bBacteria can become resistant not only by horizontal gene transfer or other forms of exchange of genetic information but also by de novo by adaptation at the gene expression level and through DNA mutations. The interrelationship between changes in gene expression and DNA mutations during acquisition of resistance is not well documented. In addition, it is not known whether the DNA mutations leading to resistance always occur in the same order and whether the final result is always identical. The expression of >4,000 genes in Escherichia coli was compared upon adaptation to amoxicillin, tetracycline, and enrofloxacin. During adaptation, known resistance genes were sequenced for mutations that cause resistance. The order of mutations varied within two sets of strains adapted in parallel to amoxicillin and enrofloxacin, respectively, whereas the buildup of resistance was very similar. No specific mutations were related to the rather modest increase in tetracycline resistance. Ribosome-sensed induction and efflux pump activation initially protected the cell through induction of expression and allowed it to survive low levels of antibiotics. Subsequently, mutations were promoted by the stress-induced SOS response that stimulated modulation of genetic instability, and these mutations resulted in resistance to even higher antibiotic concentrations. The initial adaptation at the expression level enabled a subsequent trial and error search for the optimal mutations. The quantitative adjustment of cellular processes at different levels accelerated the acquisition of antibiotic resistance.
The de novo acquisition of resistance against antibiotics is known to be accompanied by certain mutations and differential expression of specific genes (1-5). The "radical-based" theory (6, 7) proposes that bactericidal antibiotics cause cell death by a single mechanism, driven by the accumulation of oxygen radicals in the cells. In that case, the cellular response to sublethal concentrations of antibiotics should be similar even for compounds belonging to different classes of bactericidal drugs, such as beta-lactams or fluoroquinolones. The outcome might differ for bacteriostatic drugs, for example, tetracycline. The radical-based theory, however, is the subject of debate (8). The revelation of a common denominator for the adaptation processes to different antibiotics might illuminate the question of a single mechanism from a different angle.Resistance can easily be induced in Escherichia coli by exposure to stepwise increasing sublethal antibiotic concentrations (9). The effects of the acquisition of resistance to amoxicillin on the overall physiology is a complex set of adaptations at the gene expression level, preventing metabolic costs at the expense of the ecological range (10). After the initial stage, the prolonged exposure to antibiotics modulates the SOS response, leading in turn to mutations that cause resistance (11). The mutations generate more permanent resistance, which remains long after the antibiotic pressure has been ...