It is important to clearly define the terms isolate, strain and clone to avoid confusion. Ideally in all molecular epidemiological studies these terms should be applied using the same definitions. For example "strain" and "isolates" are often used synonymously, and this may results in problems, in particular when the definition of the terms is not standardised.

The below definitions are approved by the American Society for Microbiology:

Isolate: A population of microbial cells in pure culture derived from a single colony on an isolation plate and identified to the species level.

Strain: An isolate or group of isolates exhibiting phenotypic and/or genotypic traits belonging to the same lineage, distinct from those of other isolates of the same species.

Clone: An isolate or group of isolates descending from a common precursor strain by nonsexual reproduction exhibiting phenotypic and/or genotypic traits characterised by a strain-typing method to belong to the same group.

The terms isolate, strain and clone form a hierarchy, as illustrated in the figure below.

 [This figure was taken from Zadoks et al. 2006]

Sources and Resources:

Zadoks, R. N., and Y. H. Schukken. 2006. Use of molecular epidemiology in veterinary practice. Veterinary Clinics of North America-Food Animal Practice 22:229-261.

Riley, L. W. 2004. Molecular Epidemiology of Infectious Diseases - Principles and Practices. ASM Press, Washington, DC.