The appearance of antibiotic resistances is modulated by events of co-option, mutation, recombination and/or horizontal gene transfer between strains and, once have occurred, are subjected to natural selection that allows the widespread dispersal of the strains due to current globalization. The spread of resistance varies both temporally and geographically. Consequently, there is a temporal progression in the abundance of the corresponding antibiotic resistance genes (ARGs) and their geographical distribution that allows the occurrence of ARGs to be used to analyse the patterns of antibiotic resistance of a given population and could be useful to detect changes on these patterns. To date, studies of the distribution and epidemiology of resistance have mostly been based on, and hence biased towards, the study of pathogens isolated in the clinical environment.