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If I use antibiotic on a specific type of bacteria, some will survive because it is resistant. Was this bacteria resistant to this antibiotic before it was even used, or did the bacteria develop resistance after the antibiotic is used?

How or why some bacteria can simply mutate to form beneficial alleles which will help in survival and others can't?

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Antibiotic resistance comes from selection pressure: any bacteria that are resistant will survive and replicate, so in the next generation of bacteria you will find more resistance.

Bacteria do not simply mutate to form beneficial alleles, the alleles or genes that confer drug resistance must already be in the population; by using antibiotics, however, you're killing off their competition by killing the bacteria that don't have the resistant allele(s)/gene(s).

It's very unlikely that one individual using one antibiotic for one illness will lead to detectable antibiotic resistance. However, antibiotics aren't used in just one individual: they are used repeatedly, in many individuals, often in multiple species, etc. It is this broad use of antibiotics over time that eventually "finds" strains that are antibiotic resistant. Once these strains with resistant alleles become more prevalent, it becomes more likely that they will be present in some quantity to be selected for in the future.

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    $\begingroup$ Not that you said otherwise, but I'd like to emphasize that there need not be a dichotomy between complete resistance and no resistance. Some population with partial resistance could have a selective advantage, especially if the antibiotic dose is low (or short), and then continue to mutate towards higher resistance. $\endgroup$ – canadianer Jan 2 at 19:37
  • $\begingroup$ @canadianer Of course, I think this is a fortunate case where we've actually picked a linguistically informative word as a scientific community: resistance refers to being less susceptible to the antibiotic, that is, resistant to it, rather than invulnerable to an antibiotic, and so resistance to a given drug can be on a spectrum. It could be thought of as just a shift in the LD50 for a given drug. $\endgroup$ – Bryan Krause Jan 2 at 20:35
  • $\begingroup$ I think there is too much emphasis on alleles in this answer. Resistance to antibiotics is not a purely genetic phenomenon. Some cells may resist the antibiotic pressure through epigenetic mechanisms, e.g. upregulation of efflux pumps etc. There need not necessarily even be a specific mutation required. $\endgroup$ – Joe Healey Jan 2 at 20:39
  • $\begingroup$ @JoeHealey I'm not sure I follow. An ability to upregulate of an efflux pump is going to be due to some allele, an epigenetic mechanism is just that: a mechanism. If one organism has a different propensity towards epigenetic modification of an efflux pump, that's still an allele. $\endgroup$ – Bryan Krause Jan 2 at 20:47
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    $\begingroup$ For me 'must already be' sounds confusing. When did 'already happen? Are you talking about already drug-resistant strain (if so - where did it come from?), or any mutation that happened to happen at moment when antibiotic was poured over, or, let's say, plasmid? $\endgroup$ – Maxim Kuleshov Jan 2 at 20:56

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