The Journal of antimicrobial chemotherapy · 2018
Analysis of the presence of erroneous Qnr sequences in GenBank.
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Ruiz Joaquim
Аннотация
BACKGROUND: Twenty years ago the first transferable mechanism of quinolone resistance (TMQR), QnrA, was described. Thereafter, innumerable TMQRs, either Qnr related or not, were described. Ten years ago the exponential description of Qnr genes/alleles led to the proposal of a common nomenclature.
OBJECTIVES: This analysis aims to determine the degree of correctness of the Qnr sequences currently present in GenBank.
METHODS: The Qnr amino acid type sequence of the first allele (e.g. QnrA1) of each Qnr family present in http://www.lahey.org/qnrStudies/ was compared with what is present in GenBank. Only the first 30 obtained annealings or those with a >90% identity were considered. No synthetic or chromosomal sequences (other than those included in http://www.lahey.org/qnrStudies/) were included in the analyses.
RESULTS: Overall, 1657 amino acid sequences were analysed: 224 QnrA, 499 QnrB, 1 QnrC, 102 QnrD, 13 QnrE, 758 QnrS and 60 QnrVC. Of these, 340 (20.5%) sequences presented a major error, including erroneous gene name, erroneous Qnr family attribution, erroneous allele identification, presence of partial sequences with allele assignation and/or erroneous initial codon. In addition, 449 (27.1%) Qnr sequences were present in GenBank with a partial identification or not identified as Qnr. Finally, nine new transferable Qnr alleles were detected.
CONCLUSIONS: These data highlight the frequent presence of erroneously identified qnr genes in GenBank and the need to be fully adherent to current nomenclature rules.
OBJECTIVES: This analysis aims to determine the degree of correctness of the Qnr sequences currently present in GenBank.
METHODS: The Qnr amino acid type sequence of the first allele (e.g. QnrA1) of each Qnr family present in http://www.lahey.org/qnrStudies/ was compared with what is present in GenBank. Only the first 30 obtained annealings or those with a >90% identity were considered. No synthetic or chromosomal sequences (other than those included in http://www.lahey.org/qnrStudies/) were included in the analyses.
RESULTS: Overall, 1657 amino acid sequences were analysed: 224 QnrA, 499 QnrB, 1 QnrC, 102 QnrD, 13 QnrE, 758 QnrS and 60 QnrVC. Of these, 340 (20.5%) sequences presented a major error, including erroneous gene name, erroneous Qnr family attribution, erroneous allele identification, presence of partial sequences with allele assignation and/or erroneous initial codon. In addition, 449 (27.1%) Qnr sequences were present in GenBank with a partial identification or not identified as Qnr. Finally, nine new transferable Qnr alleles were detected.
CONCLUSIONS: These data highlight the frequent presence of erroneously identified qnr genes in GenBank and the need to be fully adherent to current nomenclature rules.