Resistome

The resistome is a proposed expression by Gerard D. Wright ^[1] for the collection of all the antibiotic resistance genes and their precursors both in pathogenic and non-pathogenic bacteria.

This complete set of antibiotic resistance genes is composed of four different types of genes:

# Resistance genes found on pathogenic bacteria. These are the fewest but also the most problematic ones at present.
# Resistance genes found on antibiotic producers. The microorganisms such as soil-dwelling bacteria and fungi that naturally produce antibiotics have their own protection mechanisms ^[2] to avoid the adverse effects of the antibiotics on them selfs. The genes which code for these resistances are a strong source ^[3] for the pathogenic bacteria.
# Cryptic resistance genes. These genes are embedded in the bacterial chromosome but do not obviously confer resistance, because their level of expression is usually low or their not expressed.
# Precursor genes. These genes do not confer antibiotic resistance. However their proteins confer some kind of basal level activity against the antibiotic molecule or have affinity to the molecule. In both cases this interaction may evolve to a full resistance gene given the appropriate selection pressure.

Note that this groups are not independent, and some overlapping is expected between them.

References

[1] Wright, Gerard D. The antibiotic resistome: the nexus of chemical and genetic diversity. "Nature Reviews Microbiology" Vol. 5, 175-186 (March 2007)

[2] Cundliffe, E. How antibiotic-producing organisms avoid suicide. "Annu. Rev. Microbiol." 43, 207–233 (1989).

[3] Benveniste, R. & Davies, J. Aminoglycoside antibioticinactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. Proc. Natl Acad. Sci. USA 70, 2276–2280 (1973).