## 8 Unconsidered Chromosomal Mutations  
The selection of _gyrA_ and/or _parC_ mutations under quinolone exposure is a well-established phenomenon [44; 50; 80; 174; 175], with these mutations altering quinolone-DNA-DNA-Gyrase interactions [46; 52; 54]. Similarly, increased efflux levels as well as porin alterations resulting in decreased quinolone intake are also selected when microorganisms are exposed to quinolones, with both alterations resulting in lower cytoplasmic concentrations of quinolones and subsequent increased levels of antibiotic resistance [44; 82; 176]. While mutations at quinolone targets or either in regulator or constitutive genes related to efflux pumps or outer membrane proteins are clearly involved in the development of quinolone resistance, alterations in other genes outside the classical scope may induce subtle alterations. While these alterations produce slight changes in quinolone susceptibility levels, they do not modify the quinolone-susceptible status of microorganisms and remain unnoticed by classical methodologies, being considered as background noise or inter-strain MIC variations. However, these alterations can impact the ability of bacteria to develop full quinolone resistance. Of note, in multiple cases, these alterations induce modifications in different bacterial pathway regulation, which, over time, result in reduced quinolone uptake within the bacterial cytoplasm (Table 2). \begin{table}
\begin{tabular}{l l l l l l l l l l} \hline \hline  & & \multicolumn{3}{c}{**Mutation**} & & & & & \\
**Gene** & **Microorg.** & \(\mathbf{D^{1}}\) & \(\mathbf{S^{2}}\) & & **Protein Encoded** & **Alt. 3** & **Effect 4** & **Impact 5** & **Reference** \\ \hline _icdA_ & _E. coli_ & _Th_ & _IS10_ & & Isocitake dehydrogenase & LF & MA & \(\uparrow\)_acrA_-_id_-_c_6 [177; 178] \\ _parB_ & _E. coli_ & _Th_ & \(-\) & & \(\mathbf{a}\)dysuccinate lyase & LF & MA & \(\uparrow\)_acrA_-_id_-_c_6 [178] \\ _cysH_ & _E. coli_ & _Th_ & \(-\) & & \(\mathbf{s}\)-phosphodiate (PAFS) & LF & MA & \(\uparrow\)_acrA_-_id_-_c_6 [178] \\ _metE_ & _E. coli_ & _Th_ & \(-\) & & homocysteine & LF & MA & \(\uparrow\)_acrA_-_id_-_c_6 [178] \\ _rpaA_ & _S. enterica_ & \(-\) & N\({}_{20\pi}\)V & methyl transferase & & TRC & TBC & & [179] \\  & & & R\({}_{20\pi}\)C, A\({}_{120\pi}\)V, & & RNA polymerase subunit & TRC & TBC & & [179] \\ _rpoB_ & _E. coli_ & \(-\) & E\({}_{20\pi}\)G, A\({}_{42\pi}\)V, & & RNA polymerase subunit & TRC & TBC & \(\downarrow\)OmpF, \(\uparrow\) & [177; 180] \\  & & & D\({}_{45\pi}\)S & & & D\({}_{45\pi}\)S & & & M\({}_{45\pi}\)S & \\ _lcaS_ & _E. coli_ & \(-\) & & L\({}_{45}\)H, D\({}_{45\pi}\)N, S\({}_{45\pi}\)P & & & & & \(\uparrow\)MdtK; \(\uparrow\) & [181] \\  & _sapS_ & _E. coli_ & \(-\) & D\({}_{20\pi}\)A & & & & & & [181] \\  & _thrS_ & _E. coli_ & \(-\) & H\({}_{45\pi}\)P, I\({}_{25\pi}\)S & & & & & & [181] \\  & _gyrA_ & _E. coli_ & \(-\) & Ser\({}_{65\pi}\)STOP & DNA-Gyrase subunit & RE & TBC & \(\downarrow\)GyrA & \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Non-classical chromosomal mutations. In this regard, when analyzing the exposure to ciprofloxacin of _E. coli_ J53 carrying cloned _qnr_ (designed below as J53-_qnr_) determinants (_qnrA1_, _qnrA3_, _qnrB1_ and _qnrS1_), [PERSON] et al. showed that while no differences in the selection of mutants were observed, the mutant prevention concentration was \(\sim\)10-fold higher than the original _E. coli_ J53 [182]. Thus, the presence of _qnr_ determinants facilitates the acquisition of quinolone resistance in the presence of higher antibiotic concentrations [182]. Surprisingly, while only 20% (65/329) of resistant isolates derived from J53-_qnr_ presented mutation(s) in quinolone targets, this finding was observed in 79% (94/119) of quinolone-resistant mutants derived from _E. coli_ J53, \(p\) < 0.0001 [182]. The authors suggested that Qnr blocks the access of quinolones to their targets, thereby favoring the selection of other mutations [182]. Other authors have observed similar phenomenon in _E. coli_, with [PERSON] et al.