tran, J. H., and G. A. Jacoby. 2002. Mechanism of plasmid-mediated quinolone resistance. Proc. Natl. Acad. Sci. U S A 99:5638-5642.
2. Li, T. et al., unpublished
3. Poirel, L., J. M. Rodriguez-Martinez, H. Mammeri, A. Liard, and P. Nordmann. 2005. Origin of plasmid-mediated quinolone resistance determinant QnrA. Antimicrob. Agents Chemother. 49:3523-3525.
4. Cambau, E., C. Lascols, W. Sougakoff, C. Bebear, R. Bonnet, J. D. Cavallo, L. Gutmann, M. C. Ploy, V. Jarlier, C. J. Soussy, and J. Robert. 2006. Occurrence of qnrA-positive clinical isolates in French teaching hospitals during 2002-2005. Clin. Microbiol. Infect. 12:1013-1020.
5. Jacoby, G. A., K. E. Walsh, D. M. Mills, V. J. Walker, H. Oh, A. Robicsek, and D. C. Hooper. 2006. qnrB, another plasmid-mediated gene for quinolone resistance. Antimicrob. Agents Chemother. 50:1178-1182.
6. Robicsek, A., J. Strahilevitz, D. F. Sahm, G. A. Jacoby, and D. C. Hooper. 2006. qnr prevalence in ceftazidime-resistant Enterobacteriaceae isolates from the United States. Antimicrob. Agents Chemother. 50:2872-2874.
7. Gay, K., A. Robicsek, J. Strahilevitz, C. H. Park, G. Jacoby, T. J. Barrett, F. Medalla, T. M. Chiller, and D. C. Hooper. 2006. Plasmid-mediated quinolone resistance in non-Typhi serotypes of Salmonella enterica. Clin. Infect. Dis. 43:297-304.
8. Ma, X, et al. unpublished
9. Cattoir, V., L. Poirel, V. Rotimi, C. J. Soussy, and P. Nordmann. 2007. Multiplex PCR for detection of plasmid-mediated quinolone resistance qnr genes in ESBL-producing enterobacterial isolates. J. Antimicrob. Chemother. 60:394-397.
10. Zhu, M, et al., unpublished
11. Quiroga, M. P., P. Andres, A. Petroni, A. J. Soler Bistué, L. Guerriero, L. J. Vargas, A. Zorreguieta, M. Tokumoto, C. Quiroga, M. E. Tolmasky, M. Galas, and D. Centrón. 2007. Complex class 1 integrons with diverse variable regions, including aac(6')-Ib-cr, and a novel allele, qnrB10, associated with ISCR1 in clinical enterobacterial isolates from Argentina. Antimicrob. Agents Chemother. 51:4466-4470.
12. Rodriguez-Zulueta, P., et al., unpublished
13. Kehrenberg, C., S. Friederichs, A. de Jong, and S. Schwarz. 2008. Novel variant of the qnrB Gene, qnrB12, in Citrobacter werkmanii. Antimicrob. Agents Chemother. 52:1206-1207.
14. Tamang, M.D., S.Y. Seol, J-Y. Oh, H.Y. Kang, J.C. Lee, Y.C. Lee, D.T. Cho, and J. Kim. 2008. Plasmid-mediated quinolone resistance detrmineds qnrA, qnrB, and qnrS among clinical isolates of Enterobacteriaceae in a Korean hospital. Antimicrob. Agents Chemother. 52: 4159-4162.
15. Sanchez-Cespedes, J., S. Marti, S. M. Soto, V. Alba, C. Melción, M. Almela, F. Marco, and J. Vila. 2009. Two chromosomally located qnrB variants, qnrB6 and the new qnrB16, in Citrobacter spp. isolates causing bacteraemia. Clin. Microbiol. Infect. 15:1132-1138.
16. Gonzalez-Lopez, J., et al., unpublished
17. Cattoir, V., P. Nordmann, J. Silva-Sanchez, P. Espinal, and L. Poirel. 2008. ISEcp1-mediated transposition of qnrB-like gene in Escherichia coli. Antimicrob. Agents Chemother. 52:2929-2932.
18. Hata, M., M. Suzuki, M. Matsumoto, M. Takahashi, K. Sato, S. Ibe, and K. Sakae. 2005. Cloning of a novel gene for quinolone resistance from a transferable plasmid in Shigella flexneri 2b. Antimicrob. Agents Chemother. 49:801-803.
19. Yue, L., H. X. Jiang, X. P. Liao, J. H. Liu, S. J. Li, X. Y. Chen, C. X. Chen, D. H. Lu, and Y. H. Liu. 2008. Prevalence of plasmid-mediated quinolone resistance qnr genes in poultry and swine clinical isolates of Escherichia coli. Vet. Microbiol. 132:414-420.
20. Yamane, K., unpublished
21. Torpdahl, M, A.M. Hammerum, C. Zachariasen, EM Nielsen. Detection of qnr genes in Salmonella isolated from humans in Denmark. 2009. J. Antimicrob. Chemother. 63:406-408.
