Antagonism, especially by bacteria to antibiotics, that is associated with changes to existing and especially non-plasmid-borne genes.
Typically these are mutations that result in modifications to antibiotic targets. Virus resistance to antivirals also occurs due to mutations associated with chromosomes, in this case the viral chromosome. Contrasting chromosomal resistance is resistance that is a consequence of plasmid acquisition by bacteria, that is, acquisition by bacteria of resistance plasmids.
When microbiologists speak of rates of bacterial mutation to resistance, it is rates of acquisition of chromosomal resistance that is being considered. These are a consequence of a combination what nucleotide changes can result in resistance to a specific antibiotic and the rate at which specific nucleotide changes occur (that is, overall mutation rate multiplied by the fraction of mutations that give rise to the specific resistance phenotype).
It typically is the evolution of chromosomal resistance that is the concern when individuals are cautioned to complete their antibiotic prescription, that is, rather than plasmid acquisition of resistance. Chronic antibiotic exposure, such as the use of antibiotics to enhance productivity in animal husbandry, can on the other hand, can facilitate the evolution of plasmid-borne antibiotic resistance as well as chromosomal resistance.
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