In 1929 British microbiologist, Alexander Fleming discovered penicillin, an antibiotic produced by the common bread mold quite by accident. It became a wonder drug that was used to treat many types of infections, including pneumonia, gonorrhea, infections caused by streptococci such as scarlet fever and strep throat and infections caused by staphylococci such as blood disorders and boils. Penicillin was widely used during World War II, but in the 1950s discoveries were made showing bacteria that was resistant to the drug. Resistance ranged from about 2% in the 1950s to around 80% in the 1990s. What can be made of such activity? Are Bacteria evolving?
Actually, no, they are not. This is what happens. Antibiotics are minute chemical compounds that are able to destroy bacteria. Nevertheless, not all of the bacteria are destroyed. What survives grows in the presence of the antibiotic. What has happened? A small number of the bacteria was already resistant to the antibiotic before it was used upon the patient. What occurred was a more resistant strain of the original bacteria was allowed to reproduce and dominate the environment. This is not evolution. It is adaptation. Adaptation and selective breeding are legitimate tools used by organic forms that produce such variety among the species.
At times mutations do occur in the DNA of the bacteria. However, these mutants are not improvements over the original bacteria. Quite the contrary, in that the new form, although resistant to the antibiotic, represents a deficiency in information. The job efficiency of the proteins is always decreased and growth is slower. On the other hand some DNA changes are not random at all but appear to be encoded in the design of the bacteria. It changes to adapt to its new environment, but the change is not through evolution, but is part of its designed defense mechanism.
Over the past 60 or 70 years we have been using antibiotics in medicine and agriculture. This resulted in the destruction of bacteria that is not resistant to the chemicals we’ve used. However, at the same time the antibiotic-resistant bacteria have been allowed to grow unhindered by the faster growing bacteria we’ve destroyed. This is natural selection at work, but it is not natural; we are the ones who provided the environment for it to occur. For example, we derive most of our medically important antibiotics from one group of bacteria, Streptomyces. One of the defense mechanisms of antibiotic-resistant bacteria is efflux pumps located in the cell membrane. This same defense is used by the Streptomyces bacteria from which we derive our antibiotics. So, Streptomyces uses the same defense mechanism to protect itself from the antibiotics it produces.
Therefore, it doesn’t appear that bacteria are evolving at all. The mechanism we battle with new strains of antibiotics is already present. It is present in the bacteria we use to produce the antibiotic, and it is present in the harmful bacteria we combat each year. There is no evidence for biological evolution here. It is all about adaptation and natural selection (i.e. humans eliminating the bacteria that can be destroyed and permitting what remains to grow unhindered alongside the antibiotic).
 Shoemaker, N.B. et al., 2001. Evidence for extensive resistance gene transfer among Bacteriodes spp. and among Bacteriodes of other genera in the human colon. Applied and Environmental Microbiology 67:561-568.