22. Wang, M., Q. Guo, X. Xu, X. Wang, X. Ye, S. Wu, D. C. Hooper, and M. Wang. 2009. New plasmid-mediated quinolone resistance gene, qnrC, found in a clinical isolate of Proteus mirabilis Antimicrob. Agents Chemother. 53:1892-1897.
23. Cavaco, L. M., H. Hasman, S. Xia, and F. M. Aarestrup. 2009. qnrD, a novel gene conferring transferable quinolone resistance in Salmonella enterica serovar Kentucky and Bovismorbificans strains of human origin. Antimicrob. Agents Chemother. 53:603-608.
24. Galvin, S., Morris, D., Cormican, M., 12/2009, personal communication.
25. Bae, I. K., I. Park, J. J. Lee, H. I. Sun, K. S. Park, J. E. Lee, J. H. Ahn, S. H. Lee, and G. J. Woo. 2010. Novel variants of the qnrB gene, qnrB22 and qnrB23, in Citrobacter werkmanii and Citrobacter freundii. Antimicrob. Agents Chemother. 54:3068-3069.
26. Zhou MTH, Zhou T, Fei J et al. 2010. Detection of a new qnrA7 genotypes in Shewanella algae. Chinese J Microbiol Immunol 30: 593–6
27. Shao, Y., Z. Xiong, X. Li, L. Hu, J. Shen, T. Li, F. Hu, and S. Chen. 2011. Prevalence of plasmid-mediated quinolone resistance determinants in Citrobacter freundii isolates from Anhui province, PR China. J Med Microbiol 60:1801-1805.
28. Guillard, T., C. de Champs, H. Moret, X. Bertrand, J. M. Scheftel, and E. Cambau. 2012. High-resolution melting analysis for rapid characterization of qnr alleles in clinical isolates and detection of two novel alleles, qnrB25 and qnrB42. J Antimicrob Chemother 67:2635-2639.
29. Xia,R., Guo,X. and Xu,H. GenBank HQ386846.
30. Jeong, H. S., I. K. Bae, J. H. Shin, S. H. Kim, C. L. Chang, J. Jeong, S. Kim, C. H. Lee, N. H. Ryoo, and J. N. Lee. 2011. Fecal colonization of Enterobacteriaceae carrying plasmid-mediated quinolone resistance determinants in Korea. Microb. Drug Resist. 17:507-12.
31. Wang, D., H. Wang, Y. Qi, Y. Liang, J. Zhang, L. Yu. 2011. Novel variants of the qnrB gene, qnrB31 and qnrB32, in Klebsiella pneumoniae. J. Med Microbiol. 60: 1849-1852.
32. Jacoby, G. A., C. M. Griffin, and D. C. Hooper. 2011. Citrobacter spp. as a source of qnrB alleles. Antimicrob Agents Chemother 55:4979-4984.
33. Jeong,H.S., Bae,I.K., Kim,S.H., Lee,J.N., Jeong,S.H. and Shin,J.H. GenBank JN166689 and JN166690.
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35. Guillard,T., Cambau,E., Moret,H., Madoux,J., Jaulhac,B. and de Champs,C. GenBank JN680743.
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37. Oh,J.-Y., Kang,M.-S., Kwon,J.-H. and Kwon,Y.-K. GenBank JQ349153.
38. Oh,J.-Y., Kang,M.-S., Kwon,J.-H. and Kwon,Y.-K. GenBank JQ349152,
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40. Oh,J.-Y., Kang,M.-S., Kwon,J.-H. and Kwon,Y.-K. GenBank JQ349155.
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50. Sang Hee Lee, 10/18/12, Personal communication.
51. Halova, D., I Papousek, I Jamborova, M. Masarikova, A. Cizek, N. Janecko, V. Oravcova, L. Zurek, A.B. Clark, A.Townsend, J.C. Ellis, I. Literak. Plasmid-mediated quinolone resistance genes in Enterobacteriaceae from American crows: high prevalence of bacteria with variable qnrB genes. Antimicrob. Agents Chemother. 58:1257-1258. 2014.
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63. Fang, Liang-Xing, 10/15/14, Personal communication
64. Leski, Tomasz, 5/10/16, Personal communication
65. Bueno, Maria Fernada, 6/2/2016, Personal Communication
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67. Pujado, Christopher Concha, 10/28/2016, Personal communication.
68. Albornoz, E., Tijet, N., De Belder, D., Gomez, S., Martino, F., Corso, A., Melano, R. G., Petroni, 2017. A. qnrE1, a member of a new family of plasmid-located quinolone resistance genes, originated from the chromosome ofEnterobacter species. Antimicrob Agents Chemother 61: e02555-16.
69. Antunes, Patricia, 10/1/2017, Personal communication
70. Sato, Toyotaka, 11/7/2017, Personal communication
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