TABLE 5.
Overall view of TMQRa
| Mechanism | TMQRc | No. of allelesb
|
Size (bp) | Yrf | Presence of integronsg | Ancestorsh | |
|---|---|---|---|---|---|---|---|
| Litd | RefSeqe | ||||||
| Target protection | QnrA | 8 | 8i | 218 | 1998 | Y | Shewanella spp. |
| QnrB | 88j | 81 | 214 | 2006 | Y | Citrobacter spp. | |
| QnrC | 1 | 1 | 221 | 2009 | Vibrio spp. | ||
| QnrD | 3 | 3 | 214 | 2009 | Morganellaceae? | ||
| QnrE | 1 | 2 | 214 | 2017 | Enterobacter spp. | ||
| QnrS | 9 | 14k | 218 | 2005 | Vibrio spp. | ||
| QnrVCl | 9 | 7 | 218 | 2008 | Y | Vibrio spp. | |
| Efflux system | QepA | 10 | 10 | 511m | 2007 | Comamonadaceae | |
| OqxAB | 14/28 | 5/7 | 391/1,050n | 2003 | Klebsiella spp.o | ||
| QacA | 1 | 2p | |||||
| QacB | 1q | 2p | 2010 | ||||
| pRSB101 | 2004 | ||||||
| Antibiotic modification | AAC(6′)Ib-cr | >5 | 7 | 2006 | Y | ||
| CrpP | >37r | 1 | 2018 | Pseudomonadaceae? | |||
| Slow growth | pKM101 | ||||||
TMQR, transferable mechanisms of quinolone resistance; Lit, data present in the literature; RefSeq, data present as reference sequence data in GenBank.
Only alleles confirmed or proposed to be involved in the development of quinolone resistance.
Only confirmed TMQR. When a TMQR was related to the presence of a specific plasmid but no gene-specific nomenclature is available, the name of the plasmid is indicated.
Based on GenBank and bibliographic searches. Regarding Qnr, only those included in the Lahey database (formerly at http://www.lahey.org/qnrStudies/) as of 31 December 2018 are shown. This database is no longer available. Other unnamed or erroneously assigned alleles may be found in GenBank (209).
Based on a RefSeq search (https://www.ncbi.nlm.nih.gov/pathogens/isolates#/refgene/gene_family:XXX, where XXX is the name of the gene) (updated on 12 April 2019).
Publication of the first allele of the family that has been considered a TMQR, irrespective of the time at which the ability to confer quinolone resistance was demonstrated. Note that previous conference presentations may have been made and that these presentations may be included in reviews reported prior to the reported data.
Y indicates that all or several alleles were detected within the integron environment.
Established or proposed original chromosomal sources.
While considered at the Lahey website, QnrA8 is not included in RefSeq. Of note, the only description of this gene was in the S. algae chromosome; therefore, transferability has not been demonstrated (331).
QnrB89 has not been included (a high number of amino acid differences with established QnrB alleles has been reported [formerly at http://www.lahey.org/qnrStudies/], and no data on the exact sequence are provided at either the Lahey website or GenBank).
QnrS3 has not been included in RefSeq. Of note, the reported sequence lacks the initial amino acid (356).
While QnrVC8 and QnrVC9 were considered at the Lahey website, they are not included in RefSeq. It is of note that in the only description of these genes, they were located within Vibrio species chromosomes; therefore, transferability has not been demonstrated (363).
The proposed QepA8 protein has a 2-amino-acid insertion leading to a final size of 513 amino acids.
Standard size of OqxA and OqxB, respectively. Note that transferable OqxA and OqxB presenting amino acid insertions have been detected (see Tables 11 and 12).
Klebsiella pneumoniae and Klebsiella aerogenes (see “OqxAB”).
No data about the ability of one of these alleles to extrude quinolones have been reported.
Only the QacBIII allele has been associated with the ability to extrude quinolones.
The presence of more than 37 closely related alleles with identity levels of >90% has been highlighted (414). Nonetheless, the effect on ciprofloxacin has been established for only one allele, with the others remaining to be studied.