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Background   Qnr  genes are known to confer a low-level resistance to fluoroquinolone in  Enterobacteriaceae . They are often found on the same resistance plasmids as extended spectrum β-lactamase (ESBL) and constitute the most common antibiotic resistance mechanism. This study aimed to detect the presence of  qn r genes in  ESBL -producing  E. coli  and  Klebsiella spp .    Methods  From May 2013 to July 2015, 91  E. coli  and 64  Klebsiella spp.  strains with phenotypic resistance to quinolone were collected from several specimens and analyzed for the detection of  qnrA, qnrB, qnrS  genes and the β-lactamase resistance genes ( blaCTX-M ,  blaTEM ,  blaSHV ) using simplex and multiplex PCR.    Results  In the present study, 107 (69%; 61  E. coli  and 46  Klebsiella spp. ) of 155 bacterial strains tested were found harboring at least one  qnr  gene consisting of 74 (47.74%)  qnrB , 73 (47.10%)  qnrS  and 4 (2.58%)  qnrA . Of the 107 strains encoding  qnr  genes, 102, 96 and 52 carried  CTX-M1 ,  TEM  and  SHV  type ESBL respectively.    Conclusion  This study identified quinolone resistance ( qnr ) gene in  ESBL -producing  E. coli  and  Klebsiella spp.  in Togo. These finding which suggest a possible resistance to quinolone are of high interest for better management of patients and control of antimicrobial resistance in Togo.    Electronic supplementary material  The online version of this article (10.1186/s13756-019-0552-0) contains supplementary material, which is available to authorized users.

Distribution of quinolone resistance gene (qnr) in ESBL-producing Escherichia coli and Klebsiella spp. in Lomé, Togo