Although much attention has been focused on antibiotic resistance in pathogens found
in hospital patients and on the bacteria that are directly responsible for adverse effects
on human health, the development of resistance to antibiotics is a natural ecological
phenomenon and is the product of billions of years of evolution. Studies of
microorganisms from pristine sites, including isolated caves and permafrost, have
shown that resistance occurs in the absence of human activity141–143. Most antibiotics that
are used in human medicine are derived from antibiotic-producing microorganisms
that expose other species in their local environment to antimicrobial molecules. This
favours selection of resistance in environmental species as well as generating resistance
or ‘immunity’ genes in the producer organisms. Although the presence of resistance in
natural environments might be a natural phenomenon, it is not innocuous because this
reservoir of resistance genes can be mobilized and can transfer into human
pathogens144–146. Human use of antibiotics has selected for the escape of genes from the
soil ‘resistome’ into human pathogens, as demonstrated by the presence of the same
genes in soil bacteria and human bacteria. Furthermore, environmental microorganisms
carry genes that encode resistance to newly licensed antibiotics, such as daptomycin,
even before the first clinical use of such antibiotics147–149