Interventions for Tuberculosis Control and Elimination
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Freeze-drying became available only in the middle of the last century and the only way to keep the bacterium before was through propagation on sub-cultures. This will lead repeatedly to mutations that might emerge under various conditions to become the predominant strain.
BCG vaccine strains have been distributed widely and differences in maintenance and other factors such as random mutations have apparently occurred repeatedly. Thus, while vaccine strain differences cannot explain all the variation, vaccine quality is a strong factor to reconcile.