With respect to this website:
what does the term clonal isolates mean?
Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) colonies need to be isolated to make sure they carry only one insert. This can be done, e.g., by plating the transformed cell culture such that individual colonies are obtained. Theoretically, one colony represents the offspring of one cell, hence the colony as a whole has one DNA insert and is a clonal isolate.