Antibiotic resistance landscapes: a quantification of theory-data incompatibility for fitness landscapes
Fitness landscapes are central in analyzing evolution, in particular for drug resistance mutations for bacteria and virus. We show that the fitness landscapes associated with antibiotic resistance are not compatible with any of the classical models; additive, uncorrelated and block fitness landscapes. The NK model is also discussed. It is frequently stated that virtually nothing is known about fitness landscapes in nature. We demonstrate that available records of antimicrobial drug mutations can reveal interesting properties of fitness landscapes in general. We apply the methods to analyze the TEM family of $\beta$-lactamases associated with antibiotic resistance. Laboratory results agree with our observations. The qualitative tools we suggest are well suited for comparisons of empirical fitness landscapes. Fitness landscapes are central in the theory of recombination and there is a potential for finding relations between the tools and recombination strategies.