Resistance gene naming and numbering: is it a new gene or not?

In the genomic era, studying the epidemiology of individual antibiotic resistance genes and resistance gene discovery are open to all. However, the identification and naming of resistance genes is not currently understandable by all owing to a plethora of competing nomenclature systems, many of which do not comply with the basic rules of bacterial gene nomenclature. Change is needed urgently. Here, we make a case for the resistance research community to begin this process by agreeing on an answer to the question of when a new gene number should be assigned. This cut-off is of necessity arbitrary and we suggest a threshold value of ≥2% difference in the sequences of the DNA, predicted protein or both as a realistic boundary for assigning a new gene number. This proposal can be a starting point for agreement or debate followed by renumbering of the affected gene families